Literature DB >> 16325753

Structure-independent and quantitative ligation of single-stranded DNA.

Tian W Li1, Kevin M Weeks.   

Abstract

Ligation of an adapter oligonucleotide to a single-stranded cDNA is central to many molecular biology techniques. Current single-stranded ligation approaches suffer from low efficiencies and are strongly inhibited by preexisting DNA secondary structure. We develop an approach for ligating low concentrations of single-stranded DNAs to a DNA adapter with near-quantitative efficiency, unaffected by secondary structure in the target DNA. This efficient DNA ligation reaction will facilitate development of robust procedures for quantifying small amounts of highly structured cDNAs and their RNA templates.

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Year:  2005        PMID: 16325753     DOI: 10.1016/j.ab.2005.11.002

Source DB:  PubMed          Journal:  Anal Biochem        ISSN: 0003-2697            Impact factor:   3.365


  12 in total

1.  Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Authors:  Julius B Lucks; Stefanie A Mortimer; Cole Trapnell; Shujun Luo; Sharon Aviran; Gary P Schroth; Lior Pachter; Jennifer A Doudna; Adam P Arkin
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-03       Impact factor: 11.205

2.  Sources of PCR-induced distortions in high-throughput sequencing data sets.

Authors:  Justus M Kebschull; Anthony M Zador
Journal:  Nucleic Acids Res       Date:  2015-07-17       Impact factor: 16.971

3.  A high-coverage genome sequence from an archaic Denisovan individual.

Authors:  Matthias Meyer; Martin Kircher; Marie-Theres Gansauge; Heng Li; Fernando Racimo; Swapan Mallick; Joshua G Schraiber; Flora Jay; Kay Prüfer; Cesare de Filippo; Peter H Sudmant; Can Alkan; Qiaomei Fu; Ron Do; Nadin Rohland; Arti Tandon; Michael Siebauer; Richard E Green; Katarzyna Bryc; Adrian W Briggs; Udo Stenzel; Jesse Dabney; Jay Shendure; Jacob Kitzman; Michael F Hammer; Michael V Shunkov; Anatoli P Derevianko; Nick Patterson; Aida M Andrés; Evan E Eichler; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Science       Date:  2012-08-30       Impact factor: 47.728

4.  Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA.

Authors:  Marie-Theres Gansauge; Matthias Meyer
Journal:  Nat Protoc       Date:  2013-03-14       Impact factor: 13.491

5.  Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication.

Authors:  Rujuta Yashodhan Gadgil; Eric J Romer; Caitlin C Goodman; S Dean Rider; French J Damewood; Joanna R Barthelemy; Kazuo Shin-Ya; Helmut Hanenberg; Michael Leffak
Journal:  J Biol Chem       Date:  2020-09-01       Impact factor: 5.157

6.  Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase - engineering a thermostable ATP independent enzyme.

Authors:  Alexander M Zhelkovsky; Larry A McReynolds
Journal:  BMC Mol Biol       Date:  2012-07-18       Impact factor: 2.946

7.  Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.

Authors:  Patricia Heyn; Udo Stenzel; Adrian W Briggs; Martin Kircher; Michael Hofreiter; Matthias Meyer
Journal:  Nucleic Acids Res       Date:  2010-06-28       Impact factor: 16.971

8.  Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come.

Authors:  Joanna Sztuba-Solinska; Stuart F J Le Grice
Journal:  Mol Biol Int       Date:  2012-05-17

9.  Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase.

Authors:  Marie-Theres Gansauge; Tobias Gerber; Isabelle Glocke; Petra Korlevic; Laurin Lippik; Sarah Nagel; Lara Maria Riehl; Anna Schmidt; Matthias Meyer
Journal:  Nucleic Acids Res       Date:  2017-06-02       Impact factor: 16.971

10.  Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics.

Authors:  Mandy Man-Ying Tin; Evan Philip Economo; Alexander Sergeyevich Mikheyev
Journal:  PLoS One       Date:  2014-05-14       Impact factor: 3.240

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