PDBsum entry 1vte

DNA

PDB id: 1vte

Contents

DNA/RNA

Waters ×72

PDB id:

1vte

Name:

DNA

Title:

Molecular structure of nicked DNA. Model a4

Structure:

DNA (5'-d( Cp Gp Cp Gp Ap Ap Ap Ap Cp Gp Cp G)-3'). Chain: a. Engineered: yes. DNA (5'-d( Cp Gp Cp Gp Tp T)-3'). Chain: b. Engineered: yes. DNA (5'-d( Tp Tp Cp Gp Cp G)-3'). Chain: c. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

3.00Å R-factor: 0.182

Authors:

J.Aymani,M.Coll,G.A.Van Der Marel,J.H.Van Boom,A.H.-J.Wang,A.Rich

Key ref:

J.Aymami et al. (1990). Molecular structure of nicked DNA: a substrate for DNA repair enzymes. Proc Natl Acad Sci U S A, 87, 2526-2530. PubMed id: 2320572 DOI: 10.1073/pnas.87.7.2526

Date:

21-May-90 Release date: 13-Jul-11

DNA/RNA chains

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

C-G-C-G-T-T 6 bases

T-T-C-G-C-G 6 bases

DOI no: 10.1073/pnas.87.7.2526

Proc Natl Acad Sci U S A 87:2526-2530 (1990)

PubMed id: 2320572

Molecular structure of nicked DNA: a substrate for DNA repair enzymes.

J.Aymami, M.Coll, G.A.van der Marel, J.H.van Boom, A.H.Wang, A.Rich.

ABSTRACT

The molecular structure of a nicked dodecamer DNA double helix, made of a ternary system containing d(CGCGAAAACGCG) + d(CGCGTT) + d(TTCGCG) oligonucleotides, has been determined by x-ray diffraction analysis at 3 A resolution. The molecule adopts a B-DNA conformation, not unlike those found in intact dodecamer DNA molecules crystallized in a somewhat different crystal lattice, despite a gap due to the absence of a phosphate group in the molecule. The helix has a distinct narrow minor groove near the center of the molecule at the AAAA region. This suggests that the internal stabilizing forces due to base stacking and hydrogen-bonding interactions are sufficient to overcome the loss of connectivity associated with the disruption of the covalent backbone of DNA.