Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding.
An important component of protein-DNA recognition is the charge neutralization of DNA backbone phosphates and subsequent protein-induced DNA bending. Replacement of phosphates by neutral methylphosphonates has previously been shown to be a model for protein-induced bending. In addition to bending, the neutralization process may change the inherent flexibility of the DNA--a feature never before tested. We have developed a method to measure the differential flexibility of duplex DNA when methylphosphonate substitutions are made and find that the local flexibility is increased up to 40%. These results imply that backbone-neutralization-dependent DNA flexibility augments DNA-binding motifs in protein-DNA recognition processes.
Okonogi
Tamara M
TM
Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195-1700, USA.
Alley
Stephen C
SC
Harwood
Eric A
EA
Hopkins
Paul B
PB
Robinson
Bruce H
BH
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D010710:Phosphates / Q000737:chemistry*; D011485:Protein Binding; D013816:Thermodynamics
D010710:Phosphates; D004247:DNA