2N89 image
Entry Detail
PDB ID:
2N89
Keywords:
Title:
Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2015-10-09
Release Date:
2016-08-17
Method Details:
Experimental Method:
Conformers Calculated:
20
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')
Chain IDs:A, B, C, D
Chain Length:6
Number of Molecules:4
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CFL A DC ?
Ligand Molecules
Primary Citation
Stabilization of i-motif structures by 2'-beta-fluorination of DNA.
Nucleic Acids Res. 44 4998 5009 (2016)
PMID: 27166371 DOI: 10.1093/nar/gkw402

Abstact

i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH(+)). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2'-endo conformation, instead of the C3'-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.

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