The antiparallel loops in gal DNA.
Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein-DNA and protein-protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamically and biologically distinct. For example, theoretical models of Gal repressor/HU-mediated DNA-looping suggest that the antiparallel DNA loops, A1 and A2, are thermodynamically quite different. They are also biologically different, since in experiments using DNA molecules engineered to form only one of the two loops, the A2 loop failed to repress in vitro transcription. Surprisingly, single molecule measurements show that both loop trajectories form and that they appear to be quite similar energetically and kinetically.
Lia
Giuseppe
G
Department of Chemistry, Harvard University, Cambridge, MA, USA.
Semsey
Szabolcs
S
Lewis
Dale E A
DE
Adhya
Sankar
S
Bensimon
David
D
Dunlap
David
D
Finzi
Laura
L
D001426:Bacterial Proteins / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism*; D013816:Thermodynamics
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C050993:Galactose repressor proteins; D012097:Repressor Proteins; C040330:histone-like protein HU, bacteria