Электронно-микроскопические исследования специфических комплексов ДНК тема диссертации и автореферата по ВАК РФ 03.00.03, доктор биологических наук Черный, Дмитрий Ильич

• Черный, Дмитрий Ильич
• доктор биологических наук
• 1999

Оглавление диссертации доктор биологических наук Черный, Дмитрий Ильич

1. Введение

2. Литературный обзор. Анализ структурных особенностей

ДНК и ее комплексов с белками и нуклеиновыми кислотами с помощью электронной микроскопии: возможности метода

2.1. Введение

2.2. Общие принципы формирования изображения биологических объектов в просвечивающем электронном микроскопе

2.3. Общие принципы приготовления образцов ДНК для электронной микроскопии.

2.4. Возможности электронной микроскопии при изучении ДНК

2.5. Изучение специфических комплексов ДНК с белками и нуклеиновыми кислотами

2.6. Возможности применения электронной микроскопии для физического картирования

Введение диссертации (часть автореферата) на тему «Электронно-микроскопические исследования специфических комплексов ДНК»

4.1.2. Материалы,методы 71

4.1.3. Результаты 74

4.1.4. Резюме 80

4.2. Изучение специфического взаимодействия метилтрансфераз с ДНК 97

4.2.1. Введение 97

4.2.2. Материалы,методы 101

4.2.3.Результаты 104

4.2.4. Резюме 111

4.3. Изучение специфического взаимодействия триплекс образующих нуклеотидов с ДНК 121

4.3.1. Введение 121

4.3.2. Материаль^методы 127

4.3.3. Результаты 131

4.3.4. Резюме 138

4.4. Изучение специфического взаимодействия пептидной нуклеиновой кислоты с ДНК 148

4.4.1. Введение 148

4.4.2. Материалы}методы 152

4.4.3. Результаты 155

4.4.4. Резюме 159

4.5. Специфическое взаимодействие с ДНК протяженных олигонуклеотидов 169

4.5.1. Введение 169

4.5.2. Материалы?методы 175

4.5.3. Результаты 177

4.5.4. Резюме 179

5. Анализ экспериментальных данных 184 Введение 184

5.1. Общий анализ достоверности электронномикроскопического картирования 184

5.2. Частный анализ карт связывания 194

5.3. Анализ структурных изменений ДНК при специфическом взаимодействии с белками или нуклеиновыми кислотами 202

6. Обсуждение и перспективы 210

7. Выводы 218

8. Список цитированной литературы 222

Введение

Структурная организация ДНК имеет важнейшее значение для реализации генетической информации и регуляции основных клеточных процессов.

Взаимодействия ДНК с белками играют ключевую роль в регуляции этих процессов. Несмотря на значительные достижения в понимании природы ДНКбелковых взаимодействий, многие аспекты узнавания ДНК белками еще не выяснены. Для правильного понимания молекулярных механизмов, лежащих в основе этих взаимодействий, необходимо получение структурной информации о комплексах ДНК с белками. Структурный полиморфизм, вариабельность, ту. многокомпонентность и мульфункциональность этих комплексов создают серьезные проблемы при их анализе. Мощным инструментом в исследованиях ДНК-белковых комплексов и получении структурной информации о них является электронная микроскопия .

В настоящее время интенсивно изучается взаимодействие ДНК с олигонуклеотидами и их аналогами^ поскольку эти соединения позволяют разрабатывать методы направленного манипулирования активностью генов. Высокая специфичность реакции взаимодействия позволяет надеятся на создание широкого спектра методов искусственной модификации ДНК. Эти соединения представляют особый интерес с точки зрения разработки методов изучения структурной организации геномов, в том числе и с помощью электронной микроскопии, причем нет принципиальных ограничений для использования электронной микроскопии для изучения этих взаимодействий.

Уникальность микроскопии состоит в том, что она позволяет видеть индивидуальные молекулы ДНК и локализовать участки специфического связывания в составе протяженных молекул ДНК длиной до нескольких сотен тысяч пар оснований. Тем самым становится возможным получение уникальной информации о структуре ДНК в комплексе с белками или олигонуйеотидами, а также определение кинетических и равновесных констант реакции связывания. Надежная информация может быть получена только в случае разработки соответствующих методов наблюдения и правильного выбора критериев анализа экспериментальных данных.

Дуализм изучения специфического узнавания ДНК белками или олигонуклеотидами с помощью электронной микроскопии состоит в том, что оно является одновременно не только предметом исследования, но и его средством. Локализация участков специфического связывания является основой для разработки методов физического картирования. Это создает принципиально новые подходы к исследованиям структурной организации генома человека.

Для реализации потенциала электронной микроскопии необходимо уметь картировать участки узнавания различного размера и состава. В связи с этим направленное изучение специфического взаимодействия ДНК с различными белками и олигонуклеотидами и их аналогами чрезвычайно важны. В ходе таких исследований могут быть получены новые данные о специфическом узнавании ДНК и сформулированы общие принципы физического картирования ДНК с помощью электронной микроскопии.

Цель данного исследования состояла в изучении специфического взаимодействия ДНК с различными белками и олигонуклеотидими и их аналогами с помощью электронной микроскопии и разработке методов физического картирования ДНК. Для выполнения поставленной цели были сформулированы следующие основные задачи:

1) разработать методы и изучить специфическое взаимодействие ДНК с РНК-полимеразой Е.соН и метилтрансферазами;

2) разработать методы и изучить специфическое взаимодействие ДНК с триплекс-образующими олигонуклеотидами (ТОО) и аналогами олигонуклеотидов типа пептидная нуклеиновая кислота (ПНК);

3) разработать подходы к физическому картированию ДНК с помощью протяженных олигонуклеотидов;

4) разработать методы количественного анализа электронно-микроскопических данных; I

5) разработать методы определения достоверности электронно-микроскопического картирования.

В данной работе для анализа ДНК автор в основном использовал методы просвечивающей электронной микроскопии. В некоторых случаях были использованы методы атомно - силовой микроскопии. Несмотря на принципиальные различия в процессах формирования изображения в электронном и атомно-силовом микроскопах, применение в атомно-силовой микроскопии одной из электронно-микроскопических методик приготовления препаратов (адсорбция на слюду с последующим высушиванием) создает серьезные предпосылки, чтобы рассматривать данные методы как взаимодополняющие, и позволяет легко адаптировать результаты, полученные с помощью атомно - силовой микроскопии для электронно-микроскопических исследований и наоборот.

Представленные в данной работе результаты демонстрируют принципиальную возможность количественного изучения специфического взаимодействия предложенных белков, олигонуклеотидов и их аналогов с ДНК. Для каждого типа взаимодействия были найдены оптимальные условия изучения и на их основе предложены новые подходы к физическому картированию протяженных фрагментов ДНК.

Заключение диссертации по теме «Молекулярная биология», Черный, Дмитрий Ильич

Выводы

1. Разработан комплекс методов для электронно-микроскопического исследования специфических комплексов ДНК с различными белками, олигонуклеотидами и их аналогами. Разработаны методы изучения транскрипции in vitro, специфического взаимодействия ДНК с РНК-полимеразой E.coli, метилтрансферазами второго типа и ферментами рестрикции-модификации первого типа, триплекс-образующими нуклеотидами, пептидной нуклеиновой кислотой.

2. Изучено взаимодействие РНК-полимеразы E.coli с ДНК. Показано, что при физиологических условиях и в отсутствие реакции синтеза РНК фермент образует прочные комплексы преимущественно в промоторных участках ДНК. Показана высокая воспроизводимость картирования промоторных участков ДНК и предложен метод определения значений кажущихся констант ассоциации фермента с участками связывания. Обнаружена высокая корреляция в расположении участков связывания фермента, зон инициации транскрипции и наиболее легкоплавких областей ДНК. Данные выводы подтверждены результатами экспериментов, проведенных с ДНК фага Т7, плазмиды ColEl и митохондриальной ДНК крысы.

3. Исследовано взаимодействие метилтрансферазы второго типа M.BspRl (участок узнавания GGCC) с ДНК в отсутствии реакции метилирования. Найдено, что фермент образует специфические комплексы с ДНК, а комплекс является маркером участка узнавания. Экспериментальные карты связывания позволяют определять положения и число участков связывания с высокой точностью. Определены характерные времена образования и жизни комплексов. Показано, что в аналогичных условиях фермент рестрикции-модификации первого типа EcoRllAl (молекулярная структура M2S) образует специфический комплекс с ДНК, а комплекс является эффективным маркером участка узнавания (GGAN7RTCG ).

4. Изучено и охарактеризовано образование различных триплексов (PuPyPu, PuPyPy, alternate-strand), возникающих при взаимодействии триплекс-образующих олйгонуклеотидов с гомопурин-гомопиримидиновыми участками в протяженных молекулах ДНК. Показано, что стрептавидин является ЭМ маркером реакции связывания для биотинилированных производных ТОО. Для С,А-содержащего ТОО измерена кажущаяся константа скорости реакции связывания. Измерена эффективность формирования комплексов ДНК с различными олигонуклеотидами при разных условиях. Показано, что слабый alternatestrand триплекс может быть обнаружен, используя биотинилированный ТОО с химически присоединенным интеркалирующим хромофором.

