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1
Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and model-building study.额外的胸腺嘧啶堆积到d(CTGGTGCGG).d(CCGCCCAG)双链体中。一项核磁共振与模型构建研究。
Nucleic Acids Res. 1988 Apr 11;16(7):2971-86. doi: 10.1093/nar/16.7.2971.
2
Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG).(CCGCCCAG). A model-building and NMR study.单链三聚体AUA和双链体（CUGGUGCGG）。（CCGCCCAG）中的突出结构。一项模型构建和核磁共振研究。
Nucleic Acids Res. 1988 Jun 10;16(11):5013-30. doi: 10.1093/nar/16.11.5013.
3
NMR studies of the exocyclic 1,N6-ethenodeoxyadenosine adduct (epsilon dA) opposite thymidine in a DNA duplex. Nonplanar alignment of epsilon dA(anti) and dT(anti) at the lesion site.DNA双链中胸腺嘧啶对面的环外1,N6-乙烯基脱氧腺苷加合物（εdA）的核磁共振研究。损伤位点处εdA（反式）和dT（反式）的非平面排列。
Biochemistry. 1991 Feb 19;30(7):1820-8. doi: 10.1021/bi00221a014.
4
Helix-coil transition of the self-complementary dG-dG-dA-dA-dT-dT-dC-dC duplex.自互补dG-dG-dA-dA-dT-dT-dC-dC双链体的螺旋-卷曲转变
Eur J Biochem. 1979 May 15;96(2):267-76. doi: 10.1111/j.1432-1033.1979.tb13037.x.
5
Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 1. The duplex form.通过1H-NMR光谱研究溶液中A(5)残基的N6-甲基化对d(C-C-G-A-A-T-T-C-G-G)构象行为的影响。1. 双链体形式。
Eur J Biochem. 1987 Mar 2;163(2):275-86. doi: 10.1111/j.1432-1033.1987.tb10798.x.
6
Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution.含胞嘧啶凸起的脱氧十三核苷酸双链体中的构象转变：额外的胞嘧啶在溶液中处于环出（低温）和堆积（高温）构象之间达到平衡。
Biochemistry. 1989 Jan 10;28(1):294-303. doi: 10.1021/bi00427a040.
7
NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA).oligo(dT) tract.对一种含有被寡聚（dA）.寡聚（dT）序列包围的额外螺旋胸腺嘧啶的脱氧核糖十核苷酸的核磁共振研究。
Biochemistry. 1990 Sep 18;29(37):8835-45. doi: 10.1021/bi00489a047.
8
Proton NMR study and conformational analysis of d(CGT), d(TCG) and d(CGTCG) in aqueous solution. The effect of a dangling thymidine and of a thymidine mismatch on DNA mini-duplexes.水溶液中d(CGT)、d(TCG)和d(CGTCG)的质子核磁共振研究与构象分析。游离胸苷和胸苷错配对DNA小双链体的影响。
Nucleic Acids Res. 1984 Jun 25;12(12):5061-78. doi: 10.1093/nar/12.12.5061.
9
Dynamics of DNA duplexes containing internal G.T, G.A, A.C, and T.C pairs: hydrogen exchange at and adjacent to mismatch sites.包含内部G.T、G.A、A.C和T.C碱基对的DNA双链体的动力学：错配位点及其相邻位置的氢交换。
Fed Proc. 1984 Aug;43(11):2663-70.
10
Structural studies of the O6meG.T interaction in the d(C-G-T-G-A-A-T-T-C-O6meG-C-G) duplex.d（C-G-T-G-A-A-T-T-C-O6meG-C-G）双链体中O6meG.T相互作用的结构研究
Biochemistry. 1986 Mar 11;25(5):1036-42. doi: 10.1021/bi00353a013.

