PDBsum entry 1ql5

DNA

PDB id

1ql5

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Contents

			DNA/RNA

PDB id:

1ql5

Links

Name:

DNA

Title:

DNA decamer duplex containing t5-t6 photoadduct

Structure:

DNA (5'-d( Cp Gp Cp Ap Tp +Tp Ap Cp Gp C)- 3'). Chain: a. Engineered: yes. Other_details: cyclobutane ring formed between c5-c6(t5) and c5- c6(t6) double bonds. DNA (5'-d( Gp Cp Gp Tp Tp Ap Tp Gp Cp G)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

1 models

Authors:

J.-H.Lee,G.-S.Hwang,B.-S.Choi

Key ref:

J.H.Lee et al. (2000). Solution structure of the DNA decamer duplex containing a 3'-T x T basepair of the cis-syn cyclobutane pyrimidine dimer: implication for the mutagenic property of the cis-syn dimer. Nucleic Acids Res, 28, 1794-1801. PubMed id: 10734199 DOI: 10.1093/nar/28.8.1794

Date:

24-Aug-99

Release date:

10-Apr-00

	Headers

	References

DNA/RNA chains

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

DOI no: 10.1093/nar/28.8.1794	Nucleic Acids Res 28:1794-1801 (2000)
PubMed id: 10734199

Solution structure of the DNA decamer duplex containing a 3'-T x T basepair of the cis-syn cyclobutane pyrimidine dimer: implication for the mutagenic property of the cis-syn dimer.
J.H.Lee, Y.J.Choi, B.S.Choi.

ABSTRACT

The cis - syn dimer is the major DNA photoproduct produced by UV irradiation. In order to determine the origin of the mutagenic property of the cis - syn dimer, we used NMR restraints and molecular dynamics to determine the solution structure of a DNA decamer duplex containing a wobble pair between the 3'-T of the cis - syn dimer and the opposite T residue (CS/TA duplex). The solution structure of the CS/TA duplex revealed that the 3'-T x T base pair of the cis - syn dimer had base pair geometry that was significantly different from the canonical Watson-Crick base pair and caused destabilization and conformational distortion of its 3'-region. However, a 3'-T x A base pair at the cis - syn dimer within this related DNA decamer maintains the normal Watson-Crick base pair geometry and causes little distortion in the conformation of its 3'-side. Our results show that in spite of its stable hydrogen bonding, the insertion of a T residue opposite the 3'-T of the cis - syn dimer is inhibited by structural distortion caused by the 3'-T x T base pair. This may explain why the frequency of the 3'-T-->A transversion, which is the major mutation produced by the cis - syn dimer, is only 4%.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18096619

Q.Du, A.Kotlyar, and A.Vologodskii (2008).
Kinking the double helix by bending deformation.

Nucleic Acids Res, 36, 1120-1128.

15121904

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

PDB codes:

1pib 1snh

12907715

J.H.Lee, C.J.Park, A.I.Arunkumar, W.J.Chazin, and B.S.Choi (2003).
NMR study on the interaction between RPA and DNA decamer containing cis-syn cyclobutane pyrimidine dimer in the presence of XPA: implication for damage verification and strand-specific dual incision in nucleotide excision repair.

Nucleic Acids Res, 31, 4747-4754.

12405150

H.M.Lee, and J.K.Kim (2002).
H-NMR studies of duplex DNA decamer containing a uracil cyclobutane dimer: implications regarding the high UV mutagenecity of CC photolesions.

Photochem Photobiol, 76, 417-422.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.