B型DNA中平面药物插入的可视化。
Visualization of planar drug intercalations in B-DNA.
作者信息
Alden C J, Arnott S
出版信息
Nucleic Acids Res. 1975 Oct;2(10):1701-17. doi: 10.1093/nar/2.10.1701.
Abstract
A computerized linked-atom modeling system was developed to examine the stereochemical requirements for intercalation of planar drugs into DNA. All classes of conformational possibilities for extending the polynucleotide backbone were examined for their ability to accommodate insertion of a drug into a base-paired region of DNA compatible with adjacent regions of B-DNA while stacking interactions, steric strain and non-bonded interatomic contacts were optimised. One conformation was found which proved superior to all others in ability to satisfy these criteria: an extension of the backbone by characteristic changes in two torsion angles to trans values, plus a change in one sugar puckering to C3'-endo to relieve strain in an adjacent residue. The turn angle distributed over three polynucleotides for this most general mode of intercalation is 90 degrees, equivalent to a helical unwinding of -18 degrees for B-DNA.
摘要
开发了一种计算机化的连接原子建模系统，以研究平面药物插入DNA的立体化学要求。研究了多核苷酸主链延伸的所有构象可能性，以考察其在堆叠相互作用、空间应变和非键合原子间接触得到优化的情况下，将药物插入与B-DNA相邻区域兼容的DNA碱基对区域的能力。发现了一种构象，在满足这些标准的能力方面优于所有其他构象：主链通过两个扭转角的特征性变化延伸至反式值，加上一个糖环构象变为C3'-内向以缓解相邻残基的应变。这种最常见的嵌入模式在三个多核苷酸上分布的转角为90度，相当于B-DNA的螺旋解旋-18度。
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本文引用的文献
1
Structural considerations in the interaction of DNA and acridines.DNA与吖啶相互作用中的结构考量
J Mol Biol. 1961 Feb;3:18-30. doi: 10.1016/s0022-2836(61)80004-1.
2
Stereochemical studies of cyclic peptides. VI. Energy calculations of the cyclic disulphide cysteinyl-cysteine.
Biochim Biophys Acta. 1969 Aug 12;188(1):1-9. doi: 10.1016/0005-2795(69)90039-7.
3
Calculation of binding isotherms for heterogenous polymers.非均相聚合物结合等温线的计算。
Biopolymers. 1968 Apr;6(4):575-84. doi: 10.1002/bip.1968.360060411.
4
Conservation of conformation in mono and poly-nucleotides.单核苷酸和多核苷酸中构象的保守性。
Nature. 1969 Nov 29;224(5222):886-8. doi: 10.1038/224886a0.
5
Resonance energy transfer between ethidium bromide molecules bound to nucleic acids. Does intercalation wind or unwind the DNA helix?与核酸结合的溴化乙锭分子间的共振能量转移。嵌入作用会使DNA螺旋缠绕还是解旋？
J Mol Biol. 1971 Jul 14;59(1):43-62. doi: 10.1016/0022-2836(71)90412-8.
6
The geometry of nucleic acids.核酸的几何学
Prog Biophys Mol Biol. 1970;21:265-319. doi: 10.1016/0079-6107(70)90027-1.
7
Peptide antibiotic-oligonucleotide interactions. Nuclear magnetic resonance investigations of complex formation between actinomycin D and d-ApTpGpCpApT in aqueous solution.肽抗生素 - 寡核苷酸相互作用。放线菌素D与d - ApTpGpCpApT在水溶液中形成复合物的核磁共振研究。
Biochemistry. 1974 May 21;13(11):2396-402. doi: 10.1021/bi00708a025.
8
Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers.B-DNA结构的优化及其对生物聚合物纤维X射线衍射数据分析的启示
J Mol Biol. 1973 Dec 5;81(2):93-105. doi: 10.1016/0022-2836(73)90182-4.
9
The dimensions and shapes of the furanose rings in nucleic acids.核酸中呋喃糖环的尺寸和形状。
Biochem J. 1972 Nov;130(2):453-65. doi: 10.1042/bj1300453.
10
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Proc Natl Acad Sci U S A. 1974 Dec;71(12):5078-82. doi: 10.1073/pnas.71.12.5078.
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