Twist, writhe, and geometry of a DNA loop containing equally spaced coplanar bends

Biopolymers
J H WhiteW R Bauer

Abstract

The formation of a topologically closed DNA loop is important in many biological processes, including the regulation of transcription, recombination, and replication. Modeling DNA as an isotropic elastic rod, we use finite element analysis to show that the dependence of the twist (delta Tw) and the writhe (Wr) upon the linking number deficit (delta Lk) is strongly influenced by intrinsic bends. We determine how the geometry of a DNA loop changes as a function of the number of uniformly spaced coplanar 20 degrees bends, oriented so as to open toward the center of the loop. We also calculate the geometry of DNA rods that are smoothly bent to the same extent. The response of both delta Tw and Wr of a bent DNA to changes in delta Lk falls into one of three categories, depending upon the number of bends. For a single bend of 20 degrees, Wr increases monotonically with delta Lk and the change in delta Tw with distance is constant along the entire DNA axis. For two to ten 20 degrees bends, Wr passes first through a local maximum, then through a local minimum, and finally increases monotonically as delta Lk increases. For eleven to eighteen 20 degrees bends, Wr again varies monotonically with delta Lk. For all numbers of bends greater ...Continue Reading

References

Oct 20, 1992·Journal of Molecular Biology·A V VologodskiiN R Cozzarelli
Oct 20, 1992·Journal of Molecular Biology·F Claverie-Martin, B Magasanik
Feb 20, 1992·Journal of Molecular Biology·T Schlick, W K Olson
Nov 22, 1991·Science·T K Kerppola, T Curran
Mar 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·F Claverie-Martin, B Magasanik
Oct 26, 1990·Science·R B Lobell, R F Schleif
Apr 15, 1988·Science·J C Wang, G N Giaever
Sep 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·S MukherjeeD Bastia
Feb 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·W R BauerJ H White

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
W R BauerJ H White
Proceedings of the National Academy of Sciences of the United States of America
C J Benham
Current Opinion in Structural Biology
W K Olson
© 2021 Meta ULC. All rights reserved