Mechanical properties of high-G·C content DNA with A-type base-stacking

Biophysical Journal

Volumn 100, Issue 8, 2011, Pages 1996-2005

  Hormeño, Silvia ^a,b   Ibarra, Borja ^a,b   Carrascosa, José L ^b   Valpuesta, José M ^b   Moreno Herrero, Fernando ^b   Arias Gonzalez, J Ricardo ^a,b  

^a INSTITUTO MADRILEÑO DE ESTUDIOS AVANZADOS EN NANOCIENCIA IMDEA NANOCIENCIA   (Spain)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959701425     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.02.051     Document Type: Article

References (43)

1. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer-Verlag, New York.
2. Baumann, C. G., S. B. Smith, C. Bustamante. 1997. Ionic effects on the elasticity of single DNA molecules. Proc. Natl. Acad. Sci. USA. 94:6185-6190. (Pubitemid 27270659)
3. Mao, H. B., J. R. Arias-Gonzalez, C. Bustamante. 2005. Temperature control methods in a laser tweezers system. Biophys. J. 89:1308-1316. (Pubitemid 41099012)
4. Leslie, A. G., S. Arnott, R. L. Ratliff. 1980. Polymorphism of DNA double helices. J. Mol. Biol. 143:49-72.
5. Ivanov, V. I., and Krylov, D. Y. 1992. A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211:111-127.
6. Gray, D. M., R. L. Ratliff, and M. R. Vaughan. 1992. Circular dichroism spectroscopy of DNA. Methods Enzymol. 211:389-406.
7. Nishimura, Y., C. Torigoe, and M. Tsuboi. 1985. An A-form poly (dG).poly (dC) in H2O solution. Biopolymers. 24:1841-1844.
8. Calladine, C. R., H. R. Drew, A. A. Travers. 2004. Understanding DNA. The Molecule and How it Works. Elsevier/Academic Press, New York.
9. Rief, M., H. Clausen-Schaumann, and H. E. Gaub. 1999. Sequencedependent mechanics of single DNA molecules. Nat. Struct. Biol. 6:346-349. (Pubitemid 29166483)
10. Nara-Inui, H., H. Akutsu, and Y. Kyogoku. 1985. Alcohol induced B-A transition of DNAs with different base compositions studied by circular dichroism. J. Biochem. 98:629-636. (Pubitemid 16216410)
11. Usatyi, A. F., and L. S. Shlyakhtenko. 1974. Melting of DNA in ethanol-water solutions. Biopolymers. 13:2435-2446.
12. Bustamante, C., Z. Bryant, and S. B. Smith. 2003. Ten years of tension: single-molecule DNA mechanics. Nature. 421:423-427. (Pubitemid 36157948)
13. Abels, J. A., F. Moreno-Herrero, N. H. Dekker. 2005. Singlemolecule measurements of the persistence length of double-stranded RNA. Biophys. J. 88:2737-2744. (Pubitemid 40976140)
14. Fang, Y., T. S. Spisz, and J. H. Hoh. 1999. Ethanol-induced structural transitions of DNA on mica. Nucleic Acids Res. 27:1943-1949. (Pubitemid 29209639)
15. Hormeño, S., and J. R. Arias-Gonzalez. 2006. Exploring mechanochemical processes in the cell with optical tweezers. Biol. Cell. 98:679-695. (Pubitemid 44896105)
16. Moukhtar, J., C. Faivre-Moskalenko, A. Arneodo. 2010. Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments. J. Phys. Chem. B. 114:5125-5143.
17. Moreno-Herrero, F., R. Seidel, N. H. Dekker. 2006. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Nucleic Acids Res. 34:3057-3066. (Pubitemid 44540432)
18. Ibarra, B., Y. R. Chemla, C. Bustamante. 2009. Proofreading dynamics of a processive DNA polymerase. EMBO J. 28:2794-2802.
19. Rivetti, C., M. Guthold, and C. Bustamante. 1996. Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J. Mol. Biol. 264:919-932. (Pubitemid 27019483)
20. Katz, E., C. J. Thompson, and D. A. Hopwood. 1983. Cloning and expression of the tyrosinase gene from Streptomyces antibioticus in Streptomyces lividans. J. Gen. Microbiol. 129:2703-2714. (Pubitemid 13024809)
21. Chen, C., J. S. Cohen, and A. Zadar. 1981. Convenient continuous sonication method for the preparation of medium-sized polydeoxynucleotides. J. Biochem. Biophys. Methods. 5:293-295.
22. Horcas, I., R. Fernández, A. M. Baro. 2007. WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev. Sci. Instrum. 78:013705.
23. Wiggins, P. A., T. van der Heijden, P. C. Nelson. 2006. High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotechnol. 1:137-141.
24. Smith, S. B., Y. Cui, and C. Bustamante. 2003. Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol. 361:134-162. (Pubitemid 36240997)
25. Kypr, J., I. Kejnovská, M. Vorlícková. 2009. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37:1713-1725.
26. Brahms, J., and W. F. Mommaerts. 1964. A study of conformation of nucleic acids in solution by means of circular dichroism. J. Mol. Biol. 10:73-88.
27. Hillen, W., and R. D. Wells. 1980. Circular dichroism studies of the B goes to A conformational transition in seven small DNA restriction fragments containing the Escherichia coli lactose control region. Nucleic Acids Res. 8:5427-5444. (Pubitemid 11221397)
28. Hagerman, P. J. 1997. Flexibility of RNA. Annu. Rev. Biophys. Biomol. Struct. 26:139-156. (Pubitemid 27255370)
29. Bustamante, C., J. F. Marko, S. Smith. 1994. Entropic elasticity of l-phage DNA. Science. 265:1599-1600.
30. Bouchiat, C., M. D. Wang, V. Croquette. 1999. Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys. J. 76:409-413. (Pubitemid 29202467)
31. Essevaz-Roulet, B., U. Bockelmann, and F. Heslot. 1997. Mechanical separation of the complementary strands of DNA. Proc. Natl. Acad. Sci. USA. 94:11935-11940. (Pubitemid 27467820)
32. Clausen-Schaumann, H., M. Rief, H. E. Gaub. 2000. Mechanical stability of single DNA molecules. Biophys. J. 78:1997-2007. (Pubitemid 30183594)
33. Marko, J. F., and E. D. Siggia. 1995. Stretching DNA. Macromolecules. 28:8759-8770.
34. Hogan, M., J. LeGrange, and B. Austin. 1983. Dependence of DNA helix flexibility on base composition. Nature. 304:752-754. (Pubitemid 13037728)
35. Olson, W. K., D. Swigon, and B. D. Coleman. 2004. Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Philos. Transact. A Math. Phys. Eng. Sci. 362:1403-1422. (Pubitemid 38846199)
36. Odijk, T. 1995. Stiff chains and filaments under tension. Macromolecules. 28:7016-7018.
37. Hobza, P., and J. Sponer. 1999. Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem. Rev. 99:3247-3276. (Pubitemid 129583053)
38. Trantírek, L., R. Stefl, J. Kypr. 2000. An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J. Mol. Biol. 297:907-922.
39. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
40. Noy, A., and R. Golestanian. 2010. The chirality of DNA: elasticity cross-terms at base-pair level including A-tracts and the influence of ionic strength. J. Phys. Chem. B. 114:8022-8031.
41. Travers, A. A. 2004. The structural basis of DNA flexibility. Philos. Transact. A Math. Phys. Eng. Sci. 362:1423-1438. (Pubitemid 38846200)
42. SantaLucia, Jr., J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465. (Pubitemid 128624151)
43. Hormeño, S., F. Moreno-Herrero, J. R. Arias-Gonzalez. 2011. Condensation prevails over B-A transition in the structure of DNA at low humidity. Biophys. J. 100:2006-2015.