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Genome Integrity

, 2:10

First Online: 20 December 2011Received: 10 November 2011Accepted: 20 December 2011

Abstract

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time SMRT DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications.

KeywordsDNA Damage Modified Bases Sequencing List of Abbreviations Used5hC5-hydroxycytosine

5hmU5-hydroxymethyluracil

5hU5-hydroxyuracil

1mA1-methyladenine

6mAN6-methyladenine

8oxoA8-oxoadenine

8oxoG8-oxoguanine

BPDEbenzoapyrene diol epoxide

IPDinterpulse duration

O4mTO4-methylthymine

O6mGO6-methylguanine

PWpulse width

SMRTSingle-Molecule, Real-Time

Electronic supplementary materialThe online version of this article doi:10.1186-2041-9414-2-10 contains supplementary material, which is available to authorized users.

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Autor: Tyson A Clark - Kristi E Spittle - Stephen W Turner - Jonas Korlach

Fuente: https://link.springer.com/







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