DNA寡聚物的¹H NMR化学位移预测
Prediction of 1H NMR chemical shifts of DNA oligomers.
作者信息
Bell R A, Alkema D, Coddington J M, Hader P A, Hughes D W, Neilson T
出版信息
Nucleic Acids Res. 1983 Feb 25;11(4):1143-9. doi: 10.1093/nar/11.4.1143.
Abstract
A set of parameters, devised for the prediction of 1H NMR chemical shifts of heterobase and anomeric protons in the high temperature (greater than 70 degrees C) spectra of RNA oligomers has been found to be applicable to the corresponding DNA oligomers. Fifteen examples of DNA oligomers that have had high temperature spectra recorded and assigned show a mean absolute difference between predicted and assigned shifts of 0.045 ppm. The parameters for uridine H-5 are applied to the calculation of thymidine methyl group shifts and give excellent agreement with experimental assigned shifts. The RNA parameter set is a practical means of assigning heterobase and anomeric protons in DNA oligomers. A programme using the RNA parameter set has been written which enables the sequence of short DNA oligomers to be predicted from their 1H NMR spectra.
摘要
已发现，为预测RNA寡聚物高温（高于70摄氏度）光谱中杂碱基和异头质子的1H NMR化学位移而设计的一组参数适用于相应的DNA寡聚物。记录并指定了高温光谱的15个DNA寡聚物示例显示，预测位移与指定位移之间的平均绝对差值为0.045 ppm。将尿苷H-5的参数应用于胸苷甲基基团位移的计算，结果与实验指定位移高度吻合。RNA参数集是指定DNA寡聚物中杂碱基和异头质子的一种实用方法。已编写了一个使用RNA参数集的程序，该程序能够根据1H NMR光谱预测短DNA寡聚物的序列。
相似文献
1
Prediction of 1H NMR chemical shifts of DNA oligomers.DNA寡聚物的¹H NMR化学位移预测
Nucleic Acids Res. 1983 Feb 25;11(4):1143-9. doi: 10.1093/nar/11.4.1143.
2
Parameters for the calculation of proton NMR chemical shifts of oligoribonucleotides.寡核糖核苷酸质子核磁共振化学位移计算的参数
J Biomol Struct Dyn. 1985 Feb;2(4):693-707. doi: 10.1080/07391102.1985.10506317.
3
Probing the three-dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements.通过核Overhauser效应测量探究溶液中DNA和RNA寡核苷酸的三维结构。
FEBS Lett. 1985 Jan 7;179(2):187-98. doi: 10.1016/0014-5793(85)80516-0.
4
DNA fragment conformations. 1H-NMR comparative studies of helix-coil transition and conformation of d(C-A-C-G-T-G) and d(G-T-G-C-A-C). Influence of helix formation on proton chemical shifts.DNA片段构象。d（C-A-C-G-T-G）和d（G-T-G-C-A-C）螺旋-卷曲转变及构象的1H-NMR比较研究。螺旋形成对质子化学位移的影响。
Eur J Biochem. 1983 Jul 1;133(3):579-89. doi: 10.1111/j.1432-1033.1983.tb07502.x.
5
Ethidium bromide-(dC-dG-dC-dG)2 complex in solution: intercalation and sequence specificity of drug binding at the tetranucleotide duplex level.溶液中的溴化乙锭 -（dC - dG - dC - dG）2 复合物：药物在四核苷酸双链水平上结合的嵌入作用和序列特异性
Proc Natl Acad Sci U S A. 1976 Oct;73(10):3343-7. doi: 10.1073/pnas.73.10.3343.
6
Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation.RNA中质子化学位移的预测。其在结构优化与验证中的应用。
J Biomol NMR. 2001 Sep;21(1):11-29. doi: 10.1023/a:1011914132531.
7
DNA fragment conformations IV - Helix-coil transition and conformation of d-CCATGG in aqueous solution by 1H-NMR spectroscopy.DNA片段构象IV - 水溶液中d-CCATGG的螺旋-卷曲转变及构象的1H-核磁共振光谱研究
Nucleic Acids Res. 1982 Sep 11;10(17):5319-32. doi: 10.1093/nar/10.17.5319.
8
Proton nuclear magnetic resonance investigations and ring current calculations of guanine N-1 and thymine N-3 hydrogen-bonded protons in double-helical deoxyribonucleotides in aqueous solution.水溶液中双螺旋脱氧核糖核苷酸中鸟嘌呤N-1和胸腺嘧啶N-3氢键质子的质子核磁共振研究及环电流计算
Proc Natl Acad Sci U S A. 1974 May;71(5):1945-8. doi: 10.1073/pnas.71.5.1945.
