PDBsum entry 1jrv

DNA

PDB id: 1jrv

Contents

DNA/RNA

PDB id:

1jrv

Name:

DNA

Title:

Solution structure of daataa DNA bulge

Structure:

5'-d( Gp Cp Ap Tp Cp Gp Ap Ap Tp Ap Ap Gp Cp Tp Ap Cp G)- 3'. Chain: a. Engineered: yes. 5'-d( Cp Gp Tp Ap Gp Cp Cp Gp Ap Tp Gp C)-3'. Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

15 models

Authors:

F.A.Gollmick,M.Lorenz,U.Dornberger,J.Von Langen,S.Diekmann, H.Fritzsche

Key ref:

F.A.Gollmick et al. (2002). Solution structure of dAATAA and dAAUAA DNA bulges. Nucleic Acids Res, 30, 2669-2677. PubMed id: 12060684 DOI: 10.1093/nar/gkf375

Date:

15-Aug-01 Release date: 19-Jun-02

DNA/RNA chains

G-C-A-T-C-G-A-A-T-A-A-G-C-T-A-C-G 17 bases

C-G-T-A-G-C-C-G-A-T-G-C 12 bases

DOI no: 10.1093/nar/gkf375

Nucleic Acids Res 30:2669-2677 (2002)

PubMed id: 12060684

Solution structure of dAATAA and dAAUAA DNA bulges.

F.A.Gollmick, M.Lorenz, U.Dornberger, J.von Langen, S.Diekmann, H.Fritzsche.

ABSTRACT

The NMR structure analysis is described for two DNA molecules of identical stem sequences with a five base loop containing a pyrimidine, thymin or uracil, in between purines. These five unpaired nucleotides are bulged out and are known to induce a kink in the duplex structure. The dAATAA bulge DNA is kinked between the third and the fourth nucleotide. This contrasts with the previously studied dAAAAA bulge DNA where we found a kink between the fourth and fifth nucleotide. The total kinking angle is approximately 104 degrees for the dAATAA bulge. The findings were supported by electrophoretic data and fluorescence resonance energy transfer measurements of a similar DNA molecule end-labeled by suitable fluorescent dyes. For the dAAUAA bulge the NMR data result in a similar structure as reported for the dAATAA bulge with a kinking angle of approximately 87 degrees. The results are discussed in comparison with a rAAUAA RNA bulge found in a group I intron. Generally, the sequence-dependent structure of bulges is important to understand the role of DNA bulges in protein recognition.