Traveling Salesman Finds Random Walk: A Curve Reconstruction Algorithm for Supercoiled DNA.

DNA supercoiling plays an important role in a variety of cellular processes, including transcription, replication, and DNA compaction. To fully understand these processes, we must uncover and characterize the dynamics of supercoiled DNA. However, supercoil dynamics are difficult to access because of the wide range of relevant length and timescales.

Simulation of DNA Supercoil Relaxation.

Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead. The bead, which also serves to manipulate DNA, experiences significant drag and thereby obscures supercoil dynamics.

Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity.

In the bacteriophage ϕ29, DNA is packed into a preassembled capsid from which it ejects under high pressure. A recent cryo-EM reconstruction of ϕ29 revealed a compact toroidal DNA structure (30-40 basepairs) lodged within the exit cavity formed by the connector-lower collar protein complex. Using multiscale models, we compute a detailed structural ensemble of intriguing DNA toroids of various lengths, all highly compatible with experimental observations.

FRET studies of a landscape of Lac repressor-mediated DNA loops.

DNA looping mediated by the Lac repressor is an archetypal test case for modeling protein and DNA flexibility. Understanding looping is fundamental to quantitative descriptions of gene expression. Systematic analysis of LacI•DNA looping was carried out using a landscape of DNA constructs with lac operators bracketing an A-tract bend, produced by varying helical phasings between operators and the bend.

DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays.

Protein-mediated DNA looping, such as that induced by the lactose repressor (LacI) of Escherichia coli, is a well-known gene regulation mechanism. Although researchers have given considerable attention to DNA looping by LacI, many unanswered questions about this mechanism, including the role of protein flexibility, remain. Recent single-molecule observations suggest that the two DNA-binding domains of LacI are capable of splaying open about the tetramerization domain into an extended conformation.

A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB.

In this study, we report what we believe to be the first multiscale simulation of the dynamic relaxation of DNA supercoils by human topoisomerase IB (topo IB). We leverage our previous molecular dynamics calculations of the free energy landscape describing the interaction between a short DNA fragment and topo IB. Herein, this landscape is used to prescribe boundary conditions for a computational, elastodynamic continuum rod model of a long length of supercoiled DNA.

Computational analysis of looping of a large family of highly bent DNA by LacI.

Sequence-dependent intrinsic curvature of DNA influences looping by regulatory proteins such as LacI and NtrC. Curvature can enhance stability and control shape, as observed in LacI loops formed with three designed sequences with operators bracketing an A-tract bend. We explore geometric, topological, and energetic effects of curvature with an analysis of a family of highly bent sequences, using the elastic rod model from previous work.