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Volumn 134, Issue 20, 2011, Pages

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

Author keywords

[No Author keywords available]

Indexed keywords

COMBINED EFFECT; DNA BASE PAIRS; ELECTRON TRANSFER; ELECTRONIC STRUCTURE CALCULATIONS; EQUIVALENT MODEL; EXCHANGE-CORRELATION FUNCTIONALS; IMPLICIT SOLVENTS; LOCALIZED BASIS SETS; METAL COMPLEXATION; METAL-DOPING; METALLIC CONDUCTIVITY; MODIFIED DNA; STACKING INTERACTION; WATER MOLECULE;

EID: 79958113643     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3593272     Document Type: Article
Times cited : (18)

References (58)
  • 2
    • 9244252182 scopus 로고    scopus 로고
    • in, edited by H. S. Nalwa (American Scientific Publishers, Stevenson Ranch, CA), Vol. 2
    • M. Di Ventra and M. Zwolak, in Encyclopedia of Nanoscience and Nanotechnology, edited by, H. S. Nalwa, (American Scientific Publishers, Stevenson Ranch, CA, 2004), Vol. 2, p. 475.
    • (2004) Encyclopedia of Nanoscience and Nanotechnology , pp. 475
    • Di Ventra, M.1    Zwolak, M.2
  • 3
    • 1842763027 scopus 로고    scopus 로고
    • Colloquium: The quest for high-conductance DNA
    • DOI 10.1103/RevModPhys.76.195
    • R. G. Endres, D. L. Cox, and R. R. P. Singh, Rev. Mod. Phys. 76, 195 (2004). 10.1103/RevModPhys.76.195 (Pubitemid 38483931)
    • (2004) Reviews of Modern Physics , vol.76 , Issue.1 , pp. 195-214
    • Endres, R.G.1    Cox, D.L.2    Singh, R.R.P.3
  • 7
    • 0037458821 scopus 로고    scopus 로고
    • A discrete self-assembled metal array in artificial DNA
    • DOI 10.1126/science.1080587
    • K. Tanaka, A. Tengeiji, T. Kato, N. Toyama, and M. Shionoya, Science 299, 1212 (2003). 10.1126/science.1080587 (Pubitemid 36237458)
    • (2003) Science , vol.299 , Issue.5610 , pp. 1212-1213
    • Tanaka, K.1    Tengeiji, A.2    Kato, T.3    Toyama, N.4    Shionoya, M.5
  • 16
    • 33947674056 scopus 로고    scopus 로고
    • Structure and transport characteristics of modified DNA with magnetic ions
    • DOI 10.1103/PhysRevLett.98.136601
    • S. S. Mallajosyula and S. K. Pati, Phys. Rev. Lett. 98, 136601 (2007). 10.1103/PhysRevLett.98.136601 (Pubitemid 46496420)
    • (2007) Physical Review Letters , vol.98 , Issue.13 , pp. 136601
    • Mallajosyula, S.S.1    Pati, S.K.2
  • 18
    • 0242332191 scopus 로고    scopus 로고
    • A Four-Base Paired Genetic Helix with Expanded Size
    • DOI 10.1126/science.1088334
    • H. Liu, J. Gao, S. R. Lynch, Y. D. Saito, L. Maynard, and E. T. Kool, Science 302, 868 (2003). 10.1126/science.1088334 (Pubitemid 37339627)
    • (2003) Science , vol.302 , Issue.5646 , pp. 868-871
    • Liu, H.1    Gao, J.2    Lynch, S.R.3    Saito, Y.D.4    Maynard, L.5    Kool, E.T.6
  • 20
    • 18844378119 scopus 로고    scopus 로고
    • Assembly of the complete eight-base artificial genetic helix, xDNA, and its interaction with the natural genetic system
    • DOI 10.1002/anie.200500069
    • J. Gao, H. Liu, and E. T. Kool, Angew. Chem., Int. Ed. 44, 3118 (2005). 10.1002/anie.200500069 (Pubitemid 40689856)
    • (2005) Angewandte Chemie - International Edition , vol.44 , Issue.20 , pp. 3118-3122
    • Gao, J.1    Liu, H.2    Kool, E.T.3
  • 21
    • 12344282567 scopus 로고    scopus 로고
    • Size-expanded analogues of dG and dC: Synthesis and pairing properties in DNA
    • DOI 10.1021/jo048357z
    • H. Liu, J. Gao, and E. T. Kool, J. Org. Chem. 70, 639 (2005). 10.1021/jo048357z (Pubitemid 40129428)
    • (2005) Journal of Organic Chemistry , vol.70 , Issue.2 , pp. 639-647
    • Liu, H.1    Gao, J.2    Kool, E.T.3
  • 22
    • 4644365696 scopus 로고    scopus 로고
    • Expanded-size bases in naturally sized DNA: Evaluation of steric effects in Watson-Crick pairing
    • DOI 10.1021/ja048499a
    • J. Gao, H. Liu, and E. T. Kool, J. Am. Chem. Soc. 126, 11826 (2004). 10.1021/ja048499a (Pubitemid 39298331)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.38 , pp. 11826-11831
    • Gao, J.1    Liu, H.2    Kool, E.T.3
  • 24
    • 13444252456 scopus 로고    scopus 로고
    • Helix-forming properties of size-expanded DNA, an alternative four-base genetic form
    • DOI 10.1021/ja046305l
    • H. Liu, J. Gao, and E. T. Kool, J. Am. Chem. Soc. 127, 1396 (2005). 10.1021/ja046305l (Pubitemid 40204514)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.5 , pp. 1396-1402
    • Liu, H.1    Gao, J.2    Kool, E.T.3
  • 25
    • 33751005291 scopus 로고    scopus 로고