5. Изучено взаимодействие гомопиримидиновых ПНК с гомопурин-гомопиримидиновыми последовательностями ДНК. Наглядно показано, что в результате специфического внедрения ПНК в двуцепочечную ДНК образуется триплекс ДНК/ПНК2 и вытесняется некомплементарная цепь ДНК. Показано, что стрептавидин является ЭМ маркером реакции связывания для биотинилированных производных ПНК. Обнаружено, что био-ПНК эффективно взаимодействует с участком узнавания в протяженных молекулах ДНК. Показано, что образование триплекса ДНК/ПНК2 приводит к изгибу двойной спирали ДНК и существенному увеличению ее конформационной гибкости в зоне триплекса.

6. Показано, что участки длиной 300-400 пар оснований произвольного состава можно выявлять в линейных молекулах ДНК с эффективностью детекции около 95%, используя метода R-петель. В суперспиральных молекулах такие участки можно надежно детектировать в результате внедрения в них протяженных 3'-концевых одноцепочечных последовательностей двухцепочечных ДНК и образования специфического комплекса за счет гомологичного спаривания в присутствии Ree А и SSB белков.

7. Предложен алгоритм определения надежности электронно-микроскопического картирования. Получены эмпирические зависимости, определяющие граничные условия для параметров реакции связывания и электронно-микроскопического эксперимента, при которых результат картирования можно считать достоверным.

8. Предложен общий подход к изучению специфического взаимодействия ДНК с лигандами различной природы (белки, олигонуклеотиды и их аналоги) с помощью электронной микроскопии, позволяющий развивать альтернативные методы физического картирования геномов.

Список литературы диссертационного исследования доктор биологических наук Черный, Дмитрий Ильич, 1999 год

1. Кантор, Ч. и Шиммел, П. Биофизическая химия, (Мир, Москва, 1985).

2. Ландау, Л.Д. и Лифшиц, Е.М. Статистическая физика, (Наука, Москва, 1976).

3. Сагитов, В.Р. и Александров, А.А. Селективность ДНК-метилазы BspRI. Доклады АН СССР 298, 1266-1268 (1988).

4. Спэнс, Д. Электронная микроскопия высокого разрешения, (Наука, Москва, 1986).

5. Хейденрайх, Р. Основы просвечивающей электронной микроскопии, (Мир, Москва, 1966).

6. Шиммель, Г. Методика электронной микроскопии, (Мир, Москва, 1972).

7. Adams, R.P.L. DNA methylation. The effect of minor bases on DNAprotein interactions. Biochem.J. 265, 309-320 (1990).

8. Allet, В., Jeppesen, P.G., Katagiri, K.J. & Delius, H. Mapping the DNA fragments produced by cleavage by lambda DNA with endonuclease RI. Nature 241, 120-3 (1973).

9. Allison, D.P., Ganesan, A.T., Olson, A.C., Snyder, C.M. & Mitra, S. Electron microscopic studies of bacteriophage M13 DNA replication. J Virol 24, 673-84(1977).

10. Allison, D.P. et al. Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules. Proc Natl Acad Sci USA 93, 8826-9(1996).

11. Allison, D.P. et al. Mapping individual cosmid DNAs by direct AFM imaging. Genomics 41, 379-84 (1997).

12. Anderson, P. & Bauer, W. Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry 17, 594-601 (1978).

13. Barcelo, F. et al. Removal of DNA curving by DNA ligands: gel electrophoresis study. Biochemistry 30, 4863-73 (1991).

14. Bayley, J.N. & McAllister, T. Mapping of promoter sites utilized by T3 RNA polymerase on T3 DNA. Nucleic Acids Res. 8, 5071-5088 (1980).

15. Bazett-Jones, D.P. & Brown, M.L. Electron microscopy reveals that transcription factor TFIIIA bends 5S DNA. Mol Cell Biol 9, 336-41 (1989).

16. Beal, P.A. & Dervan, P.B. Second structural motif for recognition of DNA by oligonucleotide- directed triple-helix formation. Science 251, 1360-3 (1991).

17. Beal, P.A. & Dervan, P.B. The influence of single base triplet changes on the stability of a pur.pur.pyr triple helix determined by affinity cleaving. Nucleic Acids Res 20, 2773-6 (1992).

18. Bednar, J. et al. Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J Mol Biol 254, 579-594 (1995).

19. Bednar, J. et al. The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. /. Mol.Biol. 235, 825-847 (1994).

20. Belotserkovskii, B.P. et al. Formation of intramolecular triplex in homopurine-homopyrimidine mirror repeats with point substitutions. Nucleic Acids Res 18, 6621-4 (1990).

21. Berg, O.G. & von Hippel, P.H. Selection of DNA binding sites by regulatory proteins. Statistical- mechanical theory and application to operators and promoters. J Mol Biol 193, 723-50 (1987).

22. Betts, L., Josey, J.A., Yeal, J.M. & Jordan, S.R. A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex. Science 270, 1838-41 (1995).

23. Boi'fa, L.C., Carpaneto, E.M. & Allfrey, Y.G. Isolation of active genes containing CAG repeats by DNA strand invasion by a peptide nucleic acid. Proc Natl Acad Sei U S A 92, 1901-5(1995).

24. Boles, T.C., White, J.H. & Cozzarelli, N.R. Structure of plectonemically supercoiled DNA. / Mol Biol 213, 931-51 (1990).

25. Bolshoy, A., McNamara, P., Harrington, R.E. & Trifonov, E.N. Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles. Proceedings of the National Academy of Sciences of USA 88, 2312-2316 (1991).

26. Bordier, C. & Dubochet, J. Electron microscopic localization of the binding sites of Escherichia coli RNA polymerase in the early promoter region of T7 DNA. Eur J Biochem 44, 617-24 (1974).

27. Borovik, A.S., Kalambet, Y.A., Lyubchenko, Y.L., Shitov, V.T. & Golovanov, E.I. Equilibrium melting of plasmid ColEl DNA: electron-microscopic visualization. Nucleic Acids Res 8, 4165-84 (1980).

28. Borowiec, J.A. & Gralla, J.D. Supercoiling response of the lac ps promoter in vitro. J Mol Biol 184, 587-98 (1985).

29. Botchan, P. An electron microscopic comparison of transcription on linear and superhelical DNA. J Mol Biol 105, 161-76 (1976).

30. Brack, C. Electron microscopic analysis of transcription: mapping of initiation sites and direction of transcription. Proc Natl Acad Sci USA 76, 3164-8 (1979).

31. Brack, C. & Delain, E. Electron-microscopic mapping of AT-rich regions and of E. coli RNA polymerase-binding sites on the circular kinetoplast DNA of Trypanosoma cruzi. J Cell Sci 17, 287-306 (1975).

32. Brack, C., Eberle, H., Bickle, T.A. & Yuan, R. Mapping of recognition sites for the restriction endonuclease from Escherichia coli K12 on bacteriophage PM2 DNA. J Mol Biol 108, 583-93 (1976).

33. Brack, C., Eberle, H., Bickle, T.A. & Yuan, R.A. A map of the sites of bactriophage PM2 DNA for the restriction endonuclease Hind III and Hpa II. J. Mol.Biol. 104, 309-313(1976).

34. Bratosin, S., Horowitz, M., Laub, O. & Aloni, Y. Electron microscopic evidence for splicing of SY40 late mRNAs. Cell 15, 1-14 (1978).

35. Brevet, J. & Tempe, J. Homology mapping of T-DNA regions on three Agrobacterium rhizogenes Ri plasmids by electron microscope heteroduplex studies. Plasmid 19, 75-83 (1988).

36. Burton, S.K., Van 't Ho, J. & Bryant, J.A. Novel DNA-binding characteristics of a protein associated with DNA polymerase-alpha in pea. Plant J 12, 357-65 (1997).

37. Bustamante, C. & Rivetti, C. Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu Rev Biophys Biomol Struct 25, 395-429 (1996).

38. Caffarelli, E., Leoni, L., Sarapaolese, B. & Savino, M. Persistence of cruciform structure and preferential location of nucleosomes on some regions of pBR322 and ColE 1 DN As. Eur J Biochem 156, 335-42 (1986).

39. Cai, W. et al. Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces. Proc Natl Acad Sci USA 92,5164-8 (1995).

40. Calladine, C.R., Collis, C.M., Drew, H.R. & Mott, M.R. A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J Mol Biol 221, 981-1005 (1991).

41. Calladine, C.R. & Drew, H.R. Principles of sequence-dependent flexure of DNA. / Mol Biol 192, 907-18 (1986).

42. Calladine, C.R., Drew, H.R. & McCall, M.J. The intrinsic curvature of DNA in solution. J Mol Biol 201, 127-37 (1988).

43. Campbell, V.W. & Jackson, D.A. The effect of divalent cations on the mode of action of DNase I. The initial reaction products produced from covalently closed circular DNA. J Biol Chem 255, 3726-35 (1980).

44. Castleman, H., Hanau, L.H., Zacharias, W. & Erlanger, B.F. Z DNA and loop structures by immunoelectronmicroscopy of supercoiled pRW751, a plasmid containing left-handed helices. Nucleic Acids Res 16, 3977-96 (1988).

