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225d
From Proteopedia
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| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS
Overview
Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.
About this Structure
225D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A tetrameric DNA structure with protonated cytosine.cytosine base pairs., Gehring K, Leroy JL, Gueron M, Nature. 1993 Jun 10;363(6429):561-5. PMID:8389423
Page seeded by OCA on Mon Mar 31 01:44:36 2008