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Structure of the 1,N(2)-etheno-2'-deoxyguanosine lesion in the 3'-G(epsilon dG)T-5' sequence opposite a one-base deletion.在碱基缺失的情况下，3'-G(epsilon dG)T-5' 序列中 1,N(2)-乙烯基-2'-脱氧鸟苷的结构。
Biochemistry. 2010 Mar 30;49(12):2615-26. doi: 10.1021/bi901516d.
2
Bulge migration of the malondialdehyde OPdG DNA adduct when placed opposite a two-base deletion in the (CpG)3 frameshift hotspot of the Salmonella typhimurium hisD3052 gene.当丙二醛OPdG DNA加合物位于鼠伤寒沙门氏菌hisD3052基因（CpG）3移码热点中的两个碱基缺失对面时的凸起迁移。
Chem Res Toxicol. 2007 Aug;20(8):1200-10. doi: 10.1021/tx700121j. Epub 2007 Jul 24.
3
Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics.通过核磁共振和受限分子动力学对含有N-（2-脱氧-β-D-赤藓糖基）甲酰胺移码的DNA双链体进行结构研究。
Nucleic Acids Res. 2003 Oct 15;31(20):5930-40. doi: 10.1093/nar/gkg803.
4
Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.DNA 八聚体中腺嘌呤凸起的构象及其对 DNA 结构的影响：分子动力学模拟研究
Biophys J. 2001 Jul;81(1):352-70. doi: 10.1016/S0006-3495(01)75705-0.
5
2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects.DNA中无碱基位点碱基堆积相互作用的2-氨基嘌呤荧光研究：金属离子和碱基序列效应
Nucleic Acids Res. 1998 Aug 15;26(16):3837-44. doi: 10.1093/nar/26.16.3837.
6
Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases.人类主要的脱嘌呤/脱嘧啶内切核酸酶和大肠杆菌脱嘌呤/脱嘧啶内切核酸酶识别无碱基位点的要素。
Nucleic Acids Res. 1998 Jun 1;26(11):2771-8. doi: 10.1093/nar/26.11.2771.
7
Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.使用溶剂和离子的连续介质模型分析DNA中腺嘌呤凸起的环出和堆叠构象的稳定性。
Biophys J. 1997 Dec;73(6):2990-3003. doi: 10.1016/S0006-3495(97)78328-0.
8
Kinking of DNA and RNA by base bulges.碱基凸起导致的DNA和RNA扭结
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9
Structure and in vitro replication of DNA templates containing 7,8-dihydro-8-oxoadenine.含有7,8-二氢-8-氧代腺嘌呤的DNA模板的结构与体外复制
Nucleic Acids Res. 1991 Apr 25;19(8):1753-8. doi: 10.1093/nar/19.8.1753.
10
Solution conformation of an oligonucleotide containing a urea deoxyribose residue in front of a thymine.胸腺嘧啶前含有脲脱氧核糖残基的寡核苷酸的溶液构象。
Nucleic Acids Res. 1992 Dec 25;20(24):6455-60. doi: 10.1093/nar/20.24.6455.

本文引用的文献

1
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.
2
Effective water resonance suppression in 1D- and 2D-FT-1H-NMR spectroscopy of biopolymers in aqueous solution.水溶液中生物聚合物一维和二维傅里叶变换氢核磁共振光谱法中有效的水共振抑制
Biopolymers. 1983 May;22(5):1259-66. doi: 10.1002/bip.360220502.
3
Sequential resonance assignments in 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy.通过二维核磁共振光谱对寡核苷酸的1H NMR光谱进行顺序共振归属。
Biochemistry. 1984 Mar 27;23(7):1371-6. doi: 10.1021/bi00302a006.
4
Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods.使用二维核磁共振方法对d（C-G-C-G-A-A-T-T-C-G-C-G）的非交换质子共振进行归属
J Mol Biol. 1983 Dec 15;171(3):319-36. doi: 10.1016/0022-2836(83)90096-7.
5
Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method.基于质子核磁共振化学位移的二磷酸单核苷m2(6)A-U堆积与自缔合的热力学：差分浓度-温度分布法
Eur J Biochem. 1982 Dec 15;129(2):343-57. doi: 10.1111/j.1432-1033.1982.tb07057.x.
6
Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G . T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G).d（C-G-C-G-A-A-T-T-C-G-C-G）双螺旋以及包含一个G·T碱基对的两个类似螺旋d（C-G-T-G-A-A-T-T-C-G-C-G）和一个额外腺嘌呤的d（C-G-C-A-G-A-A-T-T-C-G-C-G）中亚氨基质子交换的动力学
Biochemistry. 1982 Dec 7;21(25):6567-74. doi: 10.1021/bi00268a038.
7
Extrahelical bases in duplex DNA.双链DNA中的螺旋外碱基。
J Mol Biol. 1982 Sep;160(1):117-22. doi: 10.1016/0022-2836(82)90134-6.
8
Conformational analysis of a hybrid DNA-RNA double helical oligonucleotide in aqueous solution: d(CG)r(CG)d(CG) studied by 1D- and 2D-1H NMR spectroscopy.水溶液中一种DNA-RNA杂交双螺旋寡核苷酸的构象分析：通过一维和二维氢核磁共振光谱研究d(CG)r(CG)d(CG)
J Biomol Struct Dyn. 1983 Oct;1(1):131-49. doi: 10.1080/07391102.1983.10507430.
9
Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday.移码突变与遗传密码。本文谨献给西奥多修斯·杜布赞斯基教授，以庆祝他66岁生日。
Cold Spring Harb Symp Quant Biol. 1966;31:77-84. doi: 10.1101/sqb.1966.031.01.014.
10
Consequences of methylation on the amino group of adenine. A proton two-dimensional NMR study of d(GGATATCC) and d(GGm6ATATCC).腺嘌呤氨基甲基化的后果。d(GGATATCC)和d(GGm6ATATCC)的质子二维核磁共振研究。
Eur J Biochem. 1985 Oct 1;152(1):99-105. doi: 10.1111/j.1432-1033.1985.tb09168.x.