45. Castleman, H., Specthrie, L., Makowski, L. & Erlanger, B.F. Electronmicroscopy and circular dichroism of the dynamics of the formation and dissolution of supramolecular forms of Z-DNA. J Biomol Struct Dyn 2, 271-83 (1984).

46. Cech, T.R. & Pardue, M.L. Electron microscopy of DNA crosslinked with trimethylpsoralen: test of the secondary structure of eukaryotic inverted repeat sequences. Proc Natl Acad Sci USA 73, 2644-8 (1976).

47. Chamberlin, M.J. New models for the mechanism of transcription elongation and its regulation. Harvey Lect 88, 1-21 (1992).

48. Chattoraj, D.K. & Inman, R.B. Electron microscope heteroduplex mapping of P2 Hy dis bacteriophage DNA. Virology 55, 174-82 (1973).

49. Chattoraj, D.K. & Inman, R.B. Tandem duplication in bacteriophage P2: electron microscopic mapping. Proc Natl Acad Sci US A 71, 311-4 (1974).

50. Chen, C.Y., Hutchison, C.A.d. & Edgell, M.H. Isolation and genetic localization of three phi-X174 promoter regions. Nat New Biol 243, 233-6 (1973).

51. Chen, W.P., Cheng, C.M., Wang, A.H. & Kuo, T.T. Single-stranded DNA binding protein from bacteriophage cf: characterization, gene localization and protein-ssDNA complex. Biochim Biophys Acta 1309, 147-55 (1996).

52. Chiu, S.K., Wong, B.C. & Chow, S.A. Homologous pairing in duplex DNA regions and the formation of four- stranded paranemic joints promoted by RecA protein. Effects of gap length and negative superhelicity. J Biol Chem 265, 21262-8 (1990).

53. Christiansen, G. Electron microscopy of nucleic acid. Dan Med Bull 35, 3348 (1988).

54. Christiansen, G. & Griffith, J. Visualization of the paranemic joining of homologous DNA molecules catalyzed by the RecA protein of Escherichia coli. Proc Natl Acad Sci U S A 83, 2066-70 (1986).

55. Clark, R.K. et al. Restriction endonuclease analysis of herpesviruses isolated from two peninsular bighorn sheep (Ovis canadensis cremnobates). J WildlDis 29, 50-6 (1993).

56. Coggins, L.W., Slater, A.A., M, O.P. & Campo, M.S. R-loop mapping of RNA transcripts from bovine papillomavirus type 4. Br J Cancer Suppl 9, 85-8 (1988).

57. Cowan, G.M., Gann, A.A.F., Murray, N.E. & 1989. Conservation of complex DNA recognition domains between families of restriction enzymes. Cell 56, 103-109 (1989).

58. Cox, M.M. The RecA protein as a recombinational repair system. Mol Microbiol 5, 1295-9(1991).

59. Crothers, D.M., Haran, T.E. & Nadeau, J.G. Intrinsically bent DNA. J Biol Chem 265, 7093-6 (1990).

60. Dasgupta, S. & Inman, R.B. Denaturation mapping. Methods Enzymol 65, 429-36 (1980).

61. Davis, R.W., Simon, M. & Davidson, N. Electron microscope heteroduplex methods for mapping regions of base sequence homology in nucleic acids. Meth.Enzymol. 21D, 413-428 (1971).

62. De Santis, P., Fua, M., Palleschi, A. & Savino, M. Influence of dynamic fluctuations on DNA curvature. Biophys Chem 55, 261-71 (1995).

63. Delain, E., Fourcade, A., Revet, B. & Mory, C. New possibilities in the observation of nucleic acids by electron microscopic imaging. Microsc.Microanal. Microstruct. 3, 175-186 (1992).

64. Delain, E. & Le Cam, E. The spreading of nucleic acids, in Visualisation of Nucleic Acids (ed. Morel, G.) 35-56 (CRC Press Inc., Boca Raton, FL, 1995).

65. Delius, H., Westphal, H. & Axelrod, N. Length measurements of RNA synthesized in vitro by Escherichia coli RNA polymerase. J Mol Biol 74, 677-87 (1973).

66. Demidov, V.V., Frank-Kamenetskii, M.D., Egholm, M., Buchardt, O. & Nielsen, P.E. Sequence selective double strand DNA cleavage by Peptide nucleic acid (PNA) targeting using nuclease SI. Nucleic Acids Research 21, 2103-2107 (1993).

67. Demidov, Y.Y., Yavnilovich, M.V., Belotserkovskii, B.P., Frank-Kamenetskii, M.D. & Nielsen, P.E. Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA. Proc Natl Acad Sei U S A 92, 2637-41 (1995).

68. Dlakic, M. & Harrington, R.E. The effects of sequence context on DNA curvature. Proc Natl Acad Sei USA 93, 3847-52 (1996).

69. Dubey, A.K. & Roberts, R. Sequence-specific DNA binding by the Mspl DNA methyltransferase. Nucleic Acids Res. 20, 3167-3173 (1992).

70. Dubochet, J., Booy, F.P., Freeman, R., Jones, A.V. & Walter, C.A. Low temperature electron microscopy. Annu Rev Biophys Bioeng 10, 133-49 (1981).

71. Dubochet, J., Ducommun, M., Zollinger, M. & Kellenberger, E. A new preparation method for dark-field electron microscopy of biomacromolecules. J Ultrastruct Res 35, 147-67 (1971).

72. Dueholm, K.L. & Nielsen, P.E. Chemistry, properties and applications of PNA (Peptide Nucleic Acid). New J Chem 21, 19-31 (1997).

73. Edlind, T.D. & Ihler, G.M. Electron microscopic mapping of complementary sequences on single strands of bacteriophage lambda DNA. J Mol Biol 160, 23-39 (1982).

74. Egholm, M. et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365, 566-568 (1993).

75. Egholm, M., Buchardt, O., Nielsen, P.E. & Berg, R.H. Peptide nucleic acids(PNA). Oligonucleotide analogues with an achiral peptide bachbone. J.Am.Chem.Soc. 114, 1895-1897(1992).

76. Egholm, M., Buchardt, O., Nielsen, P.E. & Berg, R.H. Recognition of guanine and adenine in DNA by cytosine and thymine containing peptide nucleic acids(PNA). J.Am.Chem.Soc. 114, 9677-9678 (1992).

77. Egholm, M. et al. Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res 23, 217-22 (1995).

78. Endlich, B. & Linn, S. The DNA restriction endonuclease of Escherichia coli B. I. Studies of the DNA translocation and the ATPase activities. J Biol Chem 260, 5720-8 (1985).

79. Engler, G. et al. Physical mapping of DNA base sequence homologies between an octopine and a nopaline Ti plasmid of Agrobacterium tumefaciens. J Mol Biol 152, 183-208 (1981).

80. Erie, D.A., Yang, G., Schultz, H.C. & Bustamante, C. DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity see comments. Science 266, 1562-6 (1994).

81. Eriksson, M. & Nielsen, P.E. PNA-nucleic acid complexes. Structure, stability and dynamics. Q Rev Biophys 29, 369-94 (1996).

82. Evertsz, E.M., Rippe, K. & Jovin, T.M. Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs. Nucleic Acids Res 22, 3293-303 (1994).

83. Felsenfeld, G., Davis, D.R. & Rich, A. Formation of a three-stranded polynucleotide molecule. J.Am.Chem.Soc. 79, 2023-2024 (1957).

84. Ferguson, J. & Davis, R.W. An electron microscopic method for studying and mapping the region of weak sequence homology between simian virus 40 and polyoma DNAs. J Mol Biol 94, 135-49 (1975).

85. Francois, J.C., Saison-Behmoaras, T. & Helene, C. Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies. Nucleic Acids Res 16, 11431-40 (1988).

86. Francois, J.C., Saison-Behmoaras, T., Thuong, N.T. & Helene, C. Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides. Biochemistry 28, 9617-9 (1989).

87. Frank-Kamenetskii, M.D., Malkov, V.A., Voloshin, O.N. & Soyfer, V.N. Stabilization of PyPuPu triplexes with bivalent cations. Nucleic Acids Symp Ser , 159-62(1991).

88. Frank-Kamenetskii, M.D. & Mirkin, S.M. Triplex DNA structures. Annu Rev Biochem 64, 65-95 (1995).

89. Frontali, C. et al. An absolute method for the determination of the persistence length of native DNA from electron micrographs. Biopolymers 18, 1353-73 (1979).

90. Furrer, P. et al. Opposite effect of counterions on the persistence length of nicked and non-nicked DNA. J Mol Biol 266, 711-21 (1997).

91. Garcia, R.A., Bustamante, C.J. & Reich, N.O. Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA. Proc Natl Acad Sei U S A 93, 7618-22 (1996).

92. Giovannangeli, C. & Helene, C. Progress in developments of triplex-based strategies. Antisense Nucleic Acid Drug Dev 7, 413-21 (1997).

93. Goldstein, L., Thomas, M. & Davis, R.W. EcoRI endonuclease cleavage map of bacteriophage P4-DNA. Virology 66, 420-7 (1975).

94. Gonzalez, B., Yasquez, C., Bull, P. & Vicuna. Electron microscopy mapping of Escherichia coli RNA polymerase-binding sites on plasmids from thermophilic bacteria. Dna 3, 251-7 (1984).

