Base-sequence-dependent sliding of proteins on DNA.
The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.
Barbi
M
M
Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, case courrier 121, 4 Place Jussieu, 75252 Paris Cedex 05, France.
Place
C
C
Popkov
V
V
Salerno
M
M
D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000032:analysis / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D012321:DNA-Directed RNA Polymerases / Q000032:analysis / Q000737:chemistry*; D004058:Diffusion; D004789:Enzyme Activation; D007700:Kinetics; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D020409:Molecular Motor Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D009038:Motion; D009711:Nucleotides / Q000032:analysis / Q000737:chemistry*; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods; D013329:Structure-Activity Relationship; D014764:Viral Proteins / Q000032:analysis / Q000737:chemistry*
D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D020409:Molecular Motor Proteins; D009711:Nucleotides; D014764:Viral Proteins; D004247:DNA; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases