From 951b98ed1dedfd8b9e29e9681f8722597e1e8f97 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Mon, 4 Dec 2017 17:06:21 +0900 Subject: [PATCH] RNL2 etc. --- biblio/15205470.mdwn | 2 +- biblio/15247329.mdwn | 2 +- biblio/17018278.mdwn | 10 ++++++++++ biblio/17510325.mdwn | 2 +- biblio/21722378.mdwn | 10 ++++++++++ biblio/4000951.mdwn | 2 +- biblio/To_Do | 3 --- tags/ligase.mdwn | 13 +++++++++++-- 8 files changed, 35 insertions(+), 9 deletions(-) create mode 100644 biblio/17018278.mdwn create mode 100644 biblio/21722378.mdwn diff --git a/biblio/15205470.mdwn b/biblio/15205470.mdwn index eae98df5..e53f0f38 100644 --- a/biblio/15205470.mdwn +++ b/biblio/15205470.mdwn @@ -1,5 +1,5 @@ [[!meta title="Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes."]] -[[!tag ligation]] +[[!tag ligase]] Nucleic Acids Res. 2004 Jun 17;32(11):e86 doi:10.1093/nar/gnh085 diff --git a/biblio/15247329.mdwn b/biblio/15247329.mdwn index 449750ae..5170fe60 100644 --- a/biblio/15247329.mdwn +++ b/biblio/15247329.mdwn @@ -1,5 +1,5 @@ [[!meta title="Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry."]] -[[!tag method library ligation]] +[[!tag method library ligase]] So AP, Turner RF, Haynes CA. diff --git a/biblio/17018278.mdwn b/biblio/17018278.mdwn new file mode 100644 index 00000000..717d7bc7 --- /dev/null +++ b/biblio/17018278.mdwn @@ -0,0 +1,10 @@ +[[!meta title="RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward."]] +[[!tag ligase]] + +Nandakumar J, Shuman S, Lima CD. + +Cell. 2006 Oct 6;127(1):71-84 + +RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. + +[[!pmid 17018278 desc="Structure-function analysis of sealing of nicked duplexes."]] diff --git a/biblio/17510325.mdwn b/biblio/17510325.mdwn index 4e777658..1e457671 100644 --- a/biblio/17510325.mdwn +++ b/biblio/17510325.mdwn @@ -1,5 +1,5 @@ [[!meta title="RNA maps reveal new RNA classes and a possible function for pervasive transcription."]] -[[!tag ligation transcriptome small_RNA HepG2]] +[[!tag ligase transcriptome small_RNA HepG2]] Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. diff --git a/biblio/21722378.mdwn b/biblio/21722378.mdwn new file mode 100644 index 00000000..f23d364a --- /dev/null +++ b/biblio/21722378.mdwn @@ -0,0 +1,10 @@ +[[!meta title="T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis"]] +[[!tag ligase method enzyme]] + +Viollet S, Fuchs RT, Munafo DB, Zhuang F, Robb GB. + +BMC Biotechnol. 2011 Jul 1;11:72. doi: 10.1186/1472-6750-11-72. + +T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis + +[[!pmid 21722378 desc="The K227Q mutation prevents transfer of the adenylyl residue from the adapter to unwanted targets."]] diff --git a/biblio/4000951.mdwn b/biblio/4000951.mdwn index 7ea38871..5214692c 100644 --- a/biblio/4000951.mdwn +++ b/biblio/4000951.mdwn @@ -1,5 +1,5 @@ [[!meta title="Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase."]] -[[!tag ligation method]] +[[!tag ligase method]] Nucleic Acids Res. 1985 Mar 25;13(6):1997-2008. diff --git a/biblio/To_Do b/biblio/To_Do index 20363d95..d8454347 100644 --- a/biblio/To_Do +++ b/biblio/To_Do @@ -700,9 +700,6 @@ Reommends to use only dbSNP entries which have a phred score higher than 40. 15693942 [mining] Uses a highly replicated experimental desigh to show that metabolic genes vary in their expresison between tissues, individuals and populations. -17018278 [enzymes] -Not Read - 16698958 [enhancers] Defines the concept of "maximal N-mers". diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn index 90de02b4..2490e339 100644 --- a/tags/ligase.mdwn +++ b/tags/ligase.mdwn @@ -1,4 +1,13 @@ [[!meta title="pages tagged ligase"]] -[[!inline pages="tagged(ligase)" actions="no" archive="yes" -feedshow=10]] +Work in progress. + +On T4 RNL2: + + - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]]. + - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]]. + - The K227Q mutation prevents transfer of the andenylyl residue from the + linker to RNA ends, thus prevents unwanted ligation products. + [[Viollet et al., 2011|biblio/21722378]] + +[[!inline pages="tagged(ligase)" limit=0]] -- 2.47.3