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Volumn 130, Issue 4, 2008, Pages 1304-1308

Stacking interactions and the Twist of DNA

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DENSITY FUNCTIONAL THEORY; INFORMATION ANALYSIS; MOLECULAR INTERACTIONS; VAN DER WAALS FORCES;

EID: 38649139343     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0761941     Document Type: Article
Times cited : (171)

References (45)
  • 21
    • 38649123849 scopus 로고    scopus 로고
    • Hooper, J.; Cooper, V. R.; Thonhauser, T.; Romero, N. A.; Zerilli, F.; Langreth, D. C. (http://lanl.arxiv.org/abs/0707.3393).
    • Hooper, J.; Cooper, V. R.; Thonhauser, T.; Romero, N. A.; Zerilli, F.; Langreth, D. C. (http://lanl.arxiv.org/abs/0707.3393).
  • 25
    • 38649128029 scopus 로고    scopus 로고
    • A representative plot can be found in Supporting Information Figure 1.
    • A representative plot can be found in Supporting Information Figure 1.
  • 26
    • 38649095782 scopus 로고    scopus 로고
    • A comparative plot of vdW-DF and QC stacking energies for DNA base pair steps can be found in Supporting Information Figure 2
    • A comparative plot of vdW-DF and QC stacking energies for DNA base pair steps can be found in Supporting Information Figure 2.
  • 30
    • 38649120980 scopus 로고    scopus 로고
    • 2 has shown that, for most systems (including DNA), the additional electronic density rearrangement produced by the self consistency of the vdW interaction is negligible at typical nuclear separations, thus enabling this less expensive perturbation method to be applied.
    • 2 has shown that, for most systems (including DNA), the additional electronic density rearrangement produced by the self consistency of the vdW interaction is negligible at typical nuclear separations, thus enabling this less expensive perturbation method to be applied.
  • 36
    • 38649115501 scopus 로고    scopus 로고
    • A complete table of vdW-DF interaction energies and preferred Twist and Rise parameters for the nucleobases studied can be found in Supporting Information Table 1
    • A complete table of vdW-DF interaction energies and preferred Twist and Rise parameters for the nucleobases studied can be found in Supporting Information Table 1.
  • 37
    • 38649084267 scopus 로고    scopus 로고
    • An early calculation9,10 employing a simple parameterized method gave very little influence on Twist from stacking interactions in the absence of the backbone. We have tested this parameterization on the CO 2 dimer where vdW-DF agrees well with high level quantum chemical calculations.2 It gives a substantially weaker dependence of energy on geometry, notably in the repulsive regime that is a substantial contributor to the Twist in our DNA calculations, thus indicating a possible reason for the discrepancy. The use of methyl terminations of the backbone connections is another difference between ref 10 and this work, where hydrogen terminations are used
    • 2 It gives a substantially weaker dependence of energy on geometry, notably in the repulsive regime that is a substantial contributor to the Twist in our DNA calculations, thus indicating a possible reason for the discrepancy. The use of methyl terminations of the backbone connections is another difference between ref 10 and this work, where hydrogen terminations are used.
  • 41
    • 38649104994 scopus 로고    scopus 로고
    • Top and side views of the thymine methyl contacts can be found in Supporting Information Figure 3.
    • Top and side views of the thymine methyl contacts can be found in Supporting Information Figure 3.
  • 43
    • 26444433531 scopus 로고    scopus 로고
    • Sequence-Dependent Variability of B-DNA: An update on bending and curvature
    • Springer: Georgetown, TX, New York
    • Zhurkin, V. B.; Tolstorukov, M. Y.; Xu, F.; Colasanti, A. V.; Olson, W. K. Sequence-Dependent Variability of B-DNA: An update on bending and curvature. In DNA Conformation and Transcription; Springer: Georgetown, TX, New York, 2005; pp 18-34.
    • (2005) DNA Conformation and Transcription , pp. 18-34
    • Zhurkin, V.B.1    Tolstorukov, M.Y.2    Xu, F.3    Colasanti, A.V.4    Olson, W.K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.