    • Toward a designed, functioning genetic system with expanded-size base pairs: Solution structure of the eight-base xDNA double helix
    • DOI 10.1021/ja065606n
    • S. R. Lynch, H. Liu, J. Gao, and E. T. Kool, J. Am. Chem. Soc. 128, 14704 (2006). 10.1021/ja065606n (Pubitemid 44749874)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.45 , pp. 14704-14711
    • Lynch, S.R.1    Liu, H.2    Gao, J.3    Kool, E.T.4
  • 26
    • 28144442040 scopus 로고    scopus 로고
    • Size-expanded DNA bases: An ab initio study of their structural and electronic properties
    • DOI 10.1021/jp055210i
    • M. Fuentes-Cabrera, B. G. Sumpter, and J. C. Wells, J. Phys. Chem. B 109, 21135 (2005). 10.1021/jp055210i (Pubitemid 41698376)
    • (2005) Journal of Physical Chemistry B , vol.109 , Issue.44 , pp. 21135-21139
    • Fuentes-Cabrera, M.1    Sumpter, B.G.2    Wells, J.C.3
  • 34
    • 34547520602 scopus 로고    scopus 로고
    • Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks
    • DOI 10.1021/jp073592h
    • J. Zhang, R. I. Cukier, and X. Bu, J. Phys. Chem. B 111, 8335 (2007). 10.1021/jp073592h (Pubitemid 47184411)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.28 , pp. 8335-8341
    • Zhang, J.1    Cukier, R.I.2    Bu, Y.3
  • 35
    • 79958084509 scopus 로고    scopus 로고
    • xAg(I)-N7-3H2O is the equivalent of the corresponding metalated pair Ag(I)-N7-2H2O. Note that both in Cu(II)-xGC and Ag(I)-xGC pairs one of the explicit water molecules is not bonded to the metal cation in the relaxed structure, so that Cu(II) has its preferential tetragonal coordination and Ag(I) has its preferential trigonal coordination.
    • xAg(I)-N7-3H2O is the equivalent of the corresponding metalated pair Ag(I)-N7-2H2O. Note that both in Cu(II)-xGC and Ag(I)-xGC pairs one of the explicit water molecules is not bonded to the metal cation in the relaxed structure, so that Cu(II) has its preferential tetragonal coordination and Ag(I) has its preferential trigonal coordination.
  • 37
    • 0000189651 scopus 로고
    • 10.1063/1.464913
    • A. D. Becke, J. Chem. Phys. 98, 5648 (1993). 10.1063/1.464913
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648
    • Becke, A.D.1
  • 45
    • 79958082200 scopus 로고    scopus 로고
    • Preliminary calculations on Ag-DNA stacks with more complete basis sets [(i) 6-311++G for the bases and the Stuttgart RSC 1997 ECP pseudopotential for Ag(I) with NWCHEM; (ii) 6-31g(d,p) for the bases and the MWB28 pseudopotential for Ag(I) with G03; (iii) cc-pVTZ for all the elements with G03] support the validity of the results obtained on Ag-xDNA base pairs with the minimal basis set B1 (see isodensity plots in the Supporting Information), even if with a general underestimation of the metal component on the HOMO orbital, at least for the salient features discussed in this article.
    • Preliminary calculations on Ag-DNA stacks with more complete basis sets [(i) 6-311++G for the bases and the Stuttgart RSC 1997 ECP pseudopotential for Ag(I) with NWCHEM; (ii) 6-31g(d,p) for the bases and the MWB28 pseudopotential for Ag(I) with G03; (iii) cc-pVTZ for all the elements with G03] support the validity of the results obtained on Ag-xDNA base pairs with the minimal basis set B1 (see isodensity plots in the Supporting Information), even if with a general underestimation of the metal component on the HOMO orbital, at least for the salient features discussed in this article.
  • 49
    • 11744256643 scopus 로고
    • 10.1021/cr00031a013
    • J. Tomasi and M. Persico, Chem. Rev. 94, 2027 (1994). 10.1021/cr00031a013
    • (1994) Chem. Rev. , vol.94 , pp. 2027
    • Tomasi, J.1    Persico, M.2
  • 50
    • 79958106030 scopus 로고    scopus 로고
    • See supplementary material at E-JCPSA6-134-002121 for Tables and Figures.
    • See supplementary material at http://dx.doi.org/10.1063/1.3593272 E-JCPSA6-134-002121 for Tables and Figures.
  • 51
    • 38749148070 scopus 로고    scopus 로고
    • Theoretical study of hydrated copper(II) interactions with guanine: A computational density functional theory study
    • DOI 10.1021/jp074891+
    • M. Pavelka, M. K. Shukla, J. Leszczynski, and J. V. Burda, J. Phys. Chem. A 112, 256 (2008). 10.1021/jp074891+ (Pubitemid 351184583)
    • (2008) Journal of Physical Chemistry A , vol.112 , Issue.2 , pp. 256-267
    • Pavelka, M.1    Shukla, M.K.2    Leszczynski, J.3    Burda, J.V.4
  • 56


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.