95. Gosalvez, J. et al. Selective digestion of mouse chromosomes with restriction endonucleases. Oligonucleotide priming of single-stranded DNA produced with exonuclease III. Genome 36, 230-4 (1993).

96. Grabczyk, E. & Fishman, M.C. A long purine-pyrimidine homopolymer acts as a transcriptional diode. J Biol Chem 270, 1791-7 (1995).

97. Grellet, F. et al. Electron microscopic mapping of wheat germ RNA polymerase II binding sites on cloned CaMV DNA. Nucleic Acids Res 9, 3927-39 (1981).

98. Griffith, J., Bleyman, M., Rauch, C.A., Kitchin, P.A. & Englund, P.T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell 46, 717-24(1986).

99. Griffith, J., Dieckmann, M. & Berg, P. Electron microscope localization of a protein bound near the origin of simian virus 40 DNA replication. J Virol 15, 167-72(1975).

100. Griffith, J.D. DNA structure: evidence from electron microscopy. Science 201, 525-7(1978).

101. Griffith, J.D., Lee, S. & Wang, Y.H. Visualizing nucleic acids and their complexes using electron microscopy. Curr Opin Struct Biol 7, 362-6 (1997).

102. Guthold, M. et al. Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope. Proc Natl Acad Sci USA 91, 12927-31 (1994).

103. Hagen, F.K., Zarling, D.A. & Jovin, T.M. Electron microscopy of SV40 DNA cross-linked by anti-Z DNA IgG. Embo J 4, 837-44 (1985).

104. Hagerman, P.J. Sequence-directed curvature of DNA. Nature 321, 449-50 (1986).

105. Hagerman, P.J. Flexibility of DNA. Annu Rev Biophys Biophys Chem 17, 265-86(1988).

106. Hainfeld, J.F. & Wall, J.S. High resolution electron microscopy for structure and mapping. Basic Life Sci 46, 131-47 (1988).

107. Hale, P., Woodward, R.S. & Lebowitz, J. E. coli RNA polymerase promoters on superhelical SY40 DNA are highly selective targets for chemical modification. Nature 284, 640-4 (1980).

108. Hammermann, M. et al. Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics. Biophys J 73, 2674-87 (1997).

109. Hampel, K.J., Burkholder, G.D. & Lee, J.S. Plasmid dimerization mediated by triplex formation between polypyrimidine-polypurine repeats. Biochemistry 32, 1072-7(1993).

110. Hampel, K.J., Crosson, P. & Lee, J.S. Polyamines favor DNA triplex formation at neutral pH. Biochemistry 30, 4455-9 (1991).

111. Han, W., Dlakic, M., Zhu, Y.J., Lindsay, S.M. & Harrington, R.E. Strained DNA is kinked by low concentrations of Zn2+. Proc Natl Acad Sci U S A 94, 10565-70(1997).

112. Hansma, H.G., Browne, K.A., Bezanilla, M. & Bruice, T.C. Bending and straightening of DNA induced by the same ligand: characterization with the atomic force microscope. Biochemistry 33, 8436-41 (1994).

113. Hansma, H.G., Revenko, I., Kim, K. & Laney, D.E. Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res 24, 713-20 (1996).

114. Hanvey, J.C. et al. Antisense and antigene properties of peptide nucleic acids. Science 258, 1481-5(1992).

115. Hanvey, J.C., Shimizu, M. & Wells, R.D. Site-specific inhibition of EcoRI restriction/modification enzymes by a DNA triple helix. Nucleic Acids Res 18, 15761 (1990).

116. Harford, A.G. & Beer, M. Electron-microscopic localization of the binding of Escherichia coli RNA polymerase to T7 DNA in vitro. J.Mol.Biol. 69, 179-186 (1972).

117. Harvey, S.C. et al. What is the basis of sequence-directed curvature in DNAs containing A tracts. J.Biomol.Struct.Dyns. 13, 301-307 (1995).

118. Helene, C. Rational design of sequence-specific oncogene inhibitors based on antisense and antigene oligonucleotides. Eur J Cancer 27, 1466-71 (1991).

119. Helene, C. The anti-gene strategy: control of gene expression by triplex-forming- oligonucleotides. Anticancer Drug Des 6, 569-84 (1991).

120. Helene, C. Control of oncogene expression by antisense nucleic acids. Review. European Journal of Cancer (1994).

121. Helene, C., Giovannangeli, C., Guieysse-Peugeot, A.L. & Praseuth, D. Sequence-specific control of gene expression by antigene and clamp oligonucleotides. Ciba Found Symp 209, 94-102; discussion 102-6 (1997).

122. Helene, C. & Le Doan, T. Oligonucleotides: problems and frontiers of practical applications. Trends Biotechnol 9, 339-40 (1991).

123. Hirsch, J. & Schleif, R. High resolution electron microscopic studies of genetic regulation. J.Mol.Biol. 108, 471-490 (1976).

124. Hörne, D.A. & Dervan, P.B. Effects of an abasic site on triple helix formation characterized by affinity cleaving. Nucleic Acids Res 19, 4963-5 (1991).

125. Hsu, M.T. Electron microscopic evidence for the cruciform structure in intracellular SY40 DNA. Virology 143, 617-21 (1985).

126. Hyrup, B. & Nielsen, P.E. Peptide nucleic acids (PNA): Synthesis, properties and potential applications. Bioorganic and Medicinal Chemistry 4, 5-23 (1996).

127. Inaga, S., Osatake, H. & Tanaka, K. SEM images of double helix and nucleosomes observed by ultrahigh-resilution scanning electron microscopy. J.Electron Microsc. 40, 181-186(1991).

128. Inman, R.B. Denaturation mapping of DNA. Methods Enzymol 29, 451-8 (1974).

129. Inman, R.B. & Jackson, J.F. Mapping Z-DNA tracts in plasmid DNA using electron microscopy and gold- labeled antibodies. Gene 84, 221-6 (1989).

130. Ito, T., Smith, C.L. & Cantor, C.R. Sequence-specific DNA purification by triplex affinity capture. Proc Natl Acad Sei USA 89, 495-8 (1992).

131. Jain, S.K., Cox, M.M. & Inman, R.B. Occurrence of three-stranded DNA within a RecA protein filament. J Biol Chem 270, 4943-9 (1995).

132. Jarvis, A.W. & Meyer, J. Electron microscopic heteroduplex study and restriction endonuclease cleavage analysis of the DNA genomes of three lactic streptococcal bacteriophages. Appl Environ Microbiol 51, 566-71 (1986).

133. Jayasena, S.D. & Johnston, B.H. Intramolecular triple-helix formation at (PunPyn).(PunPyn) tracts: recognition of alternate strands via Pu.PuPy and Py.PuPy base triplets. Biochemistry 31, 320-7 (1992).

134. Jayasena, S.D. & Johnston, B.H. Oligonucleotide-directed triple helix formation at adjacent oligopurine and oligopyrimidine DNA tracts by alternate strand recognition. Nucleic Acids Res 20, 5279-88 (1992).

135. Jayasena, S.D. & Johnston, B.H. Sequence limitations of triple helix formation by alternate-strand recognition. Biochemistry 32, 2800-7 (1993).

136. Joanicot, M. & Revet, B. DNA conformational studies from electron microscopy. I. Excluded volume effect and structure dimensionality. Biopolymers 26, 315-26 (1987).

137. Johannssen, W. Electron microscopy studies of DNA complexes with restriction endonuclease SalGI. Z Allg Mikrobiol 23, 197-201 (1983).

138. Jondle, D.M., Ambrosio, L., Vesenka, J. & Henderson, E. Imaging and manipulating chromosomes with the atomic force microscope. Chromosome Res 3, 239-44(1995).

139. Kabak, D.B., Angerer, L.M. & Davidson, N. Nucleic Acids Res. 6, 24992517 (1976).

140. Kadesch, T.R., Rosenberg, S. & Chamberlin, M.J. Binding of Escherichia coli RNA polymerase holoenzyme to bacteriophage T7 DNA. Measurements ofbinding at bacteriophage T7 promoter Al using a template competition assay. J Mol Biol 155, 1-29(1982).

141. Kadesch, T.R., Williams, R.C. & Chamberlin, M.J. Electron microscopic studies of the binding of Escherichia coli RNA polymerase to DNA. II. Formation of multiple promoter-like complexes at non-promoter sites. J Mol Biol 136, 79-93(1980).

142. Kahn, J.D., Yun, E. & Crothers, D.M. Detection of localized DNA flexibility. Nature 368, 163-6 (1994).

143. Karlovsky, P. Calculation of individual cleavage rates from partial digests in restriction endonuclease kinetics. J Theor Biol 132, 7-14 (1988).

144. Kasas, S. et al. Escherichia coli RNA polymerase activity observed using atomic force microscopy. Biochemistry 36, 461-8 (1997).

145. Keegstra, W., Vereijken, J.M. & Jansz, H.S. Mapping and length measurements of restriction enzyme fragments by electron microscopy. Biochim Biophys Acta 475, 176-83 (1977).

