体外和体内测量核糖核苷酸掺入DNA的情况。
Measuring ribonucleotide incorporation into DNA in vitro and in vivo.
作者信息
Clausen Anders R, Williams Jessica S, Kunkel Thomas A
机构信息
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA.
出版信息
Methods Mol Biol. 2015;1300:123-39. doi: 10.1007/978-1-4939-2596-4_9.
Abstract
Ribonucleotides are incorporated into genomes by DNA polymerases, they can be removed, and if not removed, they can have deleterious and beneficial consequences. Here, we describe an assay to quantify stable ribonucleotide incorporation by DNA polymerases in vitro, and an assay to probe for ribonucleotides in each of the two DNA strands of the yeast nuclear genome.
摘要
核糖核苷酸可通过DNA聚合酶掺入基因组中，它们能够被去除，若未被去除，则可能产生有害和有益的后果。在此，我们描述了一种用于在体外定量DNA聚合酶稳定掺入核糖核苷酸的测定方法，以及一种用于探测酵母核基因组两条DNA链中每条链上核糖核苷酸的测定方法。
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本文引用的文献
1
Ribonucleotides in DNA: origins, repair and consequences.DNA中的核糖核苷酸：起源、修复及后果
DNA Repair (Amst). 2014 Jul;19:27-37. doi: 10.1016/j.dnarep.2014.03.029. Epub 2014 Apr 30.
2
Ribonucleotides are signals for mismatch repair of leading-strand replication errors.核苷酸是前导链复制错误的错配修复的信号。
Mol Cell. 2013 May 9;50(3):437-43. doi: 10.1016/j.molcel.2013.03.017. Epub 2013 Apr 18.
3
Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA.拓扑异构酶 1 介导的新生前导链 DNA 中核苷酸的去除。
Mol Cell. 2013 Mar 7;49(5):1010-5. doi: 10.1016/j.molcel.2012.12.021. Epub 2013 Jan 31.
4
Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ.核苷酸掺入、校正和人类 DNA 聚合酶 δ 的旁路。
DNA Repair (Amst). 2013 Feb 1;12(2):121-7. doi: 10.1016/j.dnarep.2012.11.006. Epub 2012 Dec 12.
5
Mismatch repair balances leading and lagging strand DNA replication fidelity.错配修复平衡着前导链和滞后链 DNA 复制的保真度。
PLoS Genet. 2012;8(10):e1003016. doi: 10.1371/journal.pgen.1003016. Epub 2012 Oct 11.
6
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DNA Repair (Amst). 2012 Aug 1;11(8):649-56. doi: 10.1016/j.dnarep.2012.05.004. Epub 2012 Jun 8.
7
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PLoS Genet. 2011 Dec;7(12):e1002407. doi: 10.1371/journal.pgen.1002407. Epub 2011 Dec 1.
8
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9
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10
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