Summary information and primary citation
- PDB-id
-
2fih;
SNAP-derived features in text and
JSON formats
- Class
- DNA
- Method
- X-ray (1.13 Å)
- Summary
- Crystal structure analysis of the b-DNA dodecamer
cgcgaa-au-tcgcg, with incorporated arabino-uridine
(au)
- Reference
-
Li F, Sarkhel S, Wilds CJ, Wawrzak Z, Prakash TP,
Manoharan M, Egli M (2006): "2'-Fluoroarabino-
and arabinonucleic acid show different conformations,
resulting in deviating RNA affinities and processing of
their heteroduplexes with RNA by RNase H."
Biochemistry, 45, 4141-4152.
doi: 10.1021/bi052322r.
- Abstract
- 2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and
arabinonucleic acid (ANA) paired to RNA are substrates of
RNase H. The conformation of the natural DNA/RNA hybrid
substrates appears to be neither A-form nor B-form.
Consistent with this, the conformations of FANA and ANA
were found to be intermediate between the A- and B-forms.
However, FANA opposite RNA is preferred by RNase H over
ANA, and the RNA affinity of FANA considerably exceeds that
of ANA. By investigating the conformational boundaries of
FANA and ANA residues in crystal structures of A- and
B-form DNA duplexes at atomic resolution, we demonstrate
that FANA and ANA display subtle conformational
differences. The structural data provide insight into the
structural requirements at the catalytic site of RNase H.
They also allow conclusions with regard to the relative
importance of stereoelectronic effects and hydration as
modulators of RNA affinity.
