Learn More
Determining numbers of proteins bound to large DNAs is important for understanding their chromosomal functions. Protein numbers may be affected by physical factors such as mechanical forces generated in DNA, e.g. by transcription or replication. We performed single-DNA stretching experiments with bacterial nucleoid proteins HU and Fis, verifying that the(More)
Single-DNA stretching and twisting experiments provide a sensitive means to detect binding of proteins, via detection of their modification of DNA mechanical properties. However, it is often difficult or impossible to determine the numbers of proteins bound in such experiments, especially when the proteins interact nonspecifically (bind stably at any(More)
We study a statistical-mechanical model of the binding of DNA-bending proteins to the double helix including applied tension and binding cooperativity effects. Intrinsic cooperativity of binding sharpens force-extension curves and causes enhancement of fluctuation of extension and protein occupation. This model also allows us to estimate the intrinsic(More)
We present KnIT, the Knowledge Integration Toolkit, a system for accelerating scientific discovery and predicting previously unknown protein-protein interactions. Such predictions enrich biological research and are pertinent to drug discovery and the understanding of disease. Unlike a prior study, KnIT is now fully automated and demonstrably scalable. It(More)
When a DNA molecule is stretched, the zero-force correlation length for its bending fluctuations-the persistence length A-bifurcates into two different correlation lengths-the shorter "longitudinal" correlation length ξ_{∥}(f) and the longer "transverse" correlation length ξ_{⊥}(f). In the high-force limit, ξ_{∥}(f)=ξ_{⊥}(f)/2=sqrt[k_{B}TA/f]/2. When(More)
  • 1