Article (Scientific journals)
DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
Taghavi, Amirhossein; van der Schoot, Paul; Berryman, Josh
2017In Quarterly Reviews of Biophysics, 50
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Keywords :
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 center :
ULHPC - University of Luxembourg: High Performance Computing
Disciplines :
Genetics & genetic processes
Physical, chemical, mathematical & earth Sciences: Multidisciplinary, general & others
Biochemistry, biophysics & molecular biology
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
External co-authors :
yes
Language :
English
Title :
DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
Publication date :
November 2017
Journal title :
Quarterly Reviews of Biophysics
ISSN :
1469-8994
Publisher :
Cambridge University Press
Volume :
50
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Physics and Materials Science
Name of the research project :
R-AGR-0136 - IRP13 - NANOMECH (20140315-20170314) - BERRYMAN Josh
Commentary :
Supplementary data on journal site.
Available on ORBilu :
since 20 November 2017

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