PDBsum entry 1snh

DNA

PDB id: 1snh

Contents

DNA/RNA

PDB id:

1snh

Name:

DNA

Title:

Solution structure of the DNA decamer duplex containing double tg mismatches of cis-syn cyclobutane pyrimidine dimer

Structure:

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

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

12 models

Authors:

J.H.Lee,C.J.Park,J.S.Shin,T.Ikegami,H.Akutsu,B.S.Choi

Key ref:

J.H.Lee et al. (2004). NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex. Nucleic Acids Res, 32, 2474-2481. PubMed id: 15121904 DOI: 10.1093/nar/gkh568

Date:

11-Mar-04 Release date: 18-May-04

DNA/RNA chains

C-G-C-A-T-T-A-C-G-C 10 bases

G-C-G-T-G-G-T-G-C-G 10 bases

DOI no: 10.1093/nar/gkh568

Nucleic Acids Res 32:2474-2481 (2004)

PubMed id: 15121904

NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.

J.H.Lee, C.J.Park, J.S.Shin, T.Ikegami, H.Akutsu, B.S.Choi.

ABSTRACT

The cis-syn cyclobutane pyrimidine dimer (CPD) is a cytotoxic, mutagenic and carcinogenic DNA photoproduct and is repaired by the nucleotide excision repair (NER) pathway in mammalian cells. The XPC-hHR23B complex as the initiator of global genomic NER binds to sites of certain kinds of DNA damage. Although CPDs are rarely recognized by the XPC-hHR23B complex, the presence of mismatched bases opposite a CPD significantly increased the binding affinity of the XPC-hHR23B complex to the CPD. In order to decipher the properties of the DNA structures that determine the binding affinity for XPC-hHR23B to DNA, we carried out structural analyses of the various types of CPDs by NMR spectroscopy. The DNA duplex which contains a single 3' T*G wobble pair in a CPD (CPD/GA duplex) induces little conformational distortion. However, severe distortion of the helical conformation occurs when a CPD contains double T*G wobble pairs (CPD/GG duplex) even though the T residues of the CPD form stable hydrogen bonds with the opposite G residues. The helical bending angle of the CPD/GG duplex was larger than those of the CPD/GA duplex and properly matched CPD/AA duplex. The fluctuation of the backbone conformation and significant changes in the widths of the major and minor grooves at the double T*G wobble paired site were also observed in the CPD/GG duplex. These structural features were also found in a duplex that contains the (6-4) adduct, which is efficiently recognized by the XPC-hHR23B complex. Thus, we suggest that the unique structural features of the DNA double helix (that is, helical bending, flexible backbone conformation, and significant changes of the major and/or minor grooves) might be important factors in determining the binding affinity of the XPC-hHR23B complex to DNA.