额外的胸腺嘧啶堆积到d(CTGGTGCGG).d(CCGCCCAG)双链体中。一项核磁共振与模型构建研究。

Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and model-building study.

作者信息

van den Hoogen Y T, van Beuzekom A A, van den Elst H, van der Marel G A, van Boom J H, Altona C

机构信息

Gorlaeus Laboratories, Leiden University, The Netherlands.

出版信息

Nucleic Acids Res. 1988 Apr 11;16(7):2971-86. doi: 10.1093/nar/16.7.2971.

DOI:10.1093/nar/16.7.2971
PMID:3368313
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC336445/
Abstract

NMR and model-building studies were carried out on the duplex d(CTGGTGCGG).d(CCGCCCAG), referred to as (9+8)-mer, which contains an unpaired thymidine residue. Resonances of the base and of several sugar protons of the (9+8)-mer were assigned by means of a NOESY experiment. Interresidue NOEs between dG(4) and dT(5) as well as between dT(5) and dG(6) provided evidence that the extra dT is stacked into the duplex. Thermodynamic analysis of the chemical shift vs temperature profiles yielded an average TmD value of 334 K and delta HD of -289 kJmol-1 for the duplex in equilibrium random-coil transition. The shapes of the shift profiles as well as the thermodynamic parameters obtained for the extra dT residue and its neighbours again indicate that the unpaired dT base is incorporated inside an otherwise intact duplex. This conclusion is further supported by (a) the observation of an imino-proton resonance of the unpaired dT; (b) the relatively small dispersion in 31P chemical shifts (approximately 0.5 ppm) for the (9+8)-mer, which indicates the absence of t/g or g/t combinations for the phosphate diester torsion angles alpha/zeta. An energy-minimized model of the (9+8)-mer, which fits the present collection of experimental data, is presented.

摘要

对双链体d(CTGGTGCGG).d(CCGCCCAG)（称为(9 + 8) - 聚体）进行了核磁共振（NMR）和模型构建研究，该双链体含有一个未配对的胸腺嘧啶残基。通过核Overhauser效应光谱（NOESY）实验确定了(9 + 8) - 聚体中碱基和几个糖质子的共振峰。dG(4)与dT(5)以及dT(5)与dG(6)之间的残基间核Overhauser效应（NOE）提供了额外的dT堆积在双链体中的证据。化学位移随温度变化曲线的热力学分析得出，在平衡随机卷曲转变中，双链体的平均解链温度（TmD）值为334 K，焓变（ΔHD）为 - 289 kJ/mol。额外dT残基及其相邻残基的位移曲线形状以及获得的热力学参数再次表明，未配对的dT碱基掺入了原本完整的双链体内部。这一结论得到了以下几点的进一步支持：(a) 观察到未配对dT的亚氨基质子共振；(b) (9 + 8) - 聚体的31P化学位移相对较小（约0.5 ppm），这表明磷酸二酯扭转角α/ζ不存在t/g或g/t组合。本文给出了一个能量最小化的(9 + 8) - 聚体模型，该模型符合目前收集的实验数据。