This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.107.112268v1 93/12/4342    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Goyal, S. Articles by Perkins, N. C. Search for Related Content PubMed PubMed Citation Articles by Goyal, S. Articles by Perkins, N. C.

Intrinsic Curvature of DNA Influences LacR-Mediated Looping

Sachin Goyal ^*, Todd Lillian ^*, Seth Blumberg  , Jens-Christian Meiners  , Edgar Meyhöfer ^* and N. C. Perkins ^*

^* Department of Mechanical Engineering, Department of Physics, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan

Correspondence: Address reprint requests to N. C. Perkins, E-mail: ncp{at}umich.edu.

Protein-mediated DNA looping is a common mechanism for regulating gene expression. Loops occur when a protein binds to two operators on the same DNA molecule. The probability of looping is controlled, in part, by the basepair sequence of inter-operator DNA, which influences its structural properties. One structural property is the intrinsic or stress-free curvature. In this article, we explore the influence of sequence-dependent intrinsic curvature by exercising a computational rod model for the inter-operator DNA as applied to looping of the LacR-DNA complex. Starting with known sequences for the inter-operator DNA, we first compute the intrinsic curvature of the helical axis as input to the rod model. The crystal structure of the LacR (with bound operators) then defines the requisite boundary conditions needed for the dynamic rod model that predicts the energetics and topology of the intervening DNA loop. A major contribution of this model is its ability to predict a broad range of published experimental data for highly bent (designed) sequences. The model successfully predicts the loop topologies known from fluorescence resonance energy transfer measurements, the linking number distribution known from cyclization assays with the LacR-DNA complex, the relative loop stability known from competition assays, and the relative loop size known from gel mobility assays. In addition, the computations reveal that highly curved sequences tend to lower the energetic cost of loop formation, widen the energy distribution among stable and meta-stable looped states, and substantially alter loop topology. The inclusion of sequence-dependent intrinsic curvature also leads to nonuniform twist and necessitates consideration of eight distinct binding topologies from the known crystal structure of the LacR-DNA complex.