Analysis of various sequence-specific triplexes by electron and atomic force microscopies

Biophysical Journal

Volumn 74, Issue 2 I, 1998, Pages 1015-1023

  Cherny, Dimitry I ^a,b   Fourcade, Alain ^b   Svinarchuk, Fedor ^b,d   Nielsen, Peter E ^c   Malvy, Claude ^b   Delain, Etienne ^b  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

^b INSTITUT GUSTAVE ROUSSY   (France)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; PEPTIDE NUCLEIC ACID; PLASMID DNA; STREPTAVIDIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; DNA HELIX; DNA SEQUENCE; DNA STRAND; ELECTRON MICROSCOPY; PROTEIN ANALYSIS; TRIPLE HELIX;

EID: 0031881031     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)74026-3     Document Type: Article

References (40)

1. Beal, P. A., and P. B. Dervan. 1991. Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science. 251:1360-1363.
2. Betts, L., J. A. Josey, J. M. Veal, and D. R. Jordan. 1995. A nucleic acids triple helix formed by a peptide nucleic acid-DNA complex. Science. 270:1838-1841.
3. Bouziane, M., D. I. Cherny, J.-F. Mouscadet, and C. Auclair. 1996. Alternate strand DNA triple-helix-mediated inhibition of HIV-1 U5 long terminal repeat integration in vitro. J. Biol. Chem. 271:10359-10364.
4. Brack, C. 1981. DNA electron microscopy. Crit. Rev. Biochem. 10: 113-169.
5. Cherny, D. I., B. P. Belotserkovskii, M. D. Frank-Kamenetskii, M. Egholm, O. Buchardt, R. H. Berg, and P. E. Nielsen. 1993a. DNA unwinding upon strand-displacement binding of a thymme-substituted polyamide to double-stranded DNA. Proc. Natl. Acad. Sci. USA. 90: 1667-1670.
6. Cherny, D. I., A. V. Kurakin, V. N. Lyamichev, M. D. Frank-Kamenetskii, V. E. Zinkevich, K. Firman, M. Egholm, O. Burchardt, R. H. Berg, and P. E. Nielsen. 1994. Electron microscopy studies of sequence specific recognition of duplex DNA by different ligands. J. Mol. Recognit. 7:171-176.
7. Cherny, D. I., V. A. Malkov, A. A. Volodin, and M. D. Frank-Kamenetskii. 1993b. Electron microscopy visualization of oligonucleotide binding to duplex DNA via triplex formation. J. Mol. Biol. 230:379-383.
8. Christensen, L., R. Fitzpatrick, B. Gildea, K. H. Petersen, H. F. Hansen, T. Koch, M. Egholm, O. Buchardt, P. E. Nielsen, J. Coull, and R. H. Berg. 1995. Solid-phase synthesis of peptide nucleic acids (PNA). J. Peptide Sci. 3:175-183.
9. Delain, E., A. Fourcade, J.-C. Poulin, A. Barbin, D. Coulaud, E. Le Cam, and E. Paris. 1992a. Comparative observation of biological specimens, especially DNA and filamentous actin molecules in atomic force, tunneling and electron microscopes. Microsc. Microanal. Microstruct. 3:457-470.
10. Delain, E., A. Fourcade, B. Révet, and C. Mory. 1992b. New possibilities in the observation of nucleic acids by electron spectroscopic imaging. Microsc. Microanal. Microstruct. 3:175-186.
11. Delain, E., and E. Le Cam. 1995. The spreading of nucleic acids. In Visualisation of Nucleic Acids. G. Morel, editor. CRC Press, Boca Raton, FL. 35-56.
12. Demidov, V. V., D. I. Cherny, A. V. Kurakin, M. V. Yavnilovich, V. A. Malkov, M. D. Frank-Kamenetskii, S. H. Sonnichsen, and P. E. Nielsen. 1994. Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting. Nucleic Acids Res. 22: 5218-5222.
13. Demidov, V. V., M. V. Yavnilovich, B. P. Belotserkovskii, M. D. Frank-Kamenetskii, and P. E. Nielsen. 1995. Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA. Proc. Natl. Acad. Sci. USA. 92:2637-2641.
14. Dubochet, J. 1973. High resolution dark-field electron microscopy. In Principles and Techniques of Electron Microscopy. Biological Applications, Vol. 3. M. A. Hayat, editor. Van Nostrand Reinhold Company, New York. 113-151.
15. Dubochet, J., M. Ducommun, M. Zollinger, and E. Kellenberger. 1971. A new preparation method for dark-field electron microscopy of biomacromolecules. J. Ultrastruct. Res. 35:147-167.
16. Egholm, M., L. Christensen, K. L. Dueholm, O. Buchardt, J. Coull, and P. E. Nielsen. 1995. Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res. 23:217-222.
17. Furrer, P., J. Bednar, A. Z. Stasiak, V. Katrich, D. Michoud, A. Stasiak, and J. Dubochet. 1997. Opposite effect of counterions on the persistence length of nicked and non-nicked DNA. J. Mol. Biol. 266:711-721.
18. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:256-286.
19. Hansma, H. G., M. Bezanilla, F. Zenhausern, M. Adrian, and R. L. Sinsheimer. 1993. Atomic force microscopy of DNA in aqueous solutions. Nucleic Acids Res. 21:505-512.
20. Hansma, H. G., D. E. Laney, M. Bezanilla, R. L. Sinsheimer, and P. K. Hansma. 1995. Applications for atomic force microscopy of DNA. Biophys. J. 68:1672-1677.
21. Hansma, H. G., I. Revenko, K. Kim, and D. E. Laney. 1996. Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res. 24:713-720.
22. Hélène, C. 1991. The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. Anticancer Drug Des. 6:569-584.
23. Knudsen, H., and P. E. Nielsen. 1996. Antisense properties of duplex-and triplex-forming PNAs. Nucleic Acids Res. 24:494-500.
24. Kuhn, H., V. V. Demidov, M. D. Frank-Kamenetskii, and P. E. Nielsen. 1997. Sequence specificity of bis-PNAs upon targeting of double-stranded DNA. Nucleic Acids Res. (in press).
25. Larquet, E., E. Le Cam, A. Fourcade, F. Culard, P. Furrer, and E. Delain. 1996. Complémentarité des microscopies dans l'analyse de minicercles d'ADN associés à la protéine MC1. C. R. Acad. Sci. Paris Sér. III. 319:461-471.
26. Le Cam, E., F. Fack, J. Ménissier-de-Murcia, J. A. H. Cognet, A. Barbin, V. Sarantoglou, B. Révet, E. Delain, and G. de Murcia. 1994. 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. 235:1062-1071.
27. Lee, J. S., C. Ashley, K. J. Hampel, R. Bradley, and D. G. Scraba. 1995. A stable interaction between separated pyrimidine-purine tracts in circular DNA. J. Mol. Biol. 252:283-288.
28. Lyubchenko, Yu. L., and L. S. Shlyakhtenko. 1997. Visualization of supercoiled DNA with atomic force microscopy in situ. Proc. Natl. Acad. Sci. USA. 94:496-501.
29. Møllegaard, N. E., A. I. H. Murchie, D. M. Lilley, and P. E. Nielsen. 1994. Uranyl photoprobing of a four-way DNA junction: evidence for specific metal ion binding. Nucleic Acids Res. 13:1508-1513.
30. Nielsen, P. E., M. Egholm, R. H. Berg, and O. Buchardt. 1991. Sequence selective recognition of DNA by strand displacement with a thymme-substituted polyamide. Science. 254:1497-1500.
31. Nielsen, P. E., M. Egholm, R. H. Berg, and O. Buchardt. 1993. Sequence-specific inhibition of DNA restriction enzyme cleavage by PNA. Nucleic Acids Res. 21:197-200.
32. Nielsen, P. E., M. Egholm, and O. Burchardt. 1994. Peptide nucleic acid (PNA). A DNA mimic with a peptide backbone. Bioconjug. Chem. 5:3-7.
33. Peffer, N. J., J. C. Hanvey, J. E. Bisi, S. A. Thomson, C. F. Hassman, S. A. Noble, and L. E. Babiss. 1993. Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Proc. Natl. Acad. Sci. USA. 90: 10648-10652.
34. Pfannschmidt, C., A. Schapet, G. Heim, T. M. Jovin, and J. Langowski. 1996. Sequence-specific labeling of supercoiled DNA by triple-helix formation and psoralen crosslinking. Nucleic Acids Res. 24:1702-1709.
35. Schaper, A., J. P. P. Starink, and T. M. Jovin. 1994. The scanning force microscopy of DNA in air and n-propanol using new spreading agents. FEBS Lett. 355:91-95.
36. Svinarchuk, F., J.-R. Bertrand, and C. Malvy. 1994. A short purine oligonucleotide forms a highly stable triple helix with the promoter of the murine c-pim-1 proto-oncogene. Nucleic Acids Res. 22:3742-3747.
37. Svinarchuk, F., D. I. Cherny, A. Debin, E. Delain, and C. Malvy. 1996. A new approach to overcome potassium-mediated inhibition of triplex formation. Nucleic Acids Res. 24:3858-3865.
38. Svinarchuk, F., M. Monnot, A. Merle, C. Malvy, and S. Fermandjian. 1995. The high stability of the triple helices formed between short purine oligonucleotides and SIV/HIV-2 vpx genes is determined by the targeted DNA structure. Nucleic Acids Res. 23:3831-3836.
39. Thuong, N. T., and C. Hélène. 1993. Sequence-specific recognition and modification of double-helical DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl. 32:666-690.
40. Wang, Y.-H., M. T. Howard, and J. D. Griffith. 1991. Phased adenine tracts in double-stranded RNA do not induce sequence-directed bending. Biochemistry. 30:5443-5449.