d(CGTACG)2的分子力学研究：曲古抑菌素A与中间A - T碱基对以Hoogsteen或沃森-克里克配对方式形成的复合物。
Molecular mechanical studies of d(CGTACG)2: complex of triostin A with the middle A - T base pairs in either Hoogsteen or Watson-Crick pairing.
作者信息
Singh U C, Pattabiraman N, Langridge R, Kollman P A
出版信息
Proc Natl Acad Sci U S A. 1986 Sep;83(17):6402-6. doi: 10.1073/pnas.83.17.6402.
Abstract
Computer graphics model building and molecular mechanical calculations have been carried out on d(CGTACG)2 and its bis-intercalation complexes with triostin A and an N-Me-Ala analogue of triostin A. Two conformations of the DNA have been considered both for the uncomplexed and for complexed nucleic acid: in one the central A - T base pairs are Watson-Crick base paired; in the other they are Hoogsteen base paired. The calculations offer a clear explanation why Hoogsteen base pairing is not favorable in isolated A + T-rich DNA and also suggest reasons why the bis-intercalation of triostin A might help stabilize the neighboring A - T base pairs into a Hoogsteen form. To our knowledge, this is the first study to use molecular mechanical and dynamical methods to investigate the bis-intercalator-DNA complex.
摘要
已对d(CGTACG)2及其与三嗪菌素A和三嗪菌素A的N-甲基丙氨酸类似物的双插入复合物进行了计算机图形模型构建和分子力学计算。对于未复合和复合的核酸，均考虑了DNA的两种构象：一种构象中，中央A - T碱基对为沃森-克里克碱基对；另一种构象中，它们为霍格施泰因碱基对。这些计算清楚地解释了为什么霍格施泰因碱基对在孤立的富含A + T的DNA中不利，并且还提出了三嗪菌素A的双插入可能有助于将相邻的A - T碱基对稳定成霍格施泰因形式的原因。据我们所知，这是第一项使用分子力学和动力学方法研究双嵌入剂-DNA复合物的研究。
相似文献
1
Molecular mechanical studies of d(CGTACG)2: complex of triostin A with the middle A - T base pairs in either Hoogsteen or Watson-Crick pairing.d(CGTACG)2的分子力学研究：曲古抑菌素A与中间A - T碱基对以Hoogsteen或沃森-克里克配对方式形成的复合物。
Proc Natl Acad Sci U S A. 1986 Sep;83(17):6402-6. doi: 10.1073/pnas.83.17.6402.
2
NMR investigation of Hoogsteen base pairing in quinoxaline antibiotic--DNA complexes: comparison of 2:1 echinomycin, triostin A and [N-MeCys3,N-MeCys7] TANDEM complexes with DNA oligonucleotides.喹喔啉抗生素-DNA复合物中Hoogsteen碱基配对的核磁共振研究：2:1放线菌素、三孢菌素A和[N-甲基半胱氨酸3，N-甲基半胱氨酸7]串联复合物与DNA寡核苷酸的比较
Nucleic Acids Res. 1994 Dec 11;22(24):5484-91. doi: 10.1093/nar/22.24.5484.
3
Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin A-d(GCGTACGC) complex.喹喔啉抗生素与DNA的相互作用：曲古抑菌素A-d(GCGTACGC)复合物的分子结构
J Biomol Struct Dyn. 1986 Dec;4(3):319-42. doi: 10.1080/07391102.1986.10506353.
4
Sequence specificity of quinoxaline antibiotics. 1. Solution structure of a 1:1 complex between triostin A and [d(GACGTC)]2 and comparison with the solution structure of the [N-MeCys3,N-MeCys7]TANDEM-[d(GATATC)]2 complex.
Biochemistry. 1994 Oct 18;33(41):12386-96. doi: 10.1021/bi00207a005.
5
The molecular structure of a DNA-triostin A complex.一种DNA-三奥菌素A复合物的分子结构。
Science. 1984 Sep 14;225(4667):1115-21. doi: 10.1126/science.6474168.
6
Non-Watson-Crick G.C and A.T base pairs in a DNA-antibiotic complex.DNA-抗生素复合物中的非沃森-克里克G.C和A.T碱基对。
Science. 1986 Jun 6;232(4755):1255-8. doi: 10.1126/science.3704650.
7
Watson-Crick versus Hoogsteen Base Pairs: Chemical Strategy to Encode and Express Genetic Information in Life.沃森-克里克碱基对与霍格斯坦碱基对：在生命中编码和表达遗传信息的化学策略。
Acc Chem Res. 2021 May 4;54(9):2110-2120. doi: 10.1021/acs.accounts.0c00734. Epub 2021 Feb 16.
8
Correlation of crystallographically determined and computationally predicted hydrogen-bonded pairing configurations of nucleic acid bases.核酸碱基的晶体学测定与计算预测的氢键配对构型的相关性。
Proc Natl Acad Sci U S A. 1983 Sep;80(17):5171-5. doi: 10.1073/pnas.80.17.5171.
9
Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.沃森-克里克碱基配对和霍庚斯碱基配对对 C8-苯氧基-2'-脱氧鸟苷加合物构象稳定性的影响。
J Phys Chem B. 2010 Oct 14;114(40):12995-3004. doi: 10.1021/jp105817p.
10
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.DNA中Hoogsteen - 沃森 - 克里克连接的理论研究。
Biophys J. 2006 Feb 1;90(3):1000-8. doi: 10.1529/biophysj.105.059535. Epub 2005 Nov 11.
