title: DNA linking number change induced by sequence-specific DNA-binding proteins.
abstract: Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, which in many cases induce a linking number change (Delta Lk) to the DNA-binding site. Due to the lack of a feasible approach, Delta Lk induced by sequence-specific DNA-binding proteins has not been fully explored. In this paper we successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA-binding site for one sequence-specific DNA-binding protein, such as lambda O, LacI, GalR, CRP and AraC. In this case, the protein-induced Delta Lk was greatly amplified and can be measured experimentally. Indeed, not only were we able to simultaneously determine the protein-induced Delta Lk and the DNA-binding constant for lambda O and GalR, but also we demonstrated that the protein-induced Delta Lk is an intrinsic property for these sequence-specific DNA-binding proteins. Our results also showed that protein-mediated DNA looping by AraC and LacI can induce a Delta Lk to the plasmid DNA templates. Furthermore, we demonstrated that the protein-induced Delta Lk does not correlate with the protein-induced DNA bending by the DNA-binding proteins.
authors.affiliation: Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Chen
authors.forename: Yazhong
authors.initials: Y
authors.lastname: Xiao
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.forename: Chenzhong
authors.initials: C
authors.lastname: Li
authors.forename: Fenfei
authors.initials: F
authors.lastname: Leng
mesh_terms: D051777:AraC Transcription Factor / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D002373:Cyclic AMP Receptor Protein / Q000378:metabolism; D004270:DNA, Circular / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D056968:Lac Repressors / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics; D011485:Protein Binding; D012097:Repressor Proteins / Q000378:metabolism; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D051777:AraC Transcription Factor; D002373:Cyclic AMP Receptor Protein; D004270:DNA, Circular; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C050993:Galactose repressor proteins; D056968:Lac Repressors; C027812:O protein, Bacteriophage lambda; D012097:Repressor Proteins; D014764:Viral Proteins