药物-脱氧核苷磷酸复合物的结构；与RNA和DNA片段形成的嵌入复合物的一般构象行为。
The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.
作者信息
Shieh H S, Berman H M, Dabrow M, Neidle S
出版信息
Nucleic Acids Res. 1980 Jan 11;8(1):85-97. doi: 10.1093/nar/8.1.85.
Abstract
A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry.
摘要
硫酸原黄素与脱氧胞苷酰-3',5'-鸟苷的2:2复合物已结晶，并通过X射线晶体学确定了其结构。两条二核苷磷酸链通过沃森-克里克氢键形成自我互补的双链体。一个硫酸原黄素不对称地插入碱基对之间，另一个则堆积在它们之上。核苷酸的构象不同寻常，因为一条链具有C3',C2'内向混合糖折叠，另一条链具有C3',C3'内向脱氧核糖糖。这些结果表明，3'-糖的构象对插入几何形状的重要性次之。
相似文献
1
The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.药物-脱氧核苷磷酸复合物的结构；与RNA和DNA片段形成的嵌入复合物的一般构象行为。
Nucleic Acids Res. 1980 Jan 11;8(1):85-97. doi: 10.1093/nar/8.1.85.
2
Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.磷酸二核苷-药物复合物的结构作为核酸-药物相互作用的模型
Nature. 1977 Sep 22;269(5626):304-7. doi: 10.1038/269304a0.
3
X-ray-structure of a cytidylyl-3',5'-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye.胞苷酰-3',5'-腺苷-硫酸普罗黄素复合物的X射线结构：一种带有嵌入吖啶染料的自配对平行链双螺旋二聚体。
Proc Natl Acad Sci U S A. 1980 Apr;77(4):1852-6. doi: 10.1073/pnas.77.4.1852.
4
Highly structured water network in crystals of a deoxydinucleoside---drug complex.脱氧二核苷-药物复合物晶体中的高度结构化水网络。
Nature. 1980 Nov 13;288(5787):129-33. doi: 10.1038/288129a0.
5
Molecular mechanical studies of proflavine and acridine orange intercalation.硫酸原黄素和吖啶橙嵌入的分子力学研究。
Nucleic Acids Res. 1981 Mar 25;9(6):1483-97. doi: 10.1093/nar/9.6.1483.
6
Visualization of drug-nucleic acid interactions at atomic resolution. X. Structure of a N,N-dimethylproflavine: deoxycytidylyl(3'-5')deoxyguanosine crystalline complex.药物与核酸相互作用的原子分辨率可视化。X. N,N-二甲基原黄素：脱氧胞苷酰(3'-5')脱氧鸟苷晶体复合物的结构。
J Biomol Struct Dyn. 1984 Mar;1(5):1219-27. doi: 10.1080/07391102.1984.10507513.
7
Networks of water molecules in a proflavine deoxydinucleoside phosphate complex.原黄素脱氧核苷磷酸复合物中的水分子网络
J Biomol Struct Dyn. 1983 Oct;1(1):263-85. doi: 10.1080/07391102.1983.10507439.
8
A molecular model for proflavine-DNA intercalation.原黄素-DNA嵌入的分子模型。
Nucleic Acids Res. 1988 Sep 26;16(18):8999-9016. doi: 10.1093/nar/16.18.8999.
9
Stereochemical model for proflavin intercalation in A-DNA.原黄素嵌入A-DNA的立体化学模型。
Nucleic Acids Res. 1977 Nov;4(11):3855-61. doi: 10.1093/nar/4.11.3855.
10
Conformation and dynamics of drug-DNA intercalation.药物 - DNA 嵌入的构象与动力学
J Biomol Struct Dyn. 1992 Aug;10(1):97-139. doi: 10.1080/07391102.1992.10508633.
引用本文的文献
1
High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.四链体-双链体连接的高亲和力结合：是规则而不是例外。
Nucleic Acids Res. 2022 Nov 11;50(20):11948-11964. doi: 10.1093/nar/gkac1088.
2
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.基于知识的方法，使用水合二核苷酸作为构建块预测 DNA 水合作用。
Acta Crystallogr D Struct Biol. 2022 Aug 1;78(Pt 8):1032-1045. doi: 10.1107/S2059798322006234. Epub 2022 Jul 21.
3
Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An study.芯能级光谱对腈基静电环境的敏感性：一项研究。
Struct Dyn. 2017 Sep 25;4(5):054102. doi: 10.1063/1.5003404. eCollection 2017 Sep.
4
Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches.具有C1对称性的手性氮杂-15-冠-5醚对手性有机盐的对映体识别：实验与理论方法
J Mol Model. 2015 Mar;21(3):55. doi: 10.1007/s00894-015-2604-6. Epub 2015 Feb 21.