146. Kiss, I., Boros, I., Udvardy, A., Venetianer, P. & Delius, H. RNA-polymerase binding at the promoters of the rRNA genes of Escherichia coli. Biochim Biophys Acta 609, 435-47 (1980).

147. Kleinschmidt, A.K. & Zahn, R.K. Uber deoxyribonukeinsaure-Molekulen in Protein Misschfilmen. Z.Naturforsch. 14b, 770-779 (1959).

148. Koller, T., Kubler, O., Portmann, R. & Sogo, J.M. High resolution physical mapping of specific binding sites of Escherichia coli RNA polymerase on the DNA of bacteriophage T7. J Mol Biol 120, 121-31 (1978).

149. Koncz, C., Kiss, A. & Venetianer, P. Biochemical characterization of the restriction-modification system of Bacillus sphaericus. Eur.J.Biochem. 89, 523-529 (1978).

150. Koo, H.S., Drak, J., Rice, J.A. & Crothers, D.M. Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry 29, 4227-341990).

151. Koob, M., Burkiewicz, A., Kur, J. & Szybalski, W. RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site. Nucleic Acids Res 20, 5831-6 (1992).

152. Kowalczykowski, S.C. Biochemical and biological function of Escherichia coli RecA protein: behavior of mutant RecA proteins. Biochimie 73, 289-3041991).

153. Kratky, O. & Porod, G. Recueil Trav.chim.Pays-Bas 68, 1106 (1949).

154. Kress, H., Meyerowitz, E.M. & Davidson, N. High resolution mapping of in situ hybridized biotinylated DNA to surface-spread Drosophila polytene chromosomes. Chromosomal, 113-22(1985).

155. Kruger, D.H. et al. Restriction endonucleases functionally interacting with two DNA sites. Gene 157, 165 (1995).

156. Lagutina, I.V. et al. Determination of the patterns of hexanucleotide distribution along DNA by electron microscopy. Genet Anal 13, 9-14 (1996).

157. Landgraf, R., Chen, C.H. & Sigman, D.S. R-loop stability as a function of RNA structure and size. Nucleic Acids Res 23, 3516-23 (1995).

158. Landgraf, R., Ramamurthi, K.S. & Sigman, D.S. Kinetics of spontaneous displacement of RNA from heteroduplexes by DNA. Nucleic Acids Res 24, 324652 (1996).

159. Laundon, C.H. & Griffith, J.D. Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell 52, 545-9 (1988).

160. Le Cam, E. & Delain, E. Nucleic acids-ligands interactions, in Visualisation of Nucleic Acids (ed. Morel, G.) 331-356 (CRC Press Inc., Boca Raton, FL, 1995).

161. Le Cam, E. et al Conformational analysis of a 139 base-pair DNA fragment containing a single-stranded break and its interaction with human poly(ADP-ribose) polymerase. J Mol Biol 235, 1062-71 (1994).

162. Le Cam, E., Theveny, B., Mignotte, B., Revet, B. & Delain, E. Quantitative electron microscopic analysis of DNA-protein interactions. J Electron Microsc Tech 18, 375-86 (1991).

163. Le Doan, T. et al. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-alpha.-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res 15, 7749-60 (1987).

164. Lebedev, Y.V. et al. Physical mapping of sequences homologous to an endogeneous retovirus LTR on human chromosome 19. Mol. Gen. Genet. 247, 742748 (1995).

165. Lebrun, A. & Lavery, R. Modelling extreme stretching of DNA. Nucleic Acids Res 24, 2260-2267 (1996).

166. Lee, J.S., Ashley, C., Hampel, K.J., Bradley, R. & Scraba, D.G. A stable interaction between separated pyrimidine.purine tracts in circular DNA. J Mol Biol 252, 283-8 (1995).

167. Lee, J.S. et al. Triplex DNA in plasmids and chromosomes. Gene 82, 191-9 (1989).

168. Legerski, R.J. & Robberson, D.L. Analysis and optimization of recombinant DNA joining reactions. J Mol Biol 181, 297-312 (1985).

169. Lescure, B., Chestier, A. & Yaniv, M. Transcription of polyoma virus DNA in vitro. II. Transcription of superhelical and linear polyoma DNA by RNA polymerase II. J Mol Biol 124, 73-85 (1978).

170. Lescure, B., Dauguet, C. & Yaniv, M. Transcription of polyoma virus DNA in vitro. III. Localization of calf thymus RNA polymerase II binding sites. / Mol Biol 124, 87-96(1978).

171. Lescure, B., Oudet, P., Chambon, P. & Yaniv, M. Transcription of polyoma virus DNA in vitro. Localization of Escherichia coli RNA polymerase initiation sites. J Mol Biol 108, 83-97 (1976).

172. Lescure, B. & Yaniv, M. Denaturation map of polyoma DNA. J Virol 16, 720-4(1975).

173. Levene, S.D., Wu, H.M. & Crothers, D.M. Bending and flexibility of kinetoplast DNA. Biochemistry 25, 3988-95 (1986).

174. Littlewood, R.K. & Inman, R.B. Computer-assisted DNA length measurements from electron micrographs with special reference to partial denaturation mapping. Nucleic Acids Res 10, 1691-706 (1982).

175. Liu, L.F. & Wang, J.C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci US AM, 7024-7 (1987).

176. Lower, R., Lower, J. & Kurth, R. The viruses in all of us: charactristics and biological significance of human endogeneous retrovirus sequences. Proc.Nall.Acad.Sci. USA 93, 5177-5184 (1996).

177. Lurz, R., Danbara, H., Ruckert, B. & Timmis, K.N. Plasmid replication functions. VII. Electron microscopic localization of RNA polymerase binding sites in the replication control region of plasmid R6-5. Mol Gen Genet 183, 490-6 (1981).

178. Lyamichev, V.I., Mirkin, S.M., Frank-Kamenetskii, M.D. & Cantor, C.R. A stable complex between homopyrimidine oligomers and the homologous regions of duplex DNAs. Nucleic Acids Res 16, 2165-78 (1988).

179. Lyamichev, V.I., Panyutin, I.G., Cherny, D.I. & Lyubchenko Yu, L. Localization of low-melting regions in phage T7 DNA. Nucleic Acids Res 11, 2165-76(1983).

180. Lyamichev, V.I., Voloshin, O.N., Frank-Kamenetskii, M.D. & Soyfer, V.N. Photofootprinting of DNA triplexes. Nucleic Acids Res 19, 1633-8 (1991).

181. Lyubchenko, Y.L. et al. Atomic force microscopy imaging of double stranded DNA and RNA. J Biomol Struct Dyn 10, 589-606 (1992).

182. Lyubchenko, Y.L. & Shlyakhtenko, L.S. Visualisation of supercoiled DNA with atomic force microscopy in situ. Proc.Natl.Acad.Sci. USA 94, 496-501 (1997).

183. Maher, L.J.d., Wold, B. & Dervan, P.B. Oligonucleotide-directed DNA triple-helix formation: an approach to artificial repressors? Antisense Res Dev 1, 277-81 (1991).

184. Malkov, Y.A., Soyfer, V.N. & Frank-Kamenetskii, M.D. Effect of intermolecular triplex formation on the yield of cyclobutane photodimers in DNA. Nucleic Acids Res 20, 4889-95 (1992).

185. Malkov, V.A., Voloshin, O.N., Soyfer, V.N. & Frank-Kamenetskii, M.D. Cation and sequence effects on stability of intermolecular pyrimidine- purine-purine triplex. Nucleic Acids Res 21, 585-91 (1993).

186. Maniatis, T., Fritch, E.F. & Sambrook, J. Molecular cloning: A laboratory manual, (Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1982).

187. Manor, H., Wu, M., Baran, N. & Davidson, N. Electron microscopic mapping of RNA transcribed from the late region of polyoma virus DNA. J Virol 32, 293-303 (1979).

188. Marx, R. & Doenecke, D. Binding of polylysine and ethidium bromide to nucleosomal DNA: comparison of biochemical and electron microscopical results. ZNaturforsch C. 36, 149-56 (1981).

189. May, E., Maizel, J.V. & Salzman, N.P. Mapping of transcription sites of simian virus 40-specific late 16S and 19S mRNA by electron microscopy. Proc Natl Acad Sci USA 74, 496-500 (1977).

190. Meyer, J. & Stalhammar-Carlemalm, M. Visualization of RNA polymerase bound to R-loop molecules improves electron microscopic analysis of in vitro transcription. J Ultrastruct Mol Struct Res 96, 189-93 (1986).

191. Meyer-Almes, F.J., Heumann, H. & Porschke, D. The structure of the RNA poiymerase-promoter complex. DNA-bending-angle by quantitative electrooptics. J Mol Biol 236, 1-6 (1994).

192. Michel, D., Chatelain, G., Herault, Y., Harper, F. & Brun, G. H-DNA can act as a transcriptional insulator. Cell Mol Biol Res 39, 131-40 (1993).

193. Mikami, T., Harada, T. & Kinoshita, T. Heterogeneity of circular mitochondrial DNA molecules from sugar beet with normal and male sterile cytoplasms. Curr Genet 10, 695-700 (1986).

