含有脱氧腺苷类似物1-(2'-脱氧-β-D-呋喃核糖基)咪唑-4-甲酰胺的寡脱氧核糖核苷酸的合成与稳定性
The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide.
作者信息
Johnson W T, Zhang P, Bergstrom D E
机构信息
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
出版信息
Nucleic Acids Res. 1997 Feb 1;25(3):559-67. doi: 10.1093/nar/25.3.559.
Abstract
Oligodeoxyribonucleotides containing the nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl) imidazole-4-carboxamide (1) were synthesized by solid phase phosphoramidite technology. Nucleoside 1, which contains a reactive exocyclic amide moiety, was incorporated into synthetic oligodeoxyribonucleotides with the use of a benzoyl protecting group. The corresponding oligodeoxyribonucleotides with dI or dA in the same position in the sequence were synthesized for UV comparison of helix-coil transitions. The thermal melting studies indicate that 1, which could conceptually adopt either a dA- or a dI-like hydrogen bond configuration, pairs with significantly higher affinity to T than to dC. Nucleoside 1 further resembles dA in the relative order of its base pairing preferences (T >dG >dA >dC), but may be less discriminating than dA in its bias for base pairing with T over dG.
摘要
通过固相亚磷酰胺技术合成了含有核苷类似物1-(2'-脱氧-β-D-呋喃核糖基)咪唑-4-甲酰胺(1)的寡脱氧核糖核苷酸。核苷1含有一个反应性外环酰胺部分，通过使用苯甲酰保护基将其掺入合成寡脱氧核糖核苷酸中。合成了在序列相同位置含有dI或dA的相应寡脱氧核糖核苷酸，用于螺旋-卷曲转变的紫外比较。热变性研究表明，理论上可以采用类似dA或dI氢键构型的1，与T配对的亲和力明显高于与dC配对的亲和力。核苷1在碱基配对偏好的相对顺序上(T>dG>dA>dC)进一步类似于dA，但在与T碱基配对相对于dG的偏好上可能比dA的区分度小。
相似文献
1
The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide.含有脱氧腺苷类似物1-(2'-脱氧-β-D-呋喃核糖基)咪唑-4-甲酰胺的寡脱氧核糖核苷酸的合成与稳定性
Nucleic Acids Res. 1997 Feb 1;25(3):559-67. doi: 10.1093/nar/25.3.559.
2
Exploratory studies on azole carboxamides as nucleobase analogs: thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole-3-carboxamide.作为核碱基类似物的唑类羧酰胺的探索性研究：对含吡咯-3-羧酰胺的寡脱氧核糖核苷酸双链体的热变性研究
Nucleic Acids Res. 1998 May 1;26(9):2208-15. doi: 10.1093/nar/26.9.2208.
3
Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5'-d(CGCXAATTYGCG)-3'.寡脱氧核糖核苷酸序列5'-d(CGCXAATTYGCG)-3'中一系列硝基唑核碱基类似物的碱基配对特性比较。
Nucleic Acids Res. 1997 May 15;25(10):1935-42. doi: 10.1093/nar/25.10.1935.
4
Interaction of DNA containing Fapy.dA or its C-nucleoside analogues with base excision repair enzymes. Implications for mutagenesis and enzyme inhibition.含Fapy.dA或其C-核苷类似物的DNA与碱基切除修复酶的相互作用。对诱变和酶抑制的影响。
Biochemistry. 2002 Dec 31;41(52):15838-44. doi: 10.1021/bi025903e.
5
Synthesis and enzymatic polymerisation of 5-amino-1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide-5'- triphosphate.5-氨基-1-(2'-脱氧-β-D-呋喃核糖基)咪唑-4-甲酰胺-5'-三磷酸的合成与酶促聚合
Nucleic Acids Res. 1990 Dec 11;18(23):7127-31. doi: 10.1093/nar/18.23.7127.
6
Pyrazolo[3,4-d][1,2,3]triazine DNA: synthesis and base pairing of 7-deaza-2,8-diaza-2'-deoxyadenosine.吡唑并[3,4-d][1,2,3]三嗪DNA：7-脱氮-2,8-二氮-2'-脱氧腺苷的合成与碱基配对
J Org Chem. 2004 Jul 9;69(14):4695-700. doi: 10.1021/jo040150i.
7
Synthesis and incorporation into DNA fragments of the artificial nucleobase, 2-amino-8-oxopurine.
Bioorg Med Chem Lett. 2005 Feb 15;15(4):1069-73. doi: 10.1016/j.bmcl.2004.12.021.
8
Ambiguous base pairing of the purine analogue 1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide during PCR.在聚合酶链反应（PCR）过程中嘌呤类似物1-（2-脱氧-β-D-呋喃核糖基）-咪唑-4-甲酰胺的模糊碱基配对
Nucleic Acids Res. 1996 Sep 1;24(17):3302-6. doi: 10.1093/nar/24.17.3302.
9
Synthesis of 5-amino-1-(5-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide and related 5'-deoxyimidazole ribonucleosides.5-氨基-1-(5-脱氧-β-D-呋喃核糖基)咪唑-4-甲酰胺及相关5'-脱氧咪唑核糖核苷的合成
J Med Chem. 1975 Dec;18(12):1237-40. doi: 10.1021/jm00246a013.
