PDBsum entry 1vtw

DNA

PDB id: 1vtw

Contents

DNA/RNA

PDB id:

1vtw

Name:

DNA

Title:

At base pairs are less stable than gc base pairs in z-dna: the crystal structure of d(m(5)cgtam(5)cg)

Structure:

DNA (5'-d( (Ch3)cp Gp Tp Ap (Ch3)cp G)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Resolution:

1.20Å R-factor: 0.160

Authors:

A.H.-J.Wang,T.Hakoshima,G.A.Van Der Marel,J.H.Van Boom,A.Rich

Key ref:

A.H.Wang et al. (1984). AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG). Cell, 37, 321-331. PubMed id: 6722876

Date:

18-Aug-88 Release date: 13-Jul-11

DNA/RNA chains

5CM-G-T-A-5CM-G 6 bases

5CM-G-T-A-5CM-G 6 bases

Cell 37:321-331 (1984)

PubMed id: 6722876

AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG).

A.H.Wang, T.Hakoshima, G.van der Marel, J.H.van Boom, A.Rich.

ABSTRACT

Two hexanucleoside pentaphosphates , 5-methyl and 5-bromo cytosine derivatives of d( CpGpTpApCpG ) have been synthesized, crystallized, and their three-dimensional structure solved. They both form left-handed Z-DNA and the methylated derivative has been refined to 1.2 A resolution. These are the first crystal Z-DNA structures that contain AT base pairs. The overall form of the molecule is very similar to that of the unmethylated or the fully methylated (dC-dG)3 hexamer although there are slight changes in base stacking. However, significant differences are found in the hydration of the helical groove. When GC base pairs are present, the helical groove is systematically filled with two water molecules per base pair hydrogen bonded to the bases. Both of these water molecules are not seen in the electron density map in the segments of the helix containing AT base pairs, probably because of solvent disorder. This could be one of the features that makes AT base pairs form Z-DNA less readily than GC base pairs.