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Volumn 369, Issue 2, 2006, Pages 679-687

Persistency of single-stranded DNA: The interplay between base sequences and base stacking

Author keywords

Persistence length; Sequences; Single stranded DNA; Stacking interaction

Indexed keywords

AROMATIC COMPOUNDS; MOLECULAR DYNAMICS; SOLUBILITY; STATISTICAL MECHANICS;

EID: 33745745909     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2006.01.084     Document Type: Article
Times cited : (6)

References (25)
  • 8
    • 0035132660 scopus 로고    scopus 로고
    • For simulation studies of the origin of stacking, see, for example, R. Luo, H.S.R. Gilson, M.J. Potter, M.K. Gilson, Biophys. J. 80 (2001) 140.
  • 10
    • 33745745866 scopus 로고    scopus 로고
    • C.R. Cantor, P.R. Schimmel, Biophysical chemistry, Part 1 The Conformation of Biological Macromolecules, W.H. Freeman and Company, 1980.
  • 13
    • 33745758611 scopus 로고    scopus 로고
    • Besides stacking interactions, there are other potential sources for the persistency. Depending on the ambient salt concentration, electrostatic interactions between bases can constitute an important contribution. For polyelectrolyte aspects of ssDNA-stretching experiments, see Ref. [7]. Different bases carry the same charge and contribute equally to the persistence length. This enables us to focus on stacking effects, since the electrostatic interactions are sequence independent.
  • 14
    • 0000668407 scopus 로고    scopus 로고
    • Despite seemingly dramatic simplification in the two state model, its analogues have been extensively used in the literature, especially in the context of the helix-coil transition in polypeptides and ssDNA (see, for example, B.H. Zimm, I.K. Bragg, J. Chem. Phys. 31 (1959) 526). As a result, a backbone chain is modeled as a two-state system in which each monomer is either in a helical or coil state.
  • 15
    • 33745757747 scopus 로고    scopus 로고
    • B T is used, this reduces to the same term in [...] in Eq. (1).
  • 17
    • 33745750006 scopus 로고    scopus 로고
    • Genbank Accession numbers and the species name of the sequences which we used for our computation are: NC_002578 (thermoplasma), NC_001142 (yeast), AC099849 (human chromosome-18), AC084251 (human chromosome-8), NC_001664 (human herpesvirus) and AP004824 BA000033 (staphylococcus).
  • 21
    • 18344375341 scopus 로고    scopus 로고
    • R. Golestanian, M. Kardar, T. Liverpool, Phys. Rev. Lett. 82 (1996) 4456 (1996).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.