10
Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics.通过核磁共振光谱和受限分子动力学确定的含有3,N4-乙烯基-2'-脱氧胞苷（与2'-脱氧腺苷相对的环外损伤）的寡脱氧核苷酸双链体的溶液结构。
Biochemistry. 1996 Oct 15;35(41):13310-8. doi: 10.1021/bi9605696.
引用本文的文献
1
Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life.用黏土制造分子：层状双氢氧化物、戊吡喃糖核酸与生命起源
Life (Basel). 2019 Feb 15;9(1):19. doi: 10.3390/life9010019.
2
Purine biosynthetic intermediate-containing ribose-phosphate polymers as evolutionary precursors to RNA.含嘌呤生物合成中间体的核糖磷酸聚合物作为RNA的进化前体。
J Mol Evol. 2014 Oct;79(3-4):91-104. doi: 10.1007/s00239-014-9640-1. Epub 2014 Sep 2.
3
Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes.DNA双链体中脱氧肌苷对的近邻热力学
Nucleic Acids Res. 2005 Nov 1;33(19):6258-67. doi: 10.1093/nar/gki918. Print 2005.
4
NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control.含核苷类似物1-(2'-脱氧-β-D-呋喃核糖基)-3-硝基吡咯的DNA双链体的核磁共振结构及未修饰对照的结构。
Nucleic Acids Res. 2000 Nov 15;28(22):4514-22. doi: 10.1093/nar/28.22.4514.
5
The N(8)-(2'-deoxyribofuranoside) of 8-aza-7-deazaadenine: a universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents.8-氮杂-7-脱氮腺嘌呤的N(8)-(2'-脱氧呋喃核糖苷)：一种能与四种标准DNA成分形成特定氢键的通用核苷。
Nucleic Acids Res. 2000 Sep 1;28(17):3224-32. doi: 10.1093/nar/28.17.3224.
6
A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2'-deoxyuridines.含5-取代2'-脱氧尿苷的寡脱氧核糖核苷酸热稳定性的比较研究。
Nucleic Acids Res. 1998 Jul 1;26(13):3127-35. doi: 10.1093/nar/26.13.3127.
7
Exploratory studies on azole carboxamides as nucleobase analogs: thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole-3-carboxamide.作为核碱基类似物的唑类羧酰胺的探索性研究：对含吡咯-3-羧酰胺的寡脱氧核糖核苷酸双链体的热变性研究
Nucleic Acids Res. 1998 May 1;26(9):2208-15. doi: 10.1093/nar/26.9.2208.
8
Template directed incorporation of nucleotide mixtures using azole-nucleobase analogs.使用唑-核碱基类似物进行模板导向的核苷酸混合物掺入。
Nucleic Acids Res. 1997 Dec 15;25(24):4866-71. doi: 10.1093/nar/25.24.4866.
9
Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5'-d(CGCXAATTYGCG)-3'.寡脱氧核糖核苷酸序列5'-d(CGCXAATTYGCG)-3'中一系列硝基唑核碱基类似物的碱基配对特性比较。
Nucleic Acids Res. 1997 May 15;25(10):1935-42. doi: 10.1093/nar/25.10.1935.
本文引用的文献
1
Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine.含2-氨基嘌呤的DNA双链体的光谱和量热表征
Biochemistry. 1996 Sep 24;35(38):12329-37. doi: 10.1021/bi9614545.
2
Ambiguous base pairing of the purine analogue 1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide during PCR.在聚合酶链反应（PCR）过程中嘌呤类似物1-（2-脱氧-β-D-呋喃核糖基）-咪唑-4-甲酰胺的模糊碱基配对
Nucleic Acids Res. 1996 Sep 1;24(17):3302-6. doi: 10.1093/nar/24.17.3302.
3
A universal nucleoside for use at ambiguous sites in DNA primers.一种用于DNA引物中模糊位点的通用核苷。
Nature. 1994 Jun 9;369(6480):492-3. doi: 10.1038/369492a0.
4
5-Nitroindole as an universal base analogue.5-硝基吲哚作为一种通用的碱基类似物。
Nucleic Acids Res. 1994 Oct 11;22(20):4039-43. doi: 10.1093/nar/22.20.4039.
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
Structure of a B-DNA dodecamer: conformation and dynamics.一种B型DNA十二聚体的结构：构象与动力学
Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179-83. doi: 10.1073/pnas.78.4.2179.
7
Salt-dependent conformational transitions in the self-complementary deoxydodecanucleotide d(CGCAATTCGCG): evidence for hairpin formation.自互补脱氧十二聚体d(CGCAATTCGCG)中依赖盐的构象转变：发夹形成的证据
Biopolymers. 1983 Apr;22(4):1247-57. doi: 10.1002/bip.360220416.
8
In situ activation of bis-dialkylaminophosphines--a new method for synthesizing deoxyoligonucleotides on polymer supports.双二烷基氨基膦的原位活化——一种在聚合物载体上合成脱氧寡核苷酸的新方法。
Nucleic Acids Res. 1984 May 25;12(10):4051-61. doi: 10.1093/nar/12.10.4051.
9
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.
10
Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches.不完全核酸螺旋的自由能。3. 错配导致的小内部环。
J Mol Biol. 1973 Aug 5;78(2):301-19. doi: 10.1016/0022-2836(73)90118-6.
Zotero 插件