ISDA

Deposition Date 2006-02-15

Release Date 2006-03-21

Last Version Date 2024-03-13

Entry Detail

PDB ID:

2G1Z

Keywords:

DNA

Title:

X-ray structure of the oligonucleotide sequence d(AAATTT)

Biological Source:

Source Organism:

(Taxon ID: ) (Taxon ID: )

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.11 Å

R-Value Free:

0.37

R-Value Work:

0.28

R-Value Observed:

0.29

Space Group:

H 3 2

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*AP*AP*TP*TP*T)-3'
Chain IDs:A, B (auth: C), C (auth: B)
Chain Length:6
Number of Molecules:3
Biological Source:

Ligand Molecules

Primary Citation

Packing features of the all-AT oligonucleotide d(AAATTT).

Valls, N, Santaolalla, A, Campos, J.L, Subirana, J.A.Show

J.Biomol.Struct.Dyn. 24 547 552 (2007)

PMID: 17508776 DOI: 10.1080/07391102.2007.10507143

Abstact

We describe the packing features of the oligonucleotide duplex d(AAATTT)2, as determined by X-ray diffraction. There is little information on sequences that only contain A and T bases. The present structure confirms that these sequences tend to pack as a helical arrangement of stacked oligonucleotides in a B conformation with Watson-Crick hydrogen bonding. Our results demonstrate that the virtual TA base step between stacked duplexes has a negative twist that improves base stacking. This observation is consistent with the low stability of TA base steps in B-form DNA.

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Primary Citation of related structures