Cotranscriptional folding kinetics of ribonucleic acid secondary structures

نویسندگان
چکیده

برای دانلود باید عضویت طلایی داشته باشید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Cotranscriptional folding kinetics of ribonucleic acid secondary structures.

We develop a systematic helix-based computational method to predict RNA folding kinetics during transcription. In our method, the transcription is modeled as stepwise process, where each step is the transcription of a nucleotide. For each step, the kinetics algorithm predicts the population kinetics, transition pathways, folding intermediates, and the transcriptional folding products. The foldi...

متن کامل

Exact Folding Dynamics of RNA Secondary Structures

Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behavior of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the re...

متن کامل

Differences between cotranscriptional and free riboswitch folding

Riboswitches are part of noncoding regions of messenger RNA (mRNA) that act as RNA sensors regulating gene expression of the downstream gene. Typically, one out of two distinct conformations is formed depending on ligand binding when the transcript leaves RNA polymerase (RNAP). Elongation of the RNA chain by RNAP, folding and binding all occurs simultaneously and interdependently on the seconds...

متن کامل

Computing folding pathways between RNA secondary structures

Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of...

متن کامل

Building three-dimensional ribonucleic acid structures

orative research effort on ribonucleic acid (RNA) structure and function that started in 1987 in Robert Cedergren’s laboratory at the Université de Montréal. It involves multidisciplinary research in the fields of molecular biology, biochemistry, and computer science. The project ultimately produced MCSym, an intelligent system designed for building RNA three-dimensional (3D) structures. The RN...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

ژورنال

عنوان ژورنال: The Journal of Chemical Physics

سال: 2011

ISSN: 0021-9606,1089-7690

DOI: 10.1063/1.3671644