Doctoral thesis (Dissertations and theses)
Modelling the Extensionally Driven Transitions of DNA
Taghavi, Amirhossein
2018
 

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Keywords :
DNA extension; MD,MC simulations; Sigma DNA
Abstract :
[en] Empirical measurements on DNA under tension show a jump by a factor of ≈ 1.5 − 1.7 in the relative extension at applied force of ≈ 65 − 70 pN, indi- cating a structural transition. The still ambiguously characterised stretched ‘phase’ is known as S-DNA. Using atomistic and coarse-grained Monte Carlo simulations we study DNA over-stretching in the presence of organic salts Ethidium Bromide (EtBr) and Arginine (an amino acid present in the RecA binding cleft). We present planar-stacked triplet disproportionated DNA as a solution phase of the double helix under tension, and dub it ‘Σ DNA’, with the three right-facing points of the Σ character serving as a mnemonic for the three grouped bases. Like unstretched Watson-Crick base paired DNA structures, the structure of the Σ phase is linked to function: the partitioning of bases into codons of three base-pairs each is the first stage of operation of recombinase enzymes such as RecA, facilitating alignment of homologous or near-homologous sequences for genetic exchange or repair. By showing that this process does not require any very sophisticated manipulation of the DNA, we position it as potentially appearing as an early step in the de- velopment of life, and correlate the postulated sequence of incorporation of amino acids (GADV then GADVESPLIT and then the full 20 residue set of canonical amino acids) into molecular biology with the ease of Σ-formation for sequences including the associated codons. To further investigate the de- pendence of stretching behaviour on the concentration of intercalating salt molecules, we present a physically motivated coarse-grained force-field for DNA under tension and use it to qualitatively reproduce regimes of force- extension behaviour which are not atomistically accessible.
Research center :
Faculté des Sciences, de la Technologie et de la Communication
Disciplines :
Physics
Author, co-author :
Taghavi, Amirhossein ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit
Language :
English
Title :
Modelling the Extensionally Driven Transitions of DNA
Defense date :
22 February 2018
Number of pages :
133
Institution :
Unilu - University of Luxembourg, Luxembourg, Luxembourg
Degree :
DOCTEUR DE L’UNIVERSITÉ DU LUXEMBOURG EN PHYSIQUE
Promotor :
Schilling, Tanja
​ Berryman, Joshua​​ ​ T.
Jury member :
LAGERWALL, Jan
OTT, Albrecht
NOY, Agnes
Focus Area :
Physics and Materials Science
Name of the research project :
R-AGR-0136 - IRP13 - NANOMECH (20140315-20170314) - BERRYMAN Josh
Funders :
University of Luxembourg - UL
Available on ORBilu :
since 04 April 2018

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