Direct comparison of theoretical and experimental melting profiles for RFII ΦX174 DNA

Abstract

The determination by Sanger et al. of the comple nucleotide sequence for phiX174 DNA has made it possible for the first time to compare directly theoretical and experimental DNA melting profiles. The comparison shows that the theory predicts the observed shape of the differential melting curve surprisingly well. Calculation of the denaturation maps allows the peaks on the curve to be correlated with cooperative melting out of concrete regions on the sequence of nucleotides.

Statistical Physics of Unzipping DNA

“…A reasonable guess for more realistic models with heterogeneity is that while the transition may be less sharp (weakly bound regions melt before more tightly bound ones), a real finite temperature phase transition survives. Lyubchenko et al [23] have calculated numerically the effect of sequence heterogeneity on the DNA differential melting curves for the 5375 nucleotides of the virus φX174. For a recent theory of thermal denaturation of heterogeneous DNA, see…”

“…The effect of sequence heterogeneity on thermal denaturation of DNA at zero force is a subtle and still not completely resolved problem, [19,23,24]. Understanding inhomogeneous base pairing energies near the first-order force-induced unzipping transition appears to be more tractable.…”

Premelting of superhelical DNA: an expression for superhelical energy

“…The calculations were performed using the algorithm in [10]. We used the thermodynamic parameters of linear DNA corresponding to the conditions in [7,8]: melting temperature of AT-pairs TAT = 16°C; melting temperature of GC-pairs TGC = 58°C; the enthalpy of melting of AT pairs UAT = 7.1 kcal/mol, corresponding to the melting temperature observed; cooperatively factor 0 = 5 × 10-s, loop weighting factor ~ = 3/2, as usual (see, e.g., [18]). As the sequence ofPM2 DNA is unknown, we used in our calculation the sequence of ¢X174 DNA [19] which has nearly the same GC-content.…”

Unzipping DNA from the condensed globule state—Effects of unraveling

“…In this way the response of single DNA molecules to external torques [13,14] and its mechanical unzipping in the absence of enzymes [15][16][17][18][19] have been studied. The latter topic has only recently been subjected to theoretical investigations [20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35], while the theoretical studies of thermal denaturation of DNA have even a much longer history [36][37][38][39][40][41][42][43][44][45][46][47]. Understanding DNA denaturation under conditions of constant force could provide insights into the complicated process by which DNA replicates during bacterial cell division [48].…”