Methods: Nucleic acid modification

Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool

Evgeny S. GerasimovAnna A. GasparyanIosif KaurovBoris TichýMaria D. Logacheva …

Nucleic Acids Research, gkx1202, https://doi.org/10.1093/nar/gkx1202

Published: 06 December 2017

Abstract

Supplementary data

 

Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy

Meng ZhaoFabio D. SteffenRichard BörnerMichelle F. SchafferRoland K. O. Sigel …

Nucleic Acids Research, gkx1100, https://doi.org/10.1093/nar/gkx1100

Published: 09 November 2017

Abstract

Supplementary data

 

Self-biotinylation of DNA G-quadruplexes via intrinsic peroxidase activity

Owen J. EinarsonDipankar Sen

Nucleic Acids Research, Volume 45, Issue 17, 29 September 2017, Pages 9813–9822, https://doi.org/10.1093/nar/gkx765

Published: 29 August 2017

Abstract

Supplementary data

 

Entirely enzymatic nanofabrication of DNA–protein conjugates

Giulio BernardinelliBjörn Högberg

Nucleic Acids Research, Volume 45, Issue 18, 13 October 2017, Pages e160, https://doi.org/10.1093/nar/gkx707

Published: 16 August 2017

Abstract

Supplementary data

 

Combining asymmetric 13 C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment

Regan M. LeBlancAndrew P. LonghiniStuart F.J. Le GriceBruce A. JohnsonTheodore K. Dayie

Nucleic Acids Research, Volume 45, Issue 16, 19 September 2017, Pages e146, https://doi.org/10.1093/nar/gkx591

Published: 09 August 2017

Abstract

Supplementary data

 

Post-ExSELEX stabilization of an unnatural-base DNA aptamer targeting VEGF 165 toward pharmaceutical applications

Michiko KimotoMana NakamuraIchiro Hirao

Nucleic Acids Research, Volume 44, Issue 15, 6 September 2016, Pages 7487–7494, https://doi.org/10.1093/nar/gkw619

Published: 07 July 2016

Abstract

Supplementary data

 

Complementary-addressed site-directed spin labeling of long natural RNAs

Elena S. BabaylovaAlexey A. MalyginAlexander A. LomzovDmitrii V. PyshnyiMaxim Yulikov …

Nucleic Acids Research, Volume 44, Issue 16, 19 September 2016, Pages 7935–7943, https://doi.org/10.1093/nar/gkw516

Published: 06 June 2016

Abstract

Supplementary data

 

Profiling of 2′- O -Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

Nicolai KroghMartin D. JanssonSophia J. HäfnerDisa TehlerUlf Birkedal …

Nucleic Acids Research, Volume 44, Issue 16, 19 September 2016, Pages 7884–7895, https://doi.org/10.1093/nar/gkw482

Published: 01 June 2016

Abstract

Supplementary data

 

Direct and site-specific quantification of RNA 2′-O-methylation by PCR with an engineered DNA polymerase

Joos AschenbrennerAndreas Marx

Nucleic Acids Research, Volume 44, Issue 8, 5 May 2016, Pages 3495–3502, https://doi.org/10.1093/nar/gkw200

Published: 25 March 2016

Abstract

Supplementary data

 

Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes

Xiaomei RenAfaf H. El-SagheerTom Brown

Nucleic Acids Research, Volume 44, Issue 8, 5 May 2016, Pages e79, https://doi.org/10.1093/nar/gkw028

Published: 26 January 2016

Abstract

Supplementary data

 

A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure of Schizosaccharomyces pombe ribosomal RNAs

Masato TaokaYuko NobeMasayuki HoriAiko TakeuchiShunpei Masaki …

Nucleic Acids Research, Volume 43, Issue 18, 15 October 2015, Pages e115, https://doi.org/10.1093/nar/gkv560

Published: 10 October 2015

Abstract

Supplementary data

 

The reverse transcription signature of N -1-methyladenosine in RNA-Seq is sequence dependent

Ralf HauenschildLyudmil TserovskiKatharina SchmidKathrin ThüringMarie-Luise Winz …

Nucleic Acids Research, Volume 43, Issue 20, 16 November 2015, Pages 9950–9964, https://doi.org/10.1093/nar/gkv895

Published: 13 September 2015

Abstract

Supplementary data

 

Base-resolution detection of N 4 -methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing

Miao YuLexiang JiDrexel A. NeumannDae-hwan ChungJoseph Groom …

Nucleic Acids Research, Volume 43, Issue 21, 2 December 2015, Pages e148, https://doi.org/10.1093/nar/gkv738

Published: 15 July 2015

Abstract

Supplementary data

 

Characterisation of aptamer–target interactions by branched selection and high-throughput sequencing of SELEX pools

Daniel M. DupontNiels LarsenJan. K. JensenPeter A. AndreasenJørgen Kjems

Nucleic Acids Research, Volume 43, Issue 21, 2 December 2015, Pages e139, https://doi.org/10.1093/nar/gkv700

Published: 10 July 2015

Abstract

Supplementary data

 

Nucleotidyl transferase assisted DNA labeling with different click chemistries

Marie-Luise WinzEva Christina LinderTimon AndréJuliane BeckerAndres Jäschke

Nucleic Acids Research, Volume 43, Issue 17, 30 September 2015, Pages e110, https://doi.org/10.1093/nar/gkv544

Published: 26 May 2015

Abstract

Supplementary data

 

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

Jovana MaksimovicJohann A. Gagnon-BartschTerence P. SpeedAlicia Oshlack

Nucleic Acids Research, Volume 43, Issue 16, 18 September 2015, Pages e106, https://doi.org/10.1093/nar/gkv526

Published: 18 May 2015

Abstract

Supplementary data

 

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

Paul J. SampleKirk W. GastonJuan D. AlfonzoPatrick A. Limbach

Nucleic Acids Research, Volume 43, Issue 10, 26 May 2015, Pages e64, https://doi.org/10.1093/nar/gkv145

Published: 27 March 2015

Abstract

Supplementary data

 

Mg 2+ -dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence

Elisa TurrianiClaudia HöbartnerThomas M. Jovin

Nucleic Acids Research, Volume 43, Issue 1, 9 January 2015, Pages 40–50, https://doi.org/10.1093/nar/gku1268

Published: 10 December 2014

Abstract

Supplementary data

 

qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data

Zhixing FengJing LiJing-Ren ZhangXuegong Zhang

Nucleic Acids Research, Volume 42, Issue 22, 16 December 2014, Pages 13488–13499, https://doi.org/10.1093/nar/gku1097

Published: 17 November 2014

Abstract

Supplementary data

 

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number

Yan Ling Joy PangRyan AboStuart S. LevinePeter C. Dedon

Nucleic Acids Research, Volume 42, Issue 22, 16 December 2014, Pages e170, https://doi.org/10.1093/nar/gku945

Published: 27 October 2014

Abstract

Supplementary data

 

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