Reparametrizing the loop entropy weights: Effect on DNA melting curves

Abstract

Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior loop melting. So far, in the modeling of DNA melting, the entropy of denaturated loops has been estimated from the number of configurations of a closed self-avoiding walk. It is well understood now that a loop embedded in a chain is characterized by a loop closure exponent c which is higher than that of an isolated loop. Here we report an analysis of DNA melting curves for sequences of a broad range of lengