Condensation prevails over B-A transition in the structure of DNA at low humidity

Biophysical Journal

Volumn 100, Issue 8, 2011, Pages 2006-2015

  Hormeño, Silvia ^a,b   Moreno Herrero, Fernando ^b   Ibarra, Borja ^a,b   Carrascosa, José L ^b   Valpuesta, José M ^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: 79959721229     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.02.049     Document Type: Article

References (59)

1. Calladine, C. R., H. R. Drew, A. A. Travers. 2004. Understanding DNA. The molecule and how it works. Elsevier. Academic Press.
2. Saenger, W. 1984. Principles of nucleic acid structure. Springer-Verlag, New York.
3. Arscott, P. G., C. Ma, V. A. Bloomfield. 1995. DNA condensation by cobalt hexaammine (III) in alcohol-water mixtures: dielectric constant and other solvent effects. Biopolymers. 36:345-364.
4. 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)
5. 6. J. Mol. Biol. 144:431-453.
6. Lang, D. 1969. Collapse of single DNA molecules in ethanol. J. Mol. Biol. 46:209.
7. Hud, N. V., and K. H. Downing. 2001. Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids. Proc. Natl. Acad. Sci. USA. 98:14925-14930. (Pubitemid 34013946)
8. Ivanov, V. I., L. E. Minchenkova, A. I. Poletayev. 1973. Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 12:89-110.
9. 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.
10. Girod, J. C., W. C. Johnson, Jr., M. F. Maestre. 1973. Conformation of deoxyribonucleic acid in alcohol solutions. Biochemistry. 12:5092-5096.
11. Minyat, E. E., V. I. Ivanov, A. K. Schyolkina. 1979. Spermine and spermidine-induced B to A transition of DNA in solution. J. Mol. Biol. 128:397-409. (Pubitemid 9120574)
12. Rupprecht, A., J. Piškur, G. Lahajnar. 1994. Mechanochemical study of conformational transitions and melting of Li-, Na-, K-, and CsDNA fibers in ethanol-water solutions. Biopolymers. 34:897-920.
13. Albiser, G., A. Lamiri, and S. Premilat. 2001. The A-B transition: temperature and base composition effects on hydration of DNA. Int. J. Biol. Macromol. 28:199-203. (Pubitemid 32197454)
14. Usatyi, A. F, and L. S. Shlyakhtenko. 1974. Melting of DNA in ethanol-water solutions. Biopolymers. 13:2435-2446.
15. Bauer, C, and A. H. J. Wang. 1997. Bridged cobalt amine complexes induce DNA conformational changes effectively. J. Inorg. Biochem. 68:129-135. (Pubitemid 27441169)
16. Kankia, B. I., V. Buckin, and V. A. Bloomfield. 2001. Hexamminecobalt (III)-induced condensation of calf thymus DNA: circular dichroism and hydration measurements. Nucleic Acids Res. 29:2795-2801. (Pubitemid 32685043)
17. Saenger, W., W. N. Hunter, and O. Kennard. 1986. DNA conformation is determined by economics in the hydration of phosphate groups. Nature. 324:385-388. (Pubitemid 17180118)
18. Subirana, J. A., and M. Soler-Lopez. 2003. Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. Annu. Rev. Biophys. Biomol. Struct. 32:27-45. (Pubitemid 37056220)
19. Bloomfield, V. A. 1997. DNA condensation by multivalent cations. Biopolymers. 44:269-282.
20. Gosule, L. C., and J. A. Schellman. 1976. Compact form of DNA induced by spermidine. Nature. 259:333-335.
21. Raspaud, E., I. Chaperon, F. Livolant. 1999. Spermine-induced aggregation of DNA, nucleosome, and chromatin. Biophys. J. 77:1547-1555.
22. Ivanov, V. I., L. E. Minchenkova, A. K. Schyolkina. 1974. The B to A transition of DNA in solution. J. Mol. Biol. 87:817-833.
23. Xu, Q., R. K. Shoemaker, and W. H. Braunlin. 1993. Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution. Biophys. J. 65:1039-1049. (Pubitemid 23263919)
24. Robinson, H., and A. H. Wang. 1996. Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B-to A-DNA. Nucleic Acids Res. 24:676-682. (Pubitemid 26088515)
25. Leslie, A. G., S. Arnott, R. L. Ratliff. 1980. Polymorphism of DNA double helices. J. Mol. Biol. 143:49-72.
26. Becker, M. M., and Z. Wang. 1989. B-A transitions within a 5 S ribosomal RNA gene are highly sequence-specific. J. Biol. Chem. 264:4163-4167. (Pubitemid 19072311)
27. Borovok, N., T. Molotsky, A. Kotlyar. 2007. Poly (dG)-poly (dC) DNA appears shorter than poly (dA)-poly (dT) and possibly adopts an A-related conformation on a mica surface under ambient conditions. FEBS Lett. 581:5843-5846. (Pubitemid 50008507)
28. 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)
29. Nishimura, Y., C. Torigoe, and M. Tsuboi. 1985. An A-form poly (dG).poly (dC) in H2O solution. Biopolymers. 24:1841-1844.
30. Arnott, S., and E. Selsing. 1974. Letter: the structure of polydeoxyguanylic acid with polydeoxycytidylic acid. J. Mol. Biol. 88:551-552.
31. Lang, D., T. N. Taylor, D. M. Gray. 1976. Dehydrated circular DNA: electron microscopy of ethanol-condensed molecules. J. Mol. Biol. 106:97-107.
32. Piskur, J., and A. Rupprecht. 1995. Aggregated DNA in ethanol solution. FEBS Lett. 375:174-178.
33. Herbeck, R., T. J. Yu, and W. L. Peticolas. 1976. Effect of cross-linking on the secondary structure of DNA I. Cross-linking by photodimerization. Biochemistry. 15:2656-2660.
34. Zimmerman, S. B., and B. H. Pheiffer. 1979. A direct demonstration that the ethanol-induced transition of DNA is between the A and B forms: an x-ray diffraction study. J. Mol. Biol. 135:1023-1027. (Pubitemid 10187143)
35. Subirana, J. A., M. Chiva, and R. Mayer. 1980. X-ray diffraction studies of complexes of DNA with lysine and with lysine-containing peptides. In Biomolecular Structure, Conformation, Function and Evolution. R. Srinivasan, N. Yathindra, and E. Subramanian, editors. Pergamon Press, London. 431-440.
36. Mazur, A. K. 2005. Electrostatic polymer condensation and the A/B polymorphism in DNA: Sequence effects. J. Chem. Theory Comput. 1:325-336.
37. Schnell, J. R., J. Berman, and V. A. Bloomfield. 1998. Insertion of telomere repeat sequence decreases plasmid DNA condensation by cobalt (III) hexaammine. Biophys. J. 74:1484-1491. (Pubitemid 28108556)
38. Reich, Z., R. Ghirlando, and A. Minsky. 1991. Secondary conformational polymorphism of nucleic acids as a possible functional link between cellular parameters and DNA packaging processes. Biochemistry. 30:7828-7836.
39. Zavriev, S. K., L. E. Minchenkova, V. I. Ivanov. 1978. On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule. Nucleic Acids Res. 5:2657-2663. (Pubitemid 8369759)
40. Potaman, V. N., Y. A. Bannikov, and L. S. Shlyachtenko. 1980. Sedimentation of DNA in ethanol-water solutions within the interval of B to A transition. Nucleic Acids Res. 8:635-642.
41. 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)
42. Hormeño, S., and J. R. Arias-Gonzalez. 2006. Exploring mechanochemical processes in the cell with optical tweezers. Biol. Cell. 98:679-695. (Pubitemid 44896105)
43. Bustamante, C., Z. Bryant, and S. B. Smith. 2003. Ten years of tension: single-molecule DNA mechanics. Nature. 421:423-427. (Pubitemid 36157948)
44. 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.
45. Besteman, K., K. Van Eijk, and S. G. Lemay. 2007. Charge inversion accompanies DNA condensation by multivalent ions. Nat. Phys. 3:641-644.
46. 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)
47. Hormeño, S., B. Ibarra, J. L. Carrascosa, J. M. Valpuesta, F. Moreno-Herrero., 2011. Mechanical properties of high GC-content DNA with A-type base-stacking. Biophys. J. 100:1996-2005.
48. Gray, D. M., R. L. Ratliff, and M. R. Vaughan. 1992. Circular dichroism spectroscopy of DNA. Methods Enzymol. 211:389-406.
49. 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)
50. Cluzel, P., A. Lebrun, F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794. (Pubitemid 26058929)
51. Baumann, C. G., V. A. Bloomfield, S. M. Block. 2000. Stretching of single collapsed DNA molecules. Biophys. J. 78:1965-1978. (Pubitemid 30183591)
52. Murayama, Y., Y. Sakamaki, and M. Sano. 2003. Elastic response of single DNA molecules exhibits a reentrant collapsing transition. Phys. Rev. Lett. 90:018102.
53. 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)
54. Albiser, G., M. Harmouchi, and S. Premilat. 1988. Influence of a mechanical tension on the B-A and B-C conformational transitions in DNA fibres. J. Biomol. Struct. Dyn. 6:359-366.
55. Fornells, M., J. L. Campos, and J. A. Subirana. 1983. Changes of conformation of DNA produced by mechanical forces. J. Mol. Biol. 166:249-252.
56. Harmouchi, M., G. Albiser, and S. Premilat. 1992. Effect of a mechanical tension on the hydration of DNA in fibres. Biochem. Biophys. Res. Commun. 188:78-85.
57. Schultz, J., A. Rupprecht, G. Lahajnar. 1994. A mechanochemical study of MgDNA fibers in ethanol-water solutions. Biophys. J. 66:810-819. (Pubitemid 24083001)
58. Noy, A., A. Pérez, M. Orozco. 2007. Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water. Nucleic Acids Res. 35:3330-3338. (Pubitemid 47078739)
59. 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)