在高分辨率下观察到的2'-硫代甲基修饰DNA结构中的构象转变。
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
作者信息
Pallan Pradeep S, Prakash Thazha P, Li Feng, Eoff Robert L, Manoharan Muthiah, Egli Martin
机构信息
Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
出版信息
Chem Commun (Camb). 2009 Apr 21(15):2017-9. doi: 10.1039/b822781k. Epub 2009 Feb 26.
Abstract
Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.
摘要
含有2'-硫代甲基尿苷的A-型和B-型DNA双链体的晶体结构表明，修饰后的残基呈现出类似RNA的C3'-内向型构象，这说明在寡核苷酸环境中，RNA 2'-碳上的电负性氧被硫取代似乎并未从根本上改变糖的构象偏好，且空间效应胜过立体电子效应。
相似文献
1
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.在高分辨率下观察到的2'-硫代甲基修饰DNA结构中的构象转变。
Chem Commun (Camb). 2009 Apr 21(15):2017-9. doi: 10.1039/b822781k. Epub 2009 Feb 26.
2
Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.含有5-（N-氨基己基）氨基甲酰基修饰尿嘧啶的DNA:DNA和DNA:RNA双链体的晶体结构揭示了其作为反基因和反义分子性质的基础。
Nucleic Acids Res. 2007;35(6):1969-77. doi: 10.1093/nar/gkl821. Epub 2007 Mar 6.
3
Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability.含有2'-脱氧-2'-氟阿拉伯呋喃糖基胸腺嘧啶的B-DNA晶体结构：构象预组织对双链稳定性的影响
Nucleic Acids Res. 1998 May 15;26(10):2473-80. doi: 10.1093/nar/26.10.2473.
4
X-ray analyses of hybrid duplexes between antisense oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine and their target RNAs.含有5-（N-氨基己基）氨基甲酰基-2'-O-甲基尿苷的反义寡核苷酸与其靶RNA之间杂交双链体的X射线分析。
Nucleic Acids Symp Ser (Oxf). 2005(49):65-6. doi: 10.1093/nass/49.1.65.
5
Conformational flexibility in RNA: the role of dihydrouridine.RNA中的构象灵活性：二氢尿苷的作用。
Nucleic Acids Res. 1996 Mar 15;24(6):1073-9. doi: 10.1093/nar/24.6.1073.
6
Unusual conformation of a 3'-thioformacetal linkage in a DNA duplex.DNA双链中3'-硫代缩醛连接的异常构象。
J Biomol NMR. 1994 Jan;4(1):17-34. doi: 10.1007/BF00178333.
7
X-ray analyses of DNA duplexes containing 5-(N-aminohexyl)carbamoyl modifications.对含有5-（N-氨基己基）氨基甲酰基修饰的DNA双链体的X射线分析。
Nucleic Acids Symp Ser (Oxf). 2004(48):305-6. doi: 10.1093/nass/48.1.305.
8
Conformation of formacetal and 3'-thioformacetal nucleotide linkers and stability of their antisense RNA.DNA hybrid duplexes.甲醛缩醛和3'-硫代甲醛缩醛核苷酸连接体的构象及其反义RNA·DNA杂交双链体的稳定性
Biochemistry. 1997 Jan 14;36(2):399-411. doi: 10.1021/bi961760i.
9
B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G).由3'-末端核糖介导的B型到A型的转换：嵌合体d(CCACTAGTG)r(G)的晶体结构
Nucleic Acids Res. 2000 Nov 1;28(21):4356-63. doi: 10.1093/nar/28.21.4356.
10
Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations.通过分子模拟快速传达二氢尿苷的去稳定化作用
Biopolymers. 2014 Oct;101(10):985-91. doi: 10.1002/bip.22495.
引用本文的文献
1
Chemistry, structure and function of approved oligonucleotide therapeutics.已获批的寡核苷酸治疗药物的化学、结构和功能。
Nucleic Acids Res. 2023 Apr 11;51(6):2529-2573. doi: 10.1093/nar/gkad067.
2
Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography.磷硒酸酯修饰DNA的固相合成与结构表征：一种不会产生构象偏向且有助于单波长反常散射X射线晶体学研究的主链类似物。
Chem Sci. 2019 Oct 11;10(47):10948-10957. doi: 10.1039/c9sc04098f. eCollection 2019 Dec 21.
3
2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.2’-炔基自旋标记是一种对 DNA 结构分析极小干扰的工具。
Nucleic Acids Res. 2020 Apr 6;48(6):2830-2840. doi: 10.1093/nar/gkaa086.
