PDBsum entry 179d

DNA

PDB id: 179d

Contents

DNA/RNA

PDB id:

179d

Name:

DNA

Title:

Solution structure of the d(t-c-g-a) duplex at acidic ph: a parallel- stranded helix containing c+.C, g.G and a.A pairs

Structure:

DNA (5'-d( Tp Cp Gp A)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes

NMR struc:

6 models

Authors:

Y.Wang,D.J.Patel

Key ref:

Y.Wang and D.J.Patel (1994). Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs. J Mol Biol, 242, 508-526. PubMed id: 7932707

Date:

15-Jun-94 Release date: 31-Jul-94

DNA/RNA chains

T-C-G-A 4 bases

T-C-G-A 4 bases

J Mol Biol 242:508-526 (1994)

PubMed id: 7932707

Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs.

Y.Wang, D.J.Patel.

ABSTRACT

The solution structure of the d(T-C-G-A) sequence at acidic pH has been determined by a combination of NMR and molecular dynamics calculations including NOE intensity based refinements. This sequence forms a right-handed parallel-stranded duplex with C+ .C (three hydrogen bonds along Watson-Crick edge), G.G (two symmetry related N2-H.. N3 hydrogen bonds) and A.A (two symmetry related N6-H..N7 hydrogen bonds) homo base-pair formation at acidic pH. The duplex is stabilized by intra-strand base stacking at the C2-G3 step and cross-strand base stacking at the G3-A4 step. The thymine residues on partner strands are directed towards each other and are positioned over the C+ .C base-pair. All four residues adopt anti glycosidic torsion angles and C2'-endo type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which exhibits large changes in twist angles between adjacent steps along the duplex. This study rules out previously proposed models for the structure of the d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions, which established that d(C-G) and d(C-G-A) containing sequences at acidic pH pair through parallel-stranded alignment. We have also monitored hydration patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A) duplex.