Stereochemistry of benzylic carbon substitution coupled with ring modification of 2-nitrobenzyl groups as key determinants for fast-cleaving reversible terminators.
Stereochemistry of benzylic carbon substitution coupled with ring modification of 2-nitrobenzyl groups as key determinants for fast-cleaving reversible terminators.
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DOI：
10.1002/anie.201106516
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发表时间：
2012-02-13
影响因子：
16.6
通讯作者：
Metzker, Michael L.
中科院分区：
文献类型：
--
作者：
Stupi, Brian P.;Li, Hong;Wang, Jinchun;Wu, Weidong;Morris, Sidney E.;Litosh, Vladislav A.;Muniz, Jesse;Hersh, Megan N.;Metzker, Michael L.
下一代测序（NGS）技术促进了重要的生物医学发现，但高错误率和缓慢的周期时间保证了化学的进一步改进。[1a]采用循环可逆终止（CRT）方法[1a，B]的此类技术通常使用3 0-O-封闭的可逆终止剂。[2a-c]最近，我们描述了一种基于2-硝基苄基修饰的5-羟甲基-2-脱氧尿苷（HOMedU）5-三磷酸的新型3-OH-未封闭的可逆终止剂。[3]我们的研究表明，2-硝基苄基与核碱基的接近程度以及与其α-亚甲基碳连接的烷基的大小是重要的结构特征，这些结构特征赋予这些3-OH-未封闭的核苷酸单碱基终止、有效掺入和高核苷酸选择性（即高保真度）的独特性质。[3]这些特性有可能提高CRT方法的准确度和读取长度。由于HOMedU是一种天然发现的高度修饰的核苷，[4a]我们着手鉴定其他此类实例。5-羟甲基-20-脱氧胞苷（HOMedC）天然存在于T偶噬菌体[4a，B]和哺乳动物的基因组中。[5]吡咯并嘧啶（7-脱氮嘌呤）也天然存在于核苷抗生素[6]和tRNA中。[7]因此，2-硝基苄基修饰的7-脱氮-7-羟甲基-20-脱氧腺苷的各种类似物（C7-HOMedA），[8] HOMedC，7-deaza-7-hydroxymethyl-2о-deoxyguanosine（C7-HOMedG），[9]和HOMedU的合成目标是开发一套完整的可逆终止剂理想情况下，这些终止子应表现出快速核苷酸掺入动力学、单碱基终止、高核苷酸选择性，和快速终止基团裂解。对于后者，光化学裂解速率的改变程度取决于许多因素，包括苄基碳的取代、[10a-c]官能团与苄基环的连接、[10 b-d]和离去基团的性质、[10a]以及pH、[10a、d、e]溶剂、[10 c、f、g]和光强度。[10e，g]一个
Next-generation sequencing (NGS) technologies have facilitated important biomedical discoveries, yet high error rates and slow cycle times warrant further improvements in the chemistry.[1a] Such technologies that employ the cyclic reversible termination (CRT) method [1a, b] typically utilize 3о-O-blocked reversible terminators.[2a–c] Recently, we described a novel 3о-OH-unblocked reversible terminator based on 2-nitrobenzyl-modified 5-hydroxymethyl-2о-deoxyuridine (HOMedU) 5о-triphosphate.[3] Our study revealed that the proximity of the 2-nitrobenzyl group to the nucleobase and the size of the alkyl group attached to its α-methylene carbon are important structural features that confer the unique properties of single-base termination, efficient incorporation, and high nucleotide selectivity (ie, high fidelity) to these 3о-OH-unblocked nucleotides.[3] These properties have the potential to improve accuracy and read-lengths in the CRT method. As HOMedU is a naturally found hypermodified nucleoside,[4a] we set out to identify other such examples. 5-Hydroxymethyl-2о-deoxycytidine (HOMedC) is found naturally in the genomes of T-even bacteriophages [4a, b] and mammals.[5] Pyrrolopyrimidine (7-deazapurine) is also found naturally in nucleoside antibiotics [6] and tRNAs.[7] Thus, various analogues of 2-nitrobenzyl-modified 7-deaza-7-hydroxymethyl-2о-deoxyadenosine(C7-HOMedA),[8] HOMedC, 7-deaza-7-hydroxymethyl-2о-deoxyguanosine (C7-HOMedG),[9] and HOMedU were synthesized with the goal of developing a complete set of reversible terminators (Figure 1).Ideally, these terminators should exhibit fast nucleotideincorporation kinetics, single-base termination, high nucleotide selectivity, and rapid terminating group cleavage. For the latter, the degree to which the rate of photochemical cleavage is altered depends on numerous factors including substitution of the benzylic carbon,[10a–c] attachment of functional group (s) to the benzyl ring,[10b–d] and nature of the leaving group,[10a] as well as pH,[10a, d, e] solvent,[10c, f, g] and light intensity.[10e, g] One
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影响因子：
1.3
作者：
McDougall, MG;Sun, L;Kumar, S
通讯作者：
Kumar, S
影响因子：
15
作者：
Rockhill, JK;Wilson, SR;Gumport, RI
通讯作者：
Gumport, RI
影响因子：
2.1
作者：
Hasan, A;Stengele, KP;Foote, RS
通讯作者：
Foote, RS
影响因子：
14.9
作者：
Litosh VA;Wu W;Stupi BP;Wang J;Morris SE;Hersh MN;Metzker ML
通讯作者：
Metzker ML
DOI：
10.1039/p19920001015
发表时间：
1992-04-21
期刊：
JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 1
影响因子：
--
作者：
CORRIE, JET;REID, GP;MAZID, MA
通讯作者：
MAZID, MA