4
Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine.用2'-硫代-2'-脱氧-2'-S-(芘-1-基)甲基尿苷修饰的寡脱氧核糖核苷酸的合成与表征
Bioorg Med Chem Lett. 2015 Sep 15;25(18):3999-4004. doi: 10.1016/j.bmcl.2015.07.002. Epub 2015 Jul 7.
5
Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids.2'-三氟甲硫基修饰核糖核酸令人惊讶的碱基配对和结构特性。
J Am Chem Soc. 2014 May 7;136(18):6656-63. doi: 10.1021/ja5005637. Epub 2014 Apr 25.
6
Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.5-氯尿嘧啶修饰的 A:U 和 G:U 碱基对的结构、稳定性和功能。
Nucleic Acids Res. 2013 Feb 1;41(4):2689-97. doi: 10.1093/nar/gks1316. Epub 2012 Dec 28.
7
2'-SCF3 uridine-a powerful label for probing structure and function of RNA by 19F NMR spectroscopy.2'-SCF3 尿苷 - 通过 19F NMR 光谱学探究 RNA 结构和功能的有力标记物。
Angew Chem Int Ed Engl. 2012 Dec 21;51(52):13080-4. doi: 10.1002/anie.201207128. Epub 2012 Nov 19.
8
The conformationally constrained N-methanocarba-dT analogue adopts an unexpected C4'-exo sugar pucker in the structure of a DNA hairpin.构象受限的 N-甲撑基-dT 类似物在 DNA 发夹结构中呈现出一种出人意料的 C4'-外式糖环构象。
Biochemistry. 2012 Apr 3;51(13):2639-41. doi: 10.1021/bi300215k. Epub 2012 Mar 20.
9
The many twists and turns of DNA: template, telomere, tool, and target.DNA 的诸多曲折：模板、端粒、工具和靶标。
Curr Opin Struct Biol. 2010 Jun;20(3):262-75. doi: 10.1016/j.sbi.2010.03.001. Epub 2010 Apr 8.
10
Crystallographic studies of chemically modified nucleic acids: a backward glance.化学修饰核酸的晶体学研究：回眸
Chem Biodivers. 2010 Jan;7(1):60-89. doi: 10.1002/cbdv.200900177.
本文引用的文献
1
Processing of X-ray diffraction data collected in oscillation mode.振荡模式下收集的X射线衍射数据的处理。
Methods Enzymol. 1997;276:307-26. doi: 10.1016/S0076-6879(97)76066-X.
2
Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex.通过非特异性酶-dsDNA复合物的晶体结构深入了解RNase H对RNA/DNA杂交体的识别与加工
Cell Cycle. 2008 Aug 15;7(16):2562-9. doi: 10.4161/cc.7.16.6461. Epub 2008 Aug 18.
3
SHELXL: high-resolution refinement.SHELXL：高分辨率精修。
Methods Enzymol. 1997;277:319-43.
4
Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structures.核酸的硒修饰：用于核酸结构晶体学相位分析的掺入2'-硒甲基尿苷的寡核苷酸的制备。
Nat Protoc. 2007;2(3):647-51. doi: 10.1038/nprot.2007.75.
5
2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.2'-氟阿拉伯糖核酸和阿拉伯糖核酸呈现出不同的构象，导致它们与RNA的亲和力不同，以及核糖核酸酶H对其与RNA形成的异源双链体的加工情况也不同。
Biochemistry. 2006 Apr 4;45(13):4141-52. doi: 10.1021/bi052322r.
6
Protein-DNA recognition patterns and predictions.蛋白质 - DNA 识别模式与预测
Annu Rev Biophys Biomol Struct. 2005;34:379-98. doi: 10.1146/annurev.biophys.34.040204.144537.
7
Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy.通过弱排列核磁共振光谱研究限制核苷酸环皱折引起的DNA弯曲变化。
Proc Natl Acad Sci U S A. 2005 Jan 4;102(1):24-8. doi: 10.1073/pnas.0408498102. Epub 2004 Dec 23.
8
RNA interference and chemically modified small interfering RNAs.RNA干扰与化学修饰的小干扰RNA
Curr Opin Chem Biol. 2004 Dec;8(6):570-9. doi: 10.1016/j.cbpa.2004.10.007.
9
PROSIT: pseudo-rotational online service and interactive tool, applied to a conformational survey of nucleosides and nucleotides.PROSIT：伪旋转在线服务和交互式工具，应用于核苷和核苷酸的构象研究。
J Chem Inf Comput Sci. 2004 Sep-Oct;44(5):1752-62. doi: 10.1021/ci049881+.
10
Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis.人源核糖核酸酶H1催化作用中异源双链底物催化位点的结构要求。
J Biol Chem. 2004 Aug 27;279(35):36317-26. doi: 10.1074/jbc.M405035200. Epub 2004 Jun 17.
Zotero 插件