Description: Importance of boundary effects in diffusion of hydrocarbon molecules in a one-dimensional zeolite channel

This title appears in the Scientific Report : 2010

Importance of boundary effects in diffusion of hydrocarbon molecules in a one-dimensional zeolite channel

Two recent theoretical models, Bai et al. (2004, 2007) and Tadigotla et al. (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for...

Personal Name(s):	Chatterjee, S.
	Schütz, G. M.
Contributing Institute:	Theorie der Weichen Materie und Biophysik; IFF-2
Published in:	Journal of statistical mechanics: theory and experiment (2010)
Imprint:	Bristol IOP Publ. 2010
PubMed ID:	22446379
DOI:	10.1088/1742-5468/2010/01/P01017
Document Type:	Journal Article
Research Program:	BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung
Series Title:	Journal of Statistical Mechanics : Theory and Experiment
Subject (ZB):	J driven diffusive systems (theory) stochastic particle dynamics (theory) stochastic processes (theory) diffusion
	Publikationsportal JuSER

Please use the identifier: http://dx.doi.org/10.1088/1742-5468/2010/01/P01017 in citations.

Two recent theoretical models, Bai et al. (2004, 2007) and Tadigotla et al. (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al. model is more accurate than Tadigotla et al. at higher NTP concentrations. Pausing kinetics predicted by Bai et al. is also consistent with time-course transcription reactions, while Tadigotla et al. is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al. model provides an explanation more consistent with recent single molecule observations.