1P0U

Sheared G/C Base Pair

Summary for 1P0U

• Entry DOI: 10.2210/pdb1p0u/pdb
• Descriptor: 5'-D(*GP*CP*AP*TP*CP*GP*AP*CP*GP*AP*TP*GP*C)-3' (1 entity in total)
• Functional Keywords: sheared gc base pair, single-residue loop, syn cytidine, dna
• Total number of polymer chains: 1
• Total formula weight: 3976.60

Authors

Chin, K.H.,Chou, S.H. (deposition date: 2003-04-11, release date: 2003-06-03, Last modification date: 2024-05-29)

Primary citation

Chin, K.H.,Chou, S.H.
Sheared-type G(anti).C(syn) Base-pair: A Unique d(GXC) Loop Closure Motif.
J.Mol.Biol., 329:351-361, 2003

PubMed Abstract: Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared-type (trans Watson-Crick/sugar-edge) pairing, like those occurring in the sheared mismatched G.A or A.C base-pair, to draw the two opposite strands together. The cytidine residue in the closing base-pair is transformed into the rare syn domain to form two H-bonds with the guanine base and to prevent the steric clash between the G 2NH(2) and the C H-5 protons. Besides, the sugar pucker of the syn cytidine is still located in the regular C2'-endo domain, unlike the C3'-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of the compact d(GXC) loops closed by a unique sheared-type G(anti).C(syn) base-pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins.

PubMed: 12758081
DOI: 10.1016/S0022-2836(03)00440-6

Experimental method

SOLUTION NMR