9
Two-dimensional NMR investigation of a bent DNA fragment: assignment of the proton resonances and preliminary structure analysis.弯曲DNA片段的二维核磁共振研究：质子共振归属及初步结构分析
Nucleic Acids Res. 1987 Jul 24;15(14):5845-62. doi: 10.1093/nar/15.14.5845.
10
DNA fragment conformations. 1H-NMR and relaxation studies of 2'-deoxyadenylyl(3'-5')thymidylyl-(3'-5')deoxyguanosylyl(3'-5')thymidine, d(A-T-G-T), in neutral aqueous solution.DNA片段构象。2'-脱氧腺苷酰基（3'-5'）胸苷酰基-（3'-5'）脱氧鸟苷酰基（3'-5'）胸苷，即d(A-T-G-T)在中性水溶液中的1H-NMR和弛豫研究。
Eur J Biochem. 1982 Jan;121(2):317-23. doi: 10.1111/j.1432-1033.1982.tb05788.x.
引用本文的文献
1
Random coil proton chemical shifts of deoxyribonucleic acids.脱氧核糖核酸的无规卷曲质子化学位移
J Biomol NMR. 2002 Dec;24(4):329-37. doi: 10.1023/a:1021671531438.
2
Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect.关于共价连接的RNA-DNA杂交体r(GCG)d(TATACGC)的质子核磁共振研究。通过应用核Overhauser效应确定质子共振峰。
Nucleic Acids Res. 1983 Aug 25;11(16):5717-38. doi: 10.1093/nar/11.16.5717.
本文引用的文献
1
Proton nuclear magnetic resonance study of the self-complementary hexanucleotide d(pTpA)3 and its interaction with daunomycin.自互补六核苷酸d(pTpA)3及其与柔红霉素相互作用的质子核磁共振研究
Biochemistry. 1980 Oct 14;19(21):4795-801. doi: 10.1021/bi00562a013.
2
Synthesis and structural studies of a self-complementary decadeoxynucleotide d(AATTGCAATT). II.-Proton magnetic resonance studies.自互补十聚脱氧核苷酸d(AATTGCAATT)的合成与结构研究。II. -质子磁共振研究。
Biochimie. 1981 Oct;63(10):785-90. doi: 10.1016/s0300-9084(81)80038-7.
3
Structure and energetics of a hexanucleotide duplex with stacked trinucleotide ends formed by the sequence d(GAATTCGCG).由序列d(GAATTCGCG)形成的具有堆叠三核苷酸末端的六核苷酸双链体的结构与能量学
Biochemistry. 1982 Feb 2;21(3):451-5. doi: 10.1021/bi00532a005.
4
Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution.在溶液中，额外的腺苷堆积到自身互补的d(CGCAGAATTCGCG)双链体中。
Biochemistry. 1982 Feb 2;21(3):445-51. doi: 10.1021/bi00532a004.
5
Structure, dynamics, and energetics of deoxyguanosine . thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution.溶液中自互补双链体d(CGTGAATTCGCG) 中脱氧鸟苷-胸苷摆动碱基对形成的结构、动力学和能量学
Biochemistry. 1982 Feb 2;21(3):437-44. doi: 10.1021/bi00532a003.
6
Right-handed and left-handed DNA: studies of B- and Z-DNA by using proton nuclear Overhauser effect and P NMR.右手螺旋和左手螺旋DNA：利用质子核Overhauser效应和磷核磁共振对B型和Z型DNA的研究
Proc Natl Acad Sci U S A. 1982 Mar;79(5):1413-7. doi: 10.1073/pnas.79.5.1413.
7
DNA fragment conformations. 1H-NMR and relaxation studies of 2'-deoxyadenylyl(3'-5')thymidylyl-(3'-5')deoxyguanosylyl(3'-5')thymidine, d(A-T-G-T), in neutral aqueous solution.DNA片段构象。2'-脱氧腺苷酰基（3'-5'）胸苷酰基-（3'-5'）脱氧鸟苷酰基（3'-5'）胸苷，即d(A-T-G-T)在中性水溶液中的1H-NMR和弛豫研究。
Eur J Biochem. 1982 Jan;121(2):317-23. doi: 10.1111/j.1432-1033.1982.tb05788.x.
8
A model for base overlap in RNA.
Nature. 1982 Jul 8;298(5870):198-200. doi: 10.1038/298198a0.
9
Conformation and interaction of short nucleic acid double-stranded helices. I. Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU.短核酸双链螺旋的构象与相互作用。I. 核糖基ApApGpCpUpU不可交换质子的质子磁共振研究。
Biochemistry. 1975 Nov 4;14(22):4847-63. doi: 10.1021/bi00693a012.
10
d-CpCpGpG and d-GpGpCpC self-complementary duplexes: Nmr studies of the helix-coil transition.
Biopolymers. 1977 Aug;16(8):1635-56. doi: 10.1002/bip.1977.360160804.
Zotero 插件