194. Miller, F.D. el al. Natural occurrence of left-handed (Z) regions in PM2 DNA. J Biomol Struct Dyn 1, 611-20 (1983).

195. Miwa, T., Takanami, M. & Yamagishi, H. Electron microscopic visualization of restriction sites on DNA molecules. Gene 6, 319-30 (1979).

196. Mizuuchi, K., Mizuuchi, M. & Geliert, M. Cruciform structures in palindromic DNA are favored by DNA supercoiling. J Mol Biol 156, 229-43 (1982).

197. Modrich, P. Studies on sequence recognition by type II restriction and modification enzymes. CRC Crit Rev Biochem 13, 287-323 (1982).

198. Modrich, P. Studies on sequence recognition by type II restriction and modification enzymes. CRC Crit.Revs Biochem. 13, 287-323 (1982).

199. Mollegaard, N.E., Buchardt, O., Egholm, M. & Nielsen, P.E. Peptide nucleic acid-DNA strand displacement loops as artificial transcription promoters. Proc.Natl.Acad.Sci. USA 91, 3892-3895 (1994).

200. Moore, C. & Griffith, J. Mapping restriction sites on large DNAs by electron microscopy. Gene 24, 191-8 (1983).

201. Moore, K.H., Johnson, P.H., Chandler, S.E. & Grossman, L.I. A restriction endonuclease cleavage map of mouse mitochondrial DNA. Nucleic Acids Res A, 1273-89 (1977).

202. Moreau, J., Kejzlarova-Lepesant, J., Brock, H., Lepesant, J.A. & Scherrer, K. AT-rich linkers in long range organisation of Drosophila DNA. Mol Gen Genet 199, 357-64(1985).

203. Mori, J., Beattie, P., Melton, D.W., Cohen, BJ. & Clewley, J.P. Structure and mapping of the DNA of human parvovirus B19. J Gen Virol 68, 2797-806 (1987).

204. Mory, C., Colliex, C., Revet, B. & Delain, E. Improved visualization of single- and double-strained nucleic acids by STEM. Anat Rec 194, 547-62 (1979).

205. Moser, H.E. & Dervan, P.B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238, 645-50 (1987).

206. Mou, J., Czajkowsky, D.M., Zhang, Y. & Shao, Z. High-resolution atomic-force microscopy of DNA: the pitch of the double helix. FEBS Lett 371, 279-82 (1995).

207. Mouscadet, J.F. et al. Triple helix formation with short oligonucleotide-intercalator conjugates matching the HIV-1 U3 LTR end sequence. Biochemistry 33,4187-96(1994).

208. Muller, T. et al. Imaging the asymmetrical DNA bend induced by repressor activator protein 1 with scanning tunneling microscopy. J Struct Biol 113, 1-12 (1994).

209. Muzard, G., Theveny, B. & Revet, B. Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models. Embo J 9, 1289-98 (1990).

210. Nadeau, J.G. & Crothers, D.M. Structural basis for DNA bending. Proc Natl Acad Sci USA 86, 2622-6 (1989).

211. Nesvera, J., Hochmannova, J. & Stokrova, J. An in vivo cointegrate of two plasmids from incompatibility group X. Folia Microbiol (Praha) 31, 257-66 (1986).

212. Nesvera, J., Klaus, S., Stokrova, J. & Hochmannova, J. RNA polymerase binding sites on a plasmid R6K derivative with increased copy number. J Basic Microbiol 27, 63-7 (1987).

213. Nielsen, P.E. Sequence-selective DNA recognition by synthetic ligands. Bioconjug Chem 2, 1-12 (1991).

214. Nielsen, P.E. DNA analogues with nonphosphodiester backbones. Annu Rev Biophys Biomol Struct 24, 167-83 (1995).

215. Nielsen, P.E. Peptide nucleic acid (PNA): a model structure for the primordial genetic material? Microbiol SEM 11, 209-216 (1995).

216. Nielsen, P.E., Egholm, M., Berg, R.H. & Buchardt, O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254, 1497-500 (1991).

217. Nielsen, P.E., Egholm, M., Berg, R.H. & Buchardt, O. Peptide nucleic acids (PNAs): potential antisense and anti-gene agents. Anticancer Drug Des 8, 5363 (1993).

218. Nielsen, P.E., Egholm, M., Berg, R.H. & Buchardt, O. Peptide nucleic acids (PNAs): Potential anti-sense and anti-gene agents. Anti-Cancer Drug Design 8, 53-63(1993).

219. Nielsen, P.E., Egholm, M., Berg, R.H. & Buchardt, O. Sequence specific inhibition of DNA restriction enzyme cleavage by PNA. Nucleic Acids Res 21, 197-200(1993).

220. Nielsen, P.E., Egholm, M. & Buchardt, O. Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J Mol Recognit 7, 165-70 (1994).

221. Nielsen, P.E., Egholm, M. & Buchardt, O. Sequence-specific transcription arrest by peptide nucleic acid bound to the DNA template strand. Gene 149, 139-45(1994).

222. Nielsen, P.E. et al. DNA binding and photocleavage by uranyl (IV) (UO 2+ 2) salts. / Am Chem Soc 114, 5967-4975 (1992).

223. Nordheim, A. et al. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell 31, 309-18 (1982).

224. Nordheim, A. et al. Analysis of Z-DNA in fixed polytene chromosomes with monoclonal antibodies that show base sequence-dependent selectivity in reactions with supercoiled plasmids and polynucleotides. J Biol Chem 261, 468-76 (1986).

225. Ohta, T. et al. Atomic force microscopy proposes a novel model for stem-loop structure that binds a heat shock protein in the Staphylococcus aureus HSP70 operon. Biochem Biophys Res Commun 226, 730-4 (1996).

226. Old, R., Murray, K. & Boizes, G. Recognition sequence of restriction endonuclease III from Hemophilus influenzae. J Mol Biol 92, 331-9 (1975).

227. Olson, W.K. et al. Flexing and folding double helical DNA. Biophysical Chemistry 55, 7-29 (1995).

228. Olson, W.K., Marky, N.L., Jernigan, R.L. & Zhurkin, V.B. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J Mol Biol 232, 530-54 (1993).

229. Ono, A., Chen, C.N. & Kan, L.S. DNA triplex formation of oligonucleotide analogues consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities. Proc Natl Acad Sci USA 88, 9397-401 (1991).

230. Ostrander, E.A., Benedetti, P. & Wang, J.C. Template supercoiling by a chimera of yeast GAL4 protein and phage T7 RNA polymerase. Science 249, 1261-5(1990).

231. Palchaudhuri, S. & Maas, W.K. Physical mapping of a DNA sequence common to plasmids of incompatibility group F I. Proc Natl Acad Sei U S A 74, 1190-4(1977).

232. Palecek, E. Local supercoil-stabilized DNA structures. Crit Rev Biochem Mol Biol 26, 151-226(1991).

233. Parker, A.P. & Dean, D.H. Temperate Bacillus bacteriophage SP 16 genome is circularly permuted and terminally redundant. J Bacteriol 167, 719-21 (1986).

234. Pavlov, V.M., Lyubchenko, Y.L., Borovik, A.S. & Lazurkin, Y.S. Specific fragmentation of T7 phage DNA at low-melting sites. Nucleic Acids Res 4, 4053-62(1977).

235. Peffer, N.J. et al. Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Proc Natl Acad Sei U S A 90, 10648-52 (1993).

236. Perelroyzen, M.P. & Vologodskii, A.V. Theoretical analysis of 'addressed' chemical modification of DNA. Nucleic Acids Res 16, 4693-704 (1988).

237. Perez-Martin, J. et al. Induced bending of plasmid pLSl DNA by the plasmid-encoded protein RepA. J Biol Chem 264, 21334-9 (1989).

238. Pfannschmidt, C. & Langowski, J. Superhelix organization by DNA curvature as measured through site- specific labeling. J Mol Biol 275, 601-11 (1998).

239. Pfannschmidt, C., Schaper, A., Heim, G., Jovin, T.M. & Langowski, J. Sequence-specific labeling of superhelical DNA by triple helix formation and psoralen crosslinking. Nucleic Acids Res 24, 1702-9 (1996).

240. Pietrasanta, L.I., Schaper, A. & Jovin, T.M. Probing specific molecular conformations with the scanning force microscope. Complexes of plasmid DNA and anti-Z-DNA antibodies. Nucleic Acids Res 22, 3288-92 (1994).

241. Plum, G.E., Park, Y.W., Singleton, S.F., Dervan, P.B. & Breslauer, K.J. Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc Natl Acad S ci USA 87, 9436-40 (1990).

242. Porod, G. X-ray and light scattering by chain molecules in solution. J.Polimer S ci, 10, 157-166 (1953).

243. Porschke, D. Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations. Biophys Chem 40, 169-79 (1991).

244. Porschke, D., Schmidt, E.R., Hankeln, T., Nolte, G. & Antosiewicz, J. Structure and dynamics of curved DNA fragments in solution: Evidence for slow modes of configurational transitions. Biophys Chem 47, 179-191 (1993).

245. Posfai, G., Kiss, A., Erdei, S., Posfai, J. & Yenetianer, P. Structure of the Bacillus sphaericus R modification methylase gene. J Mol Biol 170, 597-610 (1983).

