Twist-bend coupling, twist waves and the shape of DNA loops
| Autor: | Enrico Skoruppa, Michele Caraglio, Michiel Laleman, Enrico Carlon, K. Phillips, Stefanos K. Nomidis |
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| Rok vydání: | 2019 |
| Předmět: |
Models
Molecular Base pair media_common.quotation_subject Thermal fluctuations FOS: Physical sciences Bending Condensed Matter - Soft Condensed Matter 01 natural sciences Asymmetry 010305 fluids & plasmas Physics Fluids & Plasmas 0103 physical sciences Turn (geometry) Twist 010306 general physics Base Pairing Condensed Matter - Statistical Mechanics media_common Mechanical Phenomena Physics Coupling Quantitative Biology::Biomolecules Science & Technology Statistical Mechanics (cond-mat.stat-mech) Biomolecules (q-bio.BM) DNA Biomechanical Phenomena Physics Mathematical Loop (topology) Classical mechanics Quantitative Biology - Biomolecules FOS: Biological sciences Physical Sciences MECHANICS Soft Condensed Matter (cond-mat.soft) |
| DOI: | 10.48550/arxiv.1904.04677 |
| Popis: | By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an imposed bending stress, as recently found in DNA minicircles and observed in nucleosomal DNA. These twist oscillations, here referred to as twist waves, are due to the coupling between twist and bending deformations, which in turn originates from the asymmetry between DNA major and minor grooves. We introduce a simple analytical variational shape, that reproduces the exact loop energy up to the fourth significant digit, and is in very good agreement with shapes obtained from coarse-grained simulations. We, finally, analyze the loop dynamics at room temperature, and show that the twist waves are robust against thermal fluctuations. They perform a normal diffusive motion, whose origin is briefly discussed. Comment: 9 pages, 6 figures |
| Databáze: | OpenAIRE |
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