[1] DNA bending, flexibility, and helical repeat by cyclization kinetics

Abstract

This chapter discusses experimental approaches to the measurement of ring closure probability (J factor or Jacobson–Stockmayer factor) and the theory used to analyze ring closure, and thereby obtain fundamental physical information from the J factor. It illustrates these procedures with examples from the cyclization of bent DNA molecules (A tract multimers) and recent work on the application of cyclization methods to protein–DNA complexes. Cyclization kinetics is unusual among molecular biological techniques in its requirement for computation of the properties of models to interpret the experimental results in anything more than a highly qualitative way. The theory of cyclization kinetics can also be applied to other systems where DNA assumes conformations and where its ends are fixed in a defined spatial orientation. In vivo and in vitro results on lac repressor-mediated DNA loops have been interpreted using the cyclization paradigm, and the enhancement of cyclization has been used to provide evidence for looping. The chapter also highlights the analysis of topoisomer distributions established by ligation under various conditions that can provide complementary information to that available from cyclization kinetics.