Reference : DNA partitions into triplets under tension in the presence of organic cations, with s...
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Life sciences : Genetics & genetic processes
Physical, chemical, mathematical & earth Sciences : Multidisciplinary, general & others
Physics and Materials Science
http://hdl.handle.net/10993/33076
DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
English
Taghavi, Amirhossein mailto [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 mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
Nov-2017
Quarterly Reviews of Biophysics
Cambridge University Press
50
Yes (verified by ORBilu)
International
0033-5835
1469-8994
[en] DNA ; GNC ; arginine ; DNA stretching ; Sigma DNA ; S-DNA
[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.
University of Luxembourg: High Performance Computing - ULHPC
Researchers ; Professionals ; Students ; General public
http://hdl.handle.net/10993/33076
10.1017/S0033583517000130
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
Supplementary data on journal site.

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Limited access
taghavi_vanderSchoot_Berryman_qrbp-d_2017.pdfFull version is free on publishers websiteAuthor preprint8.86 MBRequest a copy

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.