Bubble Nucleation and Cooperativity in DNA Melting

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles, and the possibility of a two-state transition are studied.

Figure 1

Melting profiles for the bubble-in-the-middle sequences [3, 4, 5]. Filled circles are $p$, open circles are $f$, and squares are $l$.

Figure 2

Upper figure: $\sigma =f-p$ vs $T$ for L60B36 (circles, upper curve), L42B18 (squares, middle curve), and L33B9 (diamonds, lower curve) [3, 4, 5]. Lower figure: ${\sigma }_{\mathrm{a}\mathrm{v}}$ vs the length, $L$, of the molecule.

Figure 3

Melting profile for the L48AS and L19AS_2 sequences. Symbols are as in Fig. 1.

Figure 4

Upper figure: $\sigma =f-p$ vs $T-T_m$ ($T_m$ is the melting temperature) for L48AS (circles, top curve), L36AS (squares, second curve from top), L30AS (diamonds, third curve from top), L24AS (up triangles, second curve from bottom), and L19AS_2 (down triangles, bottom curve) [3, 4, 5]. Lower figure: ${\sigma }_{\mathrm{a}\mathrm{v}}$ vs $L$, the molecule’s length.