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SUMMARY:Thermomechanical Mapping of DNA under Coupled Salt-Temperature Con
 trol with oxDNA2 Coarse-Grained Simulations
DTSTART;VALUE=DATE-TIME:20260327T111000Z
DTEND;VALUE=DATE-TIME:20260327T113000Z
DTSTAMP;VALUE=DATE-TIME:20260426T093155Z
UID:indico-contribution-10343@events.saip.org.za
DESCRIPTION:Speakers: Isaiah Igwe (Federal University Dutsin-Ma)\nQuantify
 ing how temperature and ionic strength jointly determine the elastic prope
 rties of double-stranded DNA remains a central challenge in molecular biop
 hysics. Although individual temperature or salt dependent trends have been
  measured\, a unified\, mechanistic map across high-salt and elevated-temp
 erature regimes is still lacking. Here\, we use the oxDNA2 coarse-grained 
 model to compute a 3×9 thermodynamic ionic grid spanning 300 –373 K and
  0.5 – 1.5 M monovalent salt\, enabling controlled evaluation of elastic
  properties and structural observables under conditions where electrostati
 c screening is extremely strong. Simulations were performed on long 500-bp
  duplexes with full ensemble averaging over independent replicate trajecto
 ries at each condition. Across all salt concentrations\, DNA softens as te
 mperature increases\, but the degree of softening depends on ionic strengt
 h. At 0.5 M\, the bending persistence length drops from about 43 nm at 300
  K to 32 nm at 373 K. At 1.5 M\, the decrease is far smaller (46 → 39 nm
 )\, showing that high salt reduces thermal sensitivity by roughly 40–50%
 . Torsional stiffness shows the same pattern (110 → 92 units at 0.5 M vs
 . 118 → 105 units at 1.5 M)\, as does twist–stretch coupling\, which c
 hanges by 0.7 units at low salt but only 0.4 units at high salt. Helical t
 wist decreases by roughly 1.1–1.3° per kbp per 10 K at 0.5 M\, with a v
 isibly weaker dependence at 1.5 M. While both bending and torsional rigidi
 ties soften with temperature\, torsional elasticity remains closer to harm
 onic behavior than bending\, with anharmonic deviations staying below ~10%
  even at the highest temperatures. Structural measures\, including base-pa
 ir occupancy and stacking energies\, show that the duplex remains intact u
 p to about 95 –100 °C\, with only limited end fraying. Beyond quantifyi
 ng these trends\, the present work introduces a unified thermodynamic inte
 rpretation of DNA elasticity. The simulations demonstrate that the weakeni
 ng of base-stacking interactions precedes significant hydrogen-bond disrup
 tion and acts as the primary microscopic driver of thermoelastic softening
 . This perspective provides a compact statistical-mechanical description o
 f DNA thermoelasticity and helps reconcile observations from coarse-graine
 d simulations\, atomistic molecular dynamics\, and single-molecule experim
 ents.\n\nhttps://events.saip.org.za/event/272/contributions/10343/
LOCATION:
URL:https://events.saip.org.za/event/272/contributions/10343/
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