Quantitative analysis of RNA modifications.
RNA modifications impact numerous cellular processes such as pre-mRNA splicing and protein synthesis. The elucidation of the mechanisms by which these modifications impact cellular processes necessitates the ability to both detect and quantify the presence of these modifications within RNA molecules. Here, we present a detailed procedure that allows the detection and quantification of RNA base modifications. This procedure involves a number of techniques, including oligonucleotide-affinity selection, site-specific cleavage and radiolabeling, nuclease digestion, and thin layer chromatography.
Karijolich
John
J
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA.
Kantartzis
Athena
A
Yu
Yi-Tao
YT
D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism; D051379:Mice; D008967:Molecular Biology / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000378:metabolism; D010766:Phosphorylation; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D016914:Ribonuclease H / Q000378:metabolism; D014529:Uridine / Q000378:metabolism
D009692:Nucleic Acid Heteroduplexes; D012342:RNA, Small Nuclear; C405484:U2 small nuclear RNA; D016914:Ribonuclease H; D014529:Uridine
Biochimie. 1995;77(1-2):22-9
7599273
Methods Enzymol. 1987;155:379-96
3431467
Nucleic Acids Res. 1979 Aug 10;6(11):3443-58
386273
RNA. 1997 Mar;3(3):324-31
9056769
Eur J Biochem. 1977 Feb;72(3):465-78
402264
RNA. 2006 Nov;12(11):2025-33
16963711
Nucleic Acids Res. 1981 Nov 11;9(21):5645-58
6796940
Biochemistry. 1993 Sep 21;32(37):9754-62
8373778
Biochimie. 1995;77(1-2):142-4
7599271
J Mol Biol. 1986 Jun 20;189(4):681-99
3783688
Methods Enzymol. 2000;317:132-9
10829277
Methods Mol Biol. 1998;77:297-309
9770678
Proc Natl Acad Sci U S A. 1997 Apr 29;94(9):4262-6
9113977
J Mol Biol. 1988 May 20;201(2):289-314
3418702
RNA. 1997 Jul;3(7):807-10
9214662
Methods. 1999 May;18(1):13-21
10208812
RNA. 1997 Sep;3(9):950-1
9292493
Methods Mol Biol. 2004;265:357-91
15103084
RNA. 2008 Jan;14(1):180-7
17998290
Methods Enzymol. 2000;318:71-88
10889981
RNA. 2004 Jun;10(6):996-1002
15146083
Nucleic Acids Res. 2007;35(18):6322-9
17881375