PDBsum entry 2mvs

RNA

PDB id: 2mvs

Contents

DNA/RNA

PDB id:

2mvs

Name:

RNA

Title:

N6-methyladenosine RNA

Structure:

N-6_methyl_adenosine_rna. Chain: 1, 2. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

NMR struc:

1 models

Authors:

S.R.Lynch,E.Kool

Key ref:

C.Roost et al. (2015). Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J Am Chem Soc, 137, 2107-2115. PubMed id: 25611135 DOI: 10.1021/ja513080v

Date:

10-Oct-14 Release date: 16-Sep-15

DNA/RNA chains

G-G-6MZ-C-U-A-G-U-C-C 10 bases

G-G-6MZ-C-U-A-G-U-C-C 10 bases

DOI no: 10.1021/ja513080v

J Am Chem Soc 137:2107-2115 (2015)

PubMed id: 25611135

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification.

C.Roost, S.R.Lynch, P.J.Batista, K.Qu, H.Y.Chang, E.T.Kool.

ABSTRACT

N(6)-Methyladenosine (m(6)A) modification is hypothesized to control processes such as RNA degradation, localization, and splicing. However, the molecular mechanisms by which this occurs are unclear. Here, we measured structures of an RNA duplex containing m(6)A in the GGACU consensus, along with an unmodified RNA control, by 2D NMR. The data show that m(6)A-U pairing in the double-stranded context is accompanied by the methylamino group rotating from its energetically preferred syn geometry on the Watson-Crick face to the higher-energy anti conformation, positioning the methyl group in the major groove. Thermodynamic measurements of m(6)A in duplexes reveal that it is destabilizing by 0.5-1.7 kcal/mol. In contrast, we show that m(6)A in unpaired positions base stacks considerably more strongly than the unmodified base, adding substantial stabilization in single-stranded locations. Transcriptome-wide nuclease mapping of methylated RNA secondary structure from human cells reveals a structural transition at methylated adenosines, with a tendency to single-stranded structure adjacent to the modified base.