Structures and properties of mixed DNA bases tetrads: Nonempirical ab inito HF and DFT studies

doi:10.1021/jp992944k

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	Structures and properties of mixed DNA bases tetrads: Nonempirical ab inito HF and DFT studies
	Gu, JD; Leszczynski, J
刊名	JOURNAL OF PHYSICAL CHEMISTRY A
	2000-03-09
卷号	104 期号:9 页码:1898-1904
ISSN号	1089-5639
DOI	10.1021/jp992944k
文献子类	Article
英文摘要	Three nonplanar tetrads of the DNA bases (Watson-Crick-type TATA, Hoogsteen-type TATA, and AGAG tetrad) are studied at the HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels of theory. Both Hoogsteen and Watson-Crick type thymine-adenine-thymine-adenine tetrads are stable in the isolated form in which the Hoogsteen type TATA tetrad is about 2.3 kcal/mol more stable than the Watson-Crick type. The significant stabilization energies of over 30 kcal/mol predicted for the TATA tetrads confirm that the stabilization of this structure plays a key role in the four stranded helices. The energy of each bifurcated H-bond in the tetrads has been found to be about 8 kcal/mol for the planar structure and about 3 kcal/mol for the nonplanar tetrad. The formation of bifurcated H-bonding is the main contribution to the creation of the tetrad structure. The electrostatic potential map suggests that the presence of a cation in the system is expected to further stabilize the TATA tetrad in both forms. However, metal ions are unlikely to be stable in the center of the TATA tetrads. The V-shape structure of the AGAG tetrad and 3.5 kcal/mol of stabilizing energy (compared to the two separated AG pair) revealed in this study suggest that this tetrad structure may not be important in the tetraplexes.
WOS关键词	TELOMERIC DNA ; MOLECULAR-DYNAMICS ; QUADRUPLEX ; ENERGIES ; TETRAPLEX ; EXCHANGE ; QUARTET ; GUANINE ; REPEAT ; MODEL
WOS研究方向	Chemistry ; Physics
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000085770400015
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/274634]
专题	新药研究国家重点实验室中科院受体结构与功能重点实验室
通讯作者	Leszczynski, J
作者单位	1.Jackson State Univ, Dept Chem, Computat Ctr Mol Struct & Interact, Jackson, MS 39217 USA 2.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Shanghai 200031, Peoples R China
推荐引用方式 GB/T 7714	Gu, JD,Leszczynski, J. Structures and properties of mixed DNA bases tetrads: Nonempirical ab inito HF and DFT studies[J]. JOURNAL OF PHYSICAL CHEMISTRY A,2000,104(9):1898-1904.
APA	Gu, JD,&Leszczynski, J.(2000).Structures and properties of mixed DNA bases tetrads: Nonempirical ab inito HF and DFT studies.JOURNAL OF PHYSICAL CHEMISTRY A,104(9),1898-1904.
MLA	Gu, JD,et al."Structures and properties of mixed DNA bases tetrads: Nonempirical ab inito HF and DFT studies".JOURNAL OF PHYSICAL CHEMISTRY A 104.9(2000):1898-1904.