246. Radmacher, M., Cleveland, J.P., Fritz, M., Hansma, H.G. & Hansma, P.K. Mapping interaction forces with the atomic force microscope. Biophys J 66, 2159-65(1994).

247. Record, M.T., Jr., Lohman, M.L. & De Haseth, P. Ion effects on ligand-nucleic acid interactions. J Mol Biol 107, 145-58 (1976).

248. Reed, J., Singer, E., Kresbach, G. & Schwartz, D.C. A quantitative study of optical mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays. Anal Biochem 259, 80-8 (1998).

249. Rees, W.A., Keller, R.W., Vesenka, J.P., Yang, G. & Bustamante, C. Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science 260, 1646-9 (1993).

250. Register, J.C.d., Christiansen, G. & Griffith, J. Electron microscopic visualization of the RecA protein-mediated pairing and branch migration phases of DNA strand exchange. J Biol Chem 262, 12812-20 (1987).

251. Revet, B. & Fourcade, A. Short unligated sticky ends enable the observation of circularised DNA by atomic force and electron microscopies In Process Citation. Nucleic Acids Res 26, 2092-8 (1998).

252. Revet, B., Zarling, D.A., Jovin, T.M. & Delain, E. Different Z DNA forming sequences are revealed in phi XI74 RFI by high resolution darkfield immuno-electron microscopy. Embo J 3, 3353-8 (1984).

253. Revet, B.M., Sena, E.P. & Zarling, D.A. Homologous DNA targeting with RecA protein-coated short DNA probes and electron microscope mapping on linear duplex molecules. J Mol Biol 232, 779-91 (1993).

254. Rippe, K. & Jovin, T.M. Parallel-stranded duplex DNA. Methods Enzymol 211,199-220(1992).

255. Rippe, K., von Hippel, P.H. & Langowski, J. Action at a distance: DNAlooping and initiation of transcription. Trends Biochem Sei 20, 500-6 (1995).

256. Rivetti, C., Guthold, M. & Bustamante, C. Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J Mol Biol 264, 919-32 (1996).

257. Rivetti, C., Walker, C. & Bustamante, C. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J Mol Biol 280, 41-59 (1998).

258. Roberts, R.W. & Crothers, D.M. Specificity and stringency in DNA triplex formation. Proc Natl Acad Sei USA 88, 9397-401 (1991).

259. Rosamond, J., Endlich, B. & Linn, S. Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B. J Mol Biol 119, 619-35(1979).

260. Ruigrok, R.W.H. & DiCapua, E. On the polymerization state of recA in the absence of DNA. Biochimie 73, 191-197 (1991).

261. Rybenkov, V.V., Cozzarelli, N.R. & Vologodskii, A.V. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc Natl Acad Sei USA 90, 5307-11 (1993).

262. Rybenkov, V.V., Vologodskii, A.V. & Cozzarelli, N.R. The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucleic Acids Res 25, 1412-8 (1997).

263. Rybenkov, Y.V., Vologodskii, A.V. & Cozzarelli, N.R. The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation. J Mol Biol 267, 312-23 (1997).

264. Rybenkov, V.V., Vologodskii, A.V. & Cozzarelli, N.R. The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis. J Mol Biol 267, 299-311 (1997).

265. Saigo, K. Denaturation mapping and chromosome structure in bacteriophage T5. Virology 68, 166-72(1975).

266. Samori, B. et al. Chirality of DNA supercoiling assigned by scanning force microscopy. Proc Natl Acad Sci USA 90, 3598-601 (1993).

267. Schaper, A. & Jovin, T.M. Striving for atomic resolution in biomolecular topography: the scanning force microscope (SFM). Bioessays 18, 925-35 (1996).

268. Scheible, P.P., Rhoades, E.A. & Rhoades, M. Localization of single-chain interruptions in bacteriophage T5 DNA I. Electron microscopic studies. J Virol 23, 725-36 (1977).

269. Scheinman, A. et al Mapping the three-dimensional locations of ribosomal RNA and proteins. Biochimie 74, 307-17 (1992).

270. Schellman, J.A. Flexibility of DNA. Biopolymers 13, 217-226 (1974).

271. Schellman, J.A. The flexibility of DNA.II. Spontaneous and ligand induced distortions. Biophys Chem 11, 329-337 (1980).

272. Schellman, J.A. The flexibility of DNA. I. Thermal fluctuations. Biophys Chem 11, 321-8 (1980).

273. Schellman, J.A. & Harvey, S.C. Static contribution to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys Chem 55, 95-114(1995).

274. Schiedner, G., Wessel, R., Scheffner, M. & Stahl, H. Renaturation and DNA looping promoted by the SV40 large tumour antigen. Embo J 9, 2937-43 (1990).

275. Schwartz, D.C. et al. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262, 110-4 (1993).

276. Sclair, M., Edgell, M.H. & Hutchinson, C.A.d. Mapping of new Escherichia coli K and 15 restriction sites on specific fragments of bacteriophage phi XI74. J Virol 11, 378-85 (1973).

277. Seidman, S., Surzycki, S.J., DeLorbe, W. & Gussin, G.N. Interaction between wheat germ RNA polymerase II and adenovirus 2 DNA. Evidence for two types of stable binary complexes. Biochemistry 18, 3363-71 (1979).

278. Seiivanova, G. et al. The single-stranded DNA end binding site of p53 coincides with the C- terminal regulatory region. Nucleic Acids Res 24, 3560-7 (1996).

279. Serwer, P., Hayes, SJ. & Watson, R.H. Conformation of DNA packaged in bacteriophage T7. Analysis by use of ultraviolet light-induced DNA-capsid cross-linking. J Mol Biol 223, 999-1011 (1992).

280. Sharp, P.A., Hsu, M.T., Otsubo, E. & Davidson, N. Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli. I. Structure of F-prime factors .J Mol Biol 71, 471-97 (1972).

281. Shchyolkina, A.K. et al. Parallel purine-pyrimidine-purine triplex: experimental evidence for existence. FEBS Lett 367, 81-4 (1995).

282. Shlyakhtenko, L.S., Potaman, V.N., Sinden, R.R. & Lyubchenko, Y.L. Structure and dynamics of supercoil-stabilized DNA cruciforms. J Mol Biol 280, 61-72(1998).

283. Simonson, T., Kubista, M., Sjoback, R., Ryberg, H. & Takahashi, M. Properties of RecA-oligonucleotide complexes. J Mol Recognit 7, 199-206 (1994).

284. Sogo, J.M., Ness, P.J., Widmer, R.M., Parish, R.W. & Roller, T. Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin. J Mol Biol 178, 897-919 (1984).

285. Sogo, J.M., Portmann, R., Kaufmann, P. & Koller, T. Adsorption of DNA molecules to different support films. J Microsc 104, 187-98 (1975).

286. Sogo, J.M., Rodeno, P., Koller, T., Vinuela, E. & Salas, M. Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage phi 29 DNA. Nucleic Acids Res 7, 107-20 (1979).

287. Sperrazza, J.M., Register, J.C.d. & Griffith, J. Electron microscopy can be used to measure DNA supertwisting. Gene 31, 17-22 (1984).

288. Spindler, E. & Stein, H. R-loop mapping of calf-thymus RNA polymerase II. Transcripts in vitro on restriction fragments of adenovirus 2 DNA. Eur J Biochem 121, 289-94 (1982).

289. Sprous, D., Zacharias, W., Wood, Z.A. & Harvey, S.C. Dehydrating agents sharply reduce curvature in DNAs containing A tracts. Nucleic Acids Res 23, 1816-21 (1995).

290. Stokke, B.T. & Brant, D.A. The reliability of wormlike polysaccharide chain dimensions estimated from electron microscopy. Biopolymers 30, 1161-1181 (1990).

291. Stokrova, J., Vojtiskova, M. & Palecek, E. Electron microscopy of supercoiled pEJ4 DNA containing homopurine.homopyrimidine sequences. J Biomol Struct Dyn 6, 891-8 (1989).

292. Strobel, S.A. & Dervan, P.B. Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation. Nature 350, 172-4 (1991).

293. Strobel, S.A. & Dervan, P.B. Triple helix-mediated single-site enzymatic cleavage of megabase genomic DNA. Methods Enzymol 216, 309-21 (1992).

294. Stumph, W.E., Wu, J.R. & Bonner, J. Gene enrichment using antibodies to DNA/RNA hybrids: purification and mapping of Dictyostelium discoideum rDNA. Biochemistry 17, 5791-8 (1978).

295. Sun, J.-S. Rational design of switched triple helix-forming oligonucleotides: extention of sequences for triple helix formation, in Modelling of Biomolecular Structures and Mechanisms (ed. Pullman, A.e.a.) 267-288 , 1993).

296. Sun, J.S. et al. Sequence-specific intercalating agents: intercalation at specific sequences on duplex DNA via major groove recognition by oligonucleotide- intercalator conjugates. Proc Natl Acad Sci USA 86, 9198-202 (1989).

297. Sun, J.S. et al. Theoretical study of ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions. J Biomol Struct Dyn 9, 425-436 (1991).

298. Svinarchuk, F., Bertrand, J.R. & Malvy, C. A short purine oligonucleotide forms a highly stable triple helix with the promoter of the murine c-pim-1 proto-oncogene. Nucleic Acids Res 22, 3742-7 (1994).

