Reference : DNA partitions into triplets under tension in the presence of organic cations, with s...

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Biochemistry, biophysics & molecular biology Life sciences : Genetics & genetic processes Physical, chemical, mathematical & earth Sciences : Multidisciplinary, general & others
	Focus Areas :	Physics and Materials Science
	To cite this reference:	http://hdl.handle.net/10993/33076

Title :	DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
Language :	English
Author, co-author :	Taghavi, Amirhossein [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
	van der Schoot, Paul [Technical University of Eindhoven]
	Berryman, Josh [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
Publication date :	Nov-2017
Journal title :	Quarterly Reviews of Biophysics
Publisher :	Cambridge University Press
Volume :	50
Peer reviewed :	Yes
Audience :	International
ISSN :	0033-5835
e-ISSN :	1469-8994
Keywords :	[en] DNA ; GNC ; arginine ; DNA stretching ; Sigma DNA ; S-DNA
Abstract :	[en] Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure–function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for ‘phase 1’ amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the ‘GADV world’ hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code.
Research centres :	University of Luxembourg: High Performance Computing - ULHPC
Name of the research project :	R-AGR-0136 > NANOMECH > 15/03/2014 - 14/03/2017 > BERRYMAN Josh
Target :	Researchers ; Professionals ; Students ; General public
Permalink :	http://hdl.handle.net/10993/33076
DOI :	10.1017/S0033583517000130
Other URL :	http://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/dna-partitions-into-triplets-under-tension-in-the-presence-of-organic-cations-with-sequence-evolutionary-age-predicting-the-stability-of-the-triplet-phase/181399C9E333C317EE1C18764471FCE9
Commentary :	Supplementary data on journal site.

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	Fulltext file(s): File Commentary Version Size Access Open access taghavi_vanderSchoot_Berryman_qrbp-d_2017.pdf Full version is free on publishers website Author preprint 8.86 MB View/Open

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