| Reference : Modelling the Extensionally Driven Transitions of DNA |
| Dissertations and theses : Doctoral thesis | |||
| Physical, chemical, mathematical & earth Sciences : Physics | |||
| Physics and Materials Science | |||
| http://hdl.handle.net/10993/35419 | |||
| Modelling the Extensionally Driven Transitions of DNA | |
| English | |
Taghavi, Amirhossein  [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >] | |
| 22-Feb-2018 | |
| University of Luxembourg, Luxembourg, Luxembourg | |
| DOCTEUR DE L’UNIVERSITÉ DU LUXEMBOURG EN PHYSIQUE | |
| 133 | |
| Schilling, Tanja | |
| Berryman, Joshua T. | |
| LAGERWALL, Jan | |
| OTT, Albrecht | |
| NOY, Agnes | |
| [en] DNA extension ; MD,MC simulations ; Sigma DNA | |
| [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. | |
| Faculté des Sciences, de la Technologie et de la Communication | |
| University of Luxembourg - UL | |
| R-AGR-0136 > NANOMECH > 15/03/2014 - 14/03/2017 > BERRYMAN Josh | |
| http://hdl.handle.net/10993/35419 |
| File(s) associated to this reference | ||||||||||||||
|
Fulltext file(s):
| ||||||||||||||
All documents in ORBilu are protected by a user license.
