The antiparallel loops in gal DNA

Publication Type:

Journal Article

Source:

NUCLEIC ACIDS RESEARCH, OXFORD UNIV PRESS, Volume 36, Number 12, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND, p.4204-4210 (2008)

DOI:

10.1093/nar/gkn389

Keywords:

BINDING; COMPLEX; FUNCTIONAL SUBUNIT; INTERFERON-BETA ENHANCEOSOME; LAC REPRESSOR; LAMBDA; RNA-POLYMERASE; SINGLE-MOLECULE; SUPERCOILED DNA; TRANSCRIPTION ACTIVATOR PROTEIN

Abstract:

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 proteinDNA and proteinprotein 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.