Base pair fluctuations in helical models for nucleic acids.
J Chem Phys
; 154(19): 194102, 2021 May 21.
Article
em En
| MEDLINE
| ID: mdl-34240895
ABSTRACT
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian motion for a particle embedded in a stable helical structure. The probability to return to the initial position is computed, as a function of time, by integrating over the particle paths consistent with the physical properties of the model potential. The zero time condition for the first-passage probability defines the constraint to select the integral cutoff for various macroscopic helical conformations, obtained by tuning the twist, bending, and slide motion between adjacent base pairs along the molecule stack. Applying the method to a short homogeneous chain at room temperature, we obtain meaningful estimates for the maximum fluctuations in the twist conformation with â¼10.5 base pairs per helix turn, typical of double stranded DNA helices. Untwisting the double helix, the base pair fluctuations broaden and the integral cutoff increases. The cutoff is found to increase also in the presence of a sliding motion, which shortens the helix contour length, a situation peculiar of dsRNA molecules.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
DNA
/
RNA
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article