Modelling the Extensionally Driven Transitions of DNA

Empirical measurements on DNA under tension show a jump by a factor of
≈ 1.5 − 1.7 in the relative extension at applied force of ≈ 65 − 70 pN, indi-
cating a structural transition. The still ambiguously characterised stretched
‘phase’ is known as S-DNA. Using atomistic and coarse-grained Monte Carlo
simulations we study DNA over-stretching in the presence of organic salts
Ethidium Bromide (EtBr) and Arginine (an amino acid present in the RecA
binding cleft). We present planar-stacked triplet disproportionated DNA as
a solution phase of the double helix under tension, and dub it ‘Σ DNA’, with
the three right-facing points of the Σ character serving as a mnemonic for
the three grouped bases. Like unstretched Watson-Crick base paired DNA
structures, the structure of the Σ phase is linked to function: the partitioning
of bases into codons of three base-pairs each is the first stage of operation
of recombinase enzymes such as RecA, facilitating alignment of homologous
or near-homologous sequences for genetic exchange or repair. By showing
that this process does not require any very sophisticated manipulation of
the DNA, we position it as potentially appearing as an early step in the de-
velopment of life, and correlate the postulated sequence of incorporation of
amino acids (GADV then GADVESPLIT and then the full 20 residue set of
canonical amino acids) into molecular biology with the ease of Σ-formation
for sequences including the associated codons. To further investigate the de-
pendence of stretching behaviour on the concentration of intercalating salt
molecules, we present a physically motivated coarse-grained force-field for
DNA under tension and use it to qualitatively reproduce regimes of force-
extension behaviour which are not atomistically accessible.