Staying in the Loop
JF Beausang, C Zurla, C Manzo, D Dunlap, L Finzi, and PC Nelson,
DNA looping kinetics analyzed using diffusive hidden Markov model, Biophysical Letters section of Biophys. J., in press.
Nelson, his student, John Beausang, and colleagues at Emory University recently reported a new technique to measure rate constants of DNA loop formation and breakdown using tethered particle motion (TPM).
Their technique improves TPM as a quantitative technique with more consistent results and improved time resolution. A typical experimental arrangement, also reported in the article, uses an optically visible bead tethered to a microscope slide (left) using a strand of DNA. The method allows the extraction of DNA-looping events even from very noisy data (right).
The work will appear in the Biophysical Letters section of Biophysical Journal. The technique, a new form of hidden Markov analysis, can provide insight into the physical process of DNA looping and its influence on the biochemistry of transcription.