Εξειδίκευση τύπου :	Άρθρο σε επιστημονικό περιοδικό
Τίτλος:	Temperature dependence of the dna double helix at the nanoscale: Structure, elasticity, and fluctuations
Δημιουργός/Συγγραφέας:	Meyer S. Jost D. [EL] Θεοδωρακόπουλος, Νίκος[EN] Theodorakopoulos, Nikos Peyrard M. Lavery R. Everaers R.
Ημερομηνία:	2013
Γλώσσα:	Αγγλικά
ISSN:	0006-3495
DOI:	10.1016/j.bpj.2013.09.004
Άλλο:	PubMed ID: 24138866
Περίληψη:	Biological organisms exist over a broad temperature range of -15 C to +120 C, where many molecular processes involving DNA depend on the nanoscale properties of the double helix. Here, we present results of extensive molecular dynamics simulations of DNA oligomers at different temperatures. We show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of the DNA melting pathway. The basepair step elasticity contains a weaker, but detectable, entropic contribution in the roll, tilt, and rise degrees of freedom. To extend the validity of our results to the temperature interval beyond the standard melting transition relevant to extremophiles, we estimate the effects of superhelical stress on the stability of the basepair steps, as computed from the Benham model. We predict that although the average twist decreases with temperature in vitro, the stabilizing external torque in vivo results in an increase of ∼1 /bp (or a superhelical density of Δσâ‰+0.03) in the interval 0-100 C. In the final step, we show that the experimentally observed apparent bending persistence length of torsionally unconstrained DNA can be calculated from a hybrid model that accounts for the softening of the double helix and the presence of transient denaturation bubbles. Although the latter dominate the behavior close to the melting transition, the inclusion of helix softening is important around standard physiological temperatures.
Τίτλος πηγής δημοσίευσης:	Biophysical Journal
Τόμος/Κεφάλαιο:	105
Τεύχος:	8
Σελίδες:	1904-1914
Θεματική Κατηγορία:	[EL] Φυσική και θεωρητική χημεία[EN] Physical and theoretical chemistry [EL] Ατομική φυσική (συμπ. μοριακή φυσική, σχετικότητα, κβαντική θεωρία και φυσική στερεάς κατάστασης)[EN] Atomic physics (Incl. molecular physics, relativity, quantum theory, and solid state physics)
Αξιολόγηση από ομότιμους (peer reviewed):	Ναι
Κάτοχος πνευματικών δικαιωμάτων:	© 2013 Biophysical Society.
Όροι και προϋποθέσεις δικαιωμάτων:	All Open Access, Bronze, Green
Σημειώσεις:	ANR-12-BSV5-0009-01, ANR-12-BSV5-0017-01; Agence Nationale de la Recherche, ANR
Εμφανίζεται στις συλλογές:	Ινστιτούτο Θεωρητικής και Φυσικής Χημείας (ΙΘΦΧ) - Επιστημονικό έργο