Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes

Biophysical Journal

Volumn 90, Issue 8, 2006, Pages 2877-2889

  Liang, Xingguo ^a,b   Kuhn, Heiko ^a   Frank Kamenetskii, Maxim D ^a  

^a Boston University   (United States)

^b NAGOYA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CATENANE; OLIGODEOXYNUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CYCLIZATION; DNA SEQUENCE; DNA STRUCTURE; ELECTROPHORESIS;

EID: 33646172099     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.074104     Document Type: Article

References (49)

1. Zou, L., and S. J. Elledge. 2003. Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science. 300:1542-1548.
2. Lee, G. S., M. B. Neiditch, R. R. Sinden, and D. B. Roth. 2002. Targeted transposition by the V(D)J recombinase. Mol. Cell. Biol. 22:2068-2077.
3. Cuenoud, B., and J. W. Szostak. 1995. A DNA metalloenzyme with DNA ligase activity. Nature. 375:611-614.
4. Breaker, R. R. 1997. DNA aptamers and DNA enzymes. Curr. Opin. Chem. Biol. 1:26-31.
5. Li, Y., and R. R. Breaker. 1999. Phosphorylating DNA with DNA. Proc. Natl. Acad. Sci. USA. 96:2746-2751.
6. Sreedhara, A., Y. Li, and R. R. Breaker. 2004. Ligating DNA with DNA. J. Am. Chem. Soc. 126:3454-3460.
7. Gan, H. H., S. Pasquali, and T. Schlick. 2003. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res. 31:2926-2943.
8. Kim, N., N. Shiffeldrim, H. H. Gan, and T. Schlick. 2004. Candidates for novel RNA topologies. J. Mol. Biol. 341:1129-1144.
9. Holbrook, S. R. 2005. RNA structure: the long and the short of it. Curr. Opin. Struct. Biol. 15:302-308.
10. Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
11. Zhang, Y., H. Zhou, and Z. C. Ou-Yang. 2001. Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions. Biophys. J. 81:1133-1143.
12. Rivetti, C., C. Walker, and C. Bustamante. 1998. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J. Mol. Biol. 280:41-59.
13. Mills, J. B., E. Vacano, and P. J. Hagerman. 1999. Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). J. Mol. Biol. 285:245-257.
14. Kuznetsov, S. V., Y. Shen, A. S. Benight, and A. Ansari. 2001. A semi-flexible polymer model applied to loop formation in DNA hairpins. Biophys. J. 81:2864-2875.
15. Murphy, M. C., I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha. 2004. Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys. J. 86:2530-2537.
16. Buhot, A., and A. Halperin. 2004. Effects of stacking on the configurations and elasticity of single-stranded nucleic acids. Phys. Rev. E. 70:020902.
17. Cantor, C. R., and P. R. Schimmel. 1980. Biophysical Chemistry. Freeman, New York.
18. Bloomfield, V. A., D. M. Crothers, and I. Tinoco. 2000. Nucleic Acids: Structure, Properties, and Functions. University Science Books, Sausalito, CA.
19. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.
20. Dong, F., H. T. Allawi, T. Anderson, B. P. Neri, and V. I. Lyamichev. 2001. Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA. Nucleic Acids Res. 29:3248-3257.
21. Gaspin, C., and E. Westhof. 1995. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J. Mol. Biol. 254:163-174.
22. Wilson, W. D., M.-H. Dotrong, E. T. Zuo, and G. Zon. 1988. Unusual duplex formation in purine rich oligodeoxyribonucleotides. Nucleic Acids Res. 16:5137-5151.
23. n sequences form a parallel-stranded DNA homoduplex. EMBO J. 11:3777-3786.
24. Suda, T., Y. Mishima, H. Asakura, and R. Kominami. 1995. Formation of a parallel-stranded DNA homoduplex by d(GGA) repeat oligonucleotides. Nucleic Acids Res. 23:3771-3777.
25. n repeats form intramolecular hairpins stabilized by different base-pairing interactions. Biochemistry. 35:13125-13135.
26. Vorlickova, M., I. Kejnovska, J. Kovanda, and J. Kypr. 1999. Dimerization of the guanine-adenine repeat strands of DNA. Nucleic Acids Res. 27:581-586.
27. Sakanoto, N., K. Ohshima, L. Montermini, M. Pandolfo, and R. D. Wells. 2001. Sticky DNA, a self-associated complex formed at long GAA·TTC repeats in intron 1 of the frataxin gene, inhibits transcription. J. Biol. Chem. 276:27171-27177.
28. n sequences. J. Mol. Evol. 27:96-101.
29. Gao, Y. G., H. Robinson, R. Sanishvili, A. Joachimiak, and A. H.-J. Wang. 1999. Structure and recognition of sheared tandem GA base pairs associated with human centromere DNA sequence at atomic resolution. Biochemistry. 38:16452-16460.
30. Chou, S.-H., and K.-H. Chin. 2001. Solution structure of a DNA double helix incorporating four consecutive non-canonical base pairs. J. Mol. Biol. 312:769-781.
31. Chen, J., and N. C. Seeman. 1991. The synthesis from DNA of a molecule with the connectivity of a cube. Nature. 350:631-633.
32. Seeman, N. C., J. Chen, S. M. Du, J. E. Mueller, Y. Zhang, T. J. Fu, Y. Wang, H. Wang, and S. Zhang. 1993. Synthetic DNA knots and catenanes. New J. Chem. 17:39-55.
33. Fu, T. J., Y. C. Tse-Dinh, and N. C. Seeman. 1994. Holiday junction crossover topology. J. Mol. Biol. 236:91-105.
34. Bucka, A., and A. Stasiak. 2002. Construction and electrophoretic migration of single-stranded DNA knots and catenanes. Nucleic Acids Res. 30:e24.
35. Kuhn, H., V. V. Demidov, and M. D. Frank-Kamenetskii. 2002. Rolling-circle amplification under topological constraints. Nucleic Acids Res. 30:574-580.
36. Libchaber, A., and R. Bar-Ziv. 2001. Effects of DNA sequence and structure on binding of RecA to single-stranded DNA. Proc. Natl. Acad. Sci. USA. 98:9068-9073.
37. Shaw, S. Y., and J. C. Wang. 1993. Knotting of a DNA chain during ring closure. Science. 260:533-536.
38. Rybenkov, V. V., N. R. Cozzarelli, and A. V. Vologodskii. 1993. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA. 90:5307-5311.
39. Chen, G., B. M. Znosko, S. D. Kennedy, T. R. Krugh, and D. H. Turner. 2005. Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry. 44:2845-2856.
40. Laurie, B., V. Katritch, J. Sogo, T. Koller, J. Dubochet, and A. Stasiak. 1998. Geometry and physics of catenanes applied to the study of DNA replication. Biophys. J. 74:2815-2822.
41. Stasiak, A., V. Katritch, J. Bednar, D. Michoud, and J. Dubochet. 1996. Electrophoretic mobility of DNA knots. Nature. 384:122.
42. Vologodskii, A. V., N. J. Crisona, B. Laurie, P. Pieranski, V. Katritch, J. Dubochet, and A. Stasiak. 1998. Sedimentation and electrophoretic migration of DNA knots and catenanes. J. Mol. Biol. 278:1-3.
43. Pluen, A., B. Tinland, J. Sturm, and G. Weill. 1998. Migration of single-stranded DNA in polyacrylamide gels during electrophoresis. Electrophoresis. 19:1548-1559.
44. Hsu, T.-P., and C. Cohen. 1984. Observations on the structure of a polyacrylamide gel from electron micrographs. Polymer. 25:1419-1423.
45. Viovy, J.-L. 2000. Electrophoresis of DNA and other polyelectrolytes: physical mechanisms. Rev. Mod. Phys. 72:813-872.
46. Grosberg, A. Y., and A. R. Khokhlov. 1994. Statistical Physics of Macromolecules. AIP, New York.
47. Ng, P.-S., and D. E. Bergstrom. 2004. Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides. Nucleic Acids Res. 32:e107.
48. SantaLucia, J., and D. Hicks. 2004. The thermodynamics of DNA structure motifs. Annu. Rev. Biophys. Biomol. Struct. 33:415-440.
49. Vologodskii, A. V., X. Yang, and N. C. Seeman. 1998. Non-complementary DNA helical structure induced by positive torsional stress. Nucleic Acids Res. 126:1503-1508.