5
Crystal structures of Λ-[Ru(phen)₂dppz]²⁺ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes.寡核苷酸中包含 TA/TA 和 AT/AT 步的 Λ-[Ru(phen)₂dppz]²⁺的晶体结构显示出两种嵌入模式。
Nat Chem. 2012 Jun 24;4(8):621-8. doi: 10.1038/nchem.1397.
6
Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world.在原始生命世界中，通过嵌入碱基配对寡核苷酸来抑制环化并促进聚合。
Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5288-93. doi: 10.1073/pnas.0914172107. Epub 2010 Mar 8.
7
Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.dCpG/硫酸原黄素晶体水合物的巨正则系综蒙特卡罗模拟
Biophys J. 1996 Sep;71(3):1179-90. doi: 10.1016/S0006-3495(96)79322-0.
8
Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.核酸片段的水合作用：RNA、DNA及DNA-药物复合物高分辨率晶体结构的理论与实验比较
Biophys J. 1995 May;68(5):1639-52. doi: 10.1016/S0006-3495(95)80381-4.
9
Molecular mechanical studies of proflavine and acridine orange intercalation.硫酸原黄素和吖啶橙嵌入的分子力学研究。
Nucleic Acids Res. 1981 Mar 25;9(6):1483-97. doi: 10.1093/nar/9.6.1483.
10
Cooperative effects in water-biomolecule crystal systems.水-生物分子晶体系统中的协同效应。
Proc Natl Acad Sci U S A. 1982 Aug;79(16):4977-9. doi: 10.1073/pnas.79.16.4977.
本文引用的文献
1
Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.核苷和核苷酸中糖环的构象分析。一种使用假旋转概念的新描述。
J Am Chem Soc. 1972 Nov 15;94(23):8205-12. doi: 10.1021/ja00778a043.
2
"Non-rigid" nucleotides in tRNA: a new correlation in the conformation of a ribose.转运RNA中的“非刚性”核苷酸：核糖构象的新关联
Nature. 1976 May 20;261(5557):250-1. doi: 10.1038/261250a0.
3
Visualization of planar drug intercalations in B-DNA.B型DNA中平面药物插入的可视化。
Nucleic Acids Res. 1975 Oct;2(10):1701-17. doi: 10.1093/nar/2.10.1701.
4
RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate.原子分辨率下的RNA双螺旋片段。I. 腺苷酰-3',5'-尿苷六水合钠的晶体和分子结构。
J Mol Biol. 1976 Jun 14;104(1):109-44. doi: 10.1016/0022-2836(76)90005-x.
5
Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodocytidylyl (3'-5') guanosine.药物与核酸相互作用的原子分辨率可视化。II. 溴化乙锭/二核苷单磷酸晶体复合物的结构，溴化乙锭：5-碘胞苷酰基（3'-5'）鸟苷。
J Mol Biol. 1977 Aug 15;114(3):317-31. doi: 10.1016/0022-2836(77)90253-4.
6
Visualization of drug-nucleic acid interactions at atomic resolution. I. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodouridylyl (3'-5') adenosine.药物与核酸相互作用的原子分辨率可视化。I. 溴化乙锭/二核苷单磷酸晶体复合物的结构，溴化乙锭：5-碘尿苷酰基（3'-5'）腺苷。
J Mol Biol. 1977 Aug 15;114(3):301-15. doi: 10.1016/0022-2836(77)90252-2.
7
Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.磷酸二核苷-药物复合物的结构作为核酸-药物相互作用的模型
Nature. 1977 Sep 22;269(5626):304-7. doi: 10.1038/269304a0.
8
A 1:2 crystalline complex of ApA:proflavine: a model for binding to single-stranded regions in RNA.ApA与原黄素的1:2晶体复合物：一种与RNA单链区域结合的模型
Nucleic Acids Res. 1978 Nov;5(11):4417-22. doi: 10.1093/nar/5.11.4417.
9
Molecular structure of a double helical DNA fragment intercalator complex between deoxy CpG and a terpyridine platinum compound.脱氧胞嘧啶磷酸鸟嘌呤（CpG）与三联吡啶铂化合物之间的双螺旋DNA片段嵌入剂复合物的分子结构。
Nature. 1978 Nov 30;276(5687):471-4. doi: 10.1038/276471a0.
10
Stereochemical model for proflavin intercalation in A-DNA.原黄素嵌入A-DNA的立体化学模型。
Nucleic Acids Res. 1977 Nov;4(11):3855-61. doi: 10.1093/nar/4.11.3855.
Zotero 插件