299. Takasugi, M. et al. Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix- forming oligonucleotide. Proc Natl Acad Sci USA 88, 5602-6 (1991).

300. Takiff, H.E., Reinhold, W., Garon, C.F. & Straus, S.E. Cloning and physical mapping of enteric adenoviruses (candidate types 40 and 41). / Virol 51, 131-6 (1984).

301. Tan, R.K.-Z. & Harvey, S.C. A compatison of six bendingmodels. J.Biomol.Struct.Dynamics 5, 497-512 (1987).

302. Tanaka, K. & Yamagata, N. Ultrahigh-resolution scanning electron microscopy of biological materials. Arch Histol Cytol 55 SuppI, 5-15 (1992).

303. Taylor, A. & Smith, G.R. Unwinding and rewinding of DNA by the RecBC enzyme. Cell 22, 447-57 (1980).

304. Theveny, B. & Revet, B. DNA orientation using specific avidin-ferritin biotin end labelling. Nucleic Acids Res 15, 947-58 (1987).

305. Thomas, M., White, R.L. & Davis, R.W. Hybridization of RNA to double-stranded DNA: formation of R-loops. Proc Natl Acad Sei USA 73, 2294-8 (1976).

306. Thresher, R. & Griffith, J. Electron microscopic visualization of DNA and DNA-protein complexes as adjunct to biochemical studies. Methods Enzymol 211, 481-90(1992).

307. Thuong, N.T. & Helene, C. Sequence-specific recognition and modification of double-helical DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl. 32, 666-690 (1993).

308. Topal, M.D., Thresher, R.J., Conrad, M. & Griffith, J. Nael endonuclease binding to pBR322 DNA induces looping. Biochemistry 30, 2006-10 (1991).

309. Travers, A.A. DNA conformation and protein binding. Annu Rev Biochem 58, 427-52(1989).

310. Trifonov, E.N., Tan, R.K.-Z. & Harvey, S.C. Static persistence length of DNA. in DNA bending and curvature (eds Olson W.K., Sarma M.H., Sarma R.H. & Sundaralingam M.) 243-253 (Adenine Press, 1987).

311. Tsao, Y.P., Wu, H.Y. & Liu, L.F. Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell 56, 111-8 (1989).

312. Tung, C.S. & Harvey, S.C. Base sequence, local helix structure, and macroscopic curvature of A- DNA and B-DNA. J Biol Chem 261, 3700-9 (1986).

313. Umlauf, S.W., Cox, M.M. & Inman, R.B. Triple-helical DNA pairing intermediates formed by recA protein. J Biol Chem 265, 16898-912 (1990).

314. Upholt, W.B. & Dawid, I.B. Mapping of mitochondrial DNA of individual sheep and goats: rapid evolution in the D loop region. Cell 11, 571-83 (1977).

315. Van Tuyle, G.C. & Pavco, P.A. The rat liver mitochondrial DNA-protein complex: displaced single strands of replicative intermediates are protein coated. J Cell Biol 100, 251-7(1985).

316. Veselkov, A.G., Demidov, V.V., Nielson, P.E. & Frank-Kamenetskii, M.D. A new class of genome rare cutters. Nucleic Acids Res 24, 2483-7 (1996).

317. Vogel, F. & Scherneck, S. Electron microscopic mapping of RNA polymerase binding sites on SV 40 DNA. Gene 16, 331-334 (1981).

318. Vogel, F. & Scherneck, S. A comparison of the phage T4 gene 32 protein and Escherichia coli RNA polymerase binding sites on hamster papovavirus DNA. Biochim BiophysActa 696, 102-6 (1982).

319. Vollenweider, H.J. & Szybalski, W. Electron microscopic mapping of RNA polymerase binding to coiliphage lambda DNA. J. Mol.Biol. 123, 485-498 (1978).

320. Volodin, A.A., Smirnova, H.A. & Bocharova, T.N. Efficient interaction of RecA protein with fluorescent dye-labeled oligonucleotides. FEBS Letters 349, 6568 (1994).

321. Vologodskii, A.V. & Cozzarelli, N.R. Conformational and thermodynamic properties of supercoiled DNA. Annu Rev Biophys Biomol Struct 23, 609-43 (1994).

322. Waddell, J., Wang, X.M. & Wu, M. Electron microscopic localization of the chloroplast DNA replicative origins in Chlamydomonas reinhardii. Nucleic Acids Res 12, 3843-56 (1984).

323. Wang, X.M., Chang, C.H., Waddell, J. & Wu, M. Cloning and delimiting one chloroplast DNA replicative origin of Chlamydomonas. Nucleic Acids Res 12, 3857-72(1984).

324. Wang, Y.K., Huff, E.J. & Schwartz, D.C. Optical mapping of site-directed cleavages on single DNA molecules by the RecA-assisted restriction endonuclease technique. Proc Natl Acad Sci USA 92, 165-9 (1995).

325. Washbrook, E. & Fox, K.R. Alternate-strand DNA triple-helix formation using short acridine-linked oligonucleotides. Biochem J 301, 569-75 (1994).

326. Wells, R.D., Collier, D.A., Hanvey, J.C., Shimizu, M. & Wohlrab, F. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. Faseb J 2, 2939-49 (1988).

327. Werner, M.H., Gronenborn, A.M. & Clore, G.M. Intercalation, DNA kinking, and the control of transcription published erratum appears in Science 1996 Apr 5;272(5258): 19. Science 271, 778-84 (1996).

328. West, S.C. & Howard-Flanders, P. Duplex-duplex interactions catalyzed by RecA protein allow strand exchanges to pass double-strand breaks in DNA. Cell 37, 683-91 (1984).

329. Williams, R.C. Use of polylysine for adsorption of nuclei acids and enzymes to electron microscope specimen films. Proc Natl Acad Sei USA 74, 2311-5(1977).

330. Williams, R.C. & Chamberlin, M.J. Electron microscope studies of transient complexes formed between Escherichia coli RNA polymerase holoenzyme and T7 DNA. Proc Natl Acad Sei US Ali, 3740-4 (1977).

331. Witney, F.R. el al. Location of binding sites for RNA polymerase II from germ and from human placenta on Adenovirus 2 DNA. Mol. Gen. Genet. 179, 627646 (1980).

332. Wolstenholme, D.R. & Fauron, C.M. A partial map of the circular mitochondrial genome of Drosophila melanogaster. Location of EcoRI-sensitive sites and the adenine-thymine- rich region. J Cell Biol 71, 434-48 (1976).

333. Wu, H.M., Dattagupta, N. & Crothers, D.M. Solution structural studies of the A and Z forms of DNA. Proc Natl Acad Sei USA 78, 6808-1 1 (1981).

334. Wu, H.Y., Shyy, S.H., Wang, J.C. & Liu, L.F. Transcription generates positively and negatively supercoiled domains in the template. Cell 53, 433-40 (1988).

335. Wu, M. & Davidson, N. Use of gene 32 protein staining of single-strand polynucleotides for gene mapping by electron microscopy: application to the phi80d3ilvsu+7 system. Proc Natl Acad Sei US All, 4506-10 (1975).

336. Yager, T.D. & von Hippel, P.H. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30, 1097-118(1991).

337. Yee, J.K. & Marsh, R.C. Locations of bacteriophage T4 origins of replication. / Virol 54, 271-7 (1985).

338. Yin, H. et al. Transcription against an applied force. Science 270, 1653-7 (1995).

339. Yokota, H. et al. A new method for straightening DNA molecules for optical restriction mapping. Nucleic Acids Res 25, 1064-70 (1997).

340. Yoshimoto, M., Nagai, K. & Tamura, G. Asymmetric replication of an oriC plasmid in Escherichia coli. Mol Gen Genet 204, 214-20 (1986).

341. Young, I.T., Levistone, D., Eden, M., Tye, B.-K. & Botstein, D. Alignment of partial denaturation maps of circularly permutted DNA by computer. J. Mol.Biol. 85, 528-532(1974).

342. Yuan, R. The structure and mechanism of multifunctional restriction endonucleases. Ann.Rev.Biochem. 50, 285-315(1981).

343. Yuan, R., Hamilton, D.L., Hadi, S.M. & Bickle, T.A. Role of ATP in the cleavage mechanism of the EcoP15 restriction endonuclease. J Mol Biol 144, 50119 (1980).

344. Zarudnaya, M.I. et al. The study of DNA-RNA-polymerase complexes by kinetic formaldehyde method. Eur JBiochem 63, 607-15 (1976).

345. Zhao, B.T., Xu, H.J., Ma, S.Y., Li, L.Y. & Shen, Т. Restriction endonuclease cleavage map of mitochondrial DNA from Peking duck liver. Sei Sin B. 26, 1143-54(1983).

346. Zhurkin, V.B., Raghunathan, G., Ulyanov, N.B., Camerini-Otero, R.D. & Jernigan, R.L. A parallel DNA triplex as a model for the intermediate in homologous recombination. J Mol Biol 239, 181-200 (1994).

347. Zhurkin, V.B., Ulyanov, N.B., Gorin, A.A. & Jernigan, R.L. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc Natl Acad Sei USA 88, 7046-50 (1991).