引用本文的文献
1
Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism.两个不同药物分子通过碱基对调节使 DNA 双链交错排列，诱导不对称的骨架扭曲和结构多态性。
Nucleic Acids Res. 2022 Aug 26;50(15):8867-8881. doi: 10.1093/nar/gkac629.
2
Slow motions in A·T rich DNA sequence.富含 A·T 的 DNA 序列中的慢动作。
Sci Rep. 2020 Nov 4;10(1):19005. doi: 10.1038/s41598-020-75645-x.
3
Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.原子水平上对 DNA 中 Watson-Crick 到 Hoogsteen 转变的动力学途径的深入了解。
Nucleic Acids Res. 2019 Dec 2;47(21):11069-11076. doi: 10.1093/nar/gkz837.
4
Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically C- and N-Labeled DNA.使用核磁共振和 C 端与 N 端特异性标记的 DNA 来描绘 DNA-蛋白质复合物中的 Watson-Crick 与 Hoogsteen 碱基对。
Biochemistry. 2019 Apr 16;58(15):1963-1974. doi: 10.1021/acs.biochem.9b00027. Epub 2019 Apr 5.
5
Robust IR-based detection of stable and fractionally populated G-C and A-T Hoogsteen base pairs in duplex DNA.基于稳健红外技术检测双链DNA中稳定且部分占据的G-C和A-T Hoogsteen碱基对。
FEBS Lett. 2017 Jun;591(12):1770-1784. doi: 10.1002/1873-3468.12681. Epub 2017 Jun 19.
6
Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.从含 N1-甲基腺嘌呤（m1A）的 DNA 双链体的溶液结构和动态集合中洞察沃森-克里克/ hoogsteen 呼吸动力学及损伤修复
Nucleic Acids Res. 2017 May 19;45(9):5586-5601. doi: 10.1093/nar/gkx186.
7
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.基于结构的研究对DNA双链体中Hoogsteen碱基对的新见解。
Nucleic Acids Res. 2015 Apr 20;43(7):3420-33. doi: 10.1093/nar/gkv241. Epub 2015 Mar 26.
8
NMR investigation of Hoogsteen base pairing in quinoxaline antibiotic--DNA complexes: comparison of 2:1 echinomycin, triostin A and [N-MeCys3,N-MeCys7] TANDEM complexes with DNA oligonucleotides.喹喔啉抗生素-DNA复合物中Hoogsteen碱基配对的核磁共振研究：2:1放线菌素、三孢菌素A和[N-甲基半胱氨酸3，N-甲基半胱氨酸7]串联复合物与DNA寡核苷酸的比较
Nucleic Acids Res. 1994 Dec 11;22(24):5484-91. doi: 10.1093/nar/22.24.5484.
9
Diethyl pyrocarbonate can detect a modified DNA structure induced by the binding of quinoxaline antibiotics.焦碳酸二乙酯能够检测由喹喔啉类抗生素结合所诱导的修饰DNA结构。
Nucleic Acids Res. 1988 May 11;16(9):3655-70. doi: 10.1093/nar/16.9.3655.
10
Hoogsteen base pairs proximal and distal to echinomycin binding sites on DNA.DNA上放线菌素结合位点近端和远端的Hoogsteen碱基对。
Proc Natl Acad Sci U S A. 1987 Feb;84(4):910-4. doi: 10.1073/pnas.84.4.910.
本文引用的文献
1
Van der waals surfaces in molecular modeling: implementation with real-time computer graphics.分子建模中的范德华表面：实时计算机图形学的实现。
Science. 1983 Dec 23;222(4630):1325-7. doi: 10.1126/science.222.4630.1325.
2
Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.核酸的分子结构；脱氧核糖核酸的一种结构。
Nature. 1953 Apr 25;171(4356):737-8. doi: 10.1038/171737a0.
3
Molecular-mechanical studies of Z-DNA: a comparison of the structural and energetic properties of Z- and B-DNA.Z-DNA的分子力学研究：Z-DNA与B-DNA结构和能量性质的比较
Biopolymers. 1982 Oct;21(10):1945-69. doi: 10.1002/bip.360211003.
4
The molecular structure of a DNA-triostin A complex.一种DNA-三奥菌素A复合物的分子结构。
Science. 1984 Sep 14;225(4667):1115-21. doi: 10.1126/science.6474168.
5
Sequence preferences in the binding to DNA of triostin A and TANDEM as reported by DNase I footprinting.如通过DNA酶I足迹法所报告的，曲古抑菌素A和串联体与DNA结合时的序列偏好性。
FEBS Lett. 1984 Oct 29;176(2):414-20. doi: 10.1016/0014-5793(84)81209-0.
6
Sequence-specific binding of echinomycin to DNA: evidence for conformational changes affecting flanking sequences.放线菌素与DNA的序列特异性结合：影响侧翼序列构象变化的证据。
Nucleic Acids Res. 1984 Jun 25;12(12):4865-79. doi: 10.1093/nar/12.12.4865.
7
Echinomycin binding sites on DNA.放线菌素与DNA上的结合位点。
Science. 1984 Sep 14;225(4667):1122-7. doi: 10.1126/science.6089341.
8
Optimised parameters for A-DNA and B-DNA.A-DNA和B-DNA的优化参数。
Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9. doi: 10.1016/0006-291X(72)90243-4.
9
Echinomycin: a bifunctional intercalating antibiotic.棘霉素：一种双功能嵌入型抗生素。
Nature. 1974 Dec 20;252(5485):653-7. doi: 10.1038/252653a0.
10
A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment.棘霉素和曲奥菌素A与一个DNA片段复合后的结构比较。
Nucleic Acids Res. 1985 Apr 11;13(7):2305-23. doi: 10.1093/nar/13.7.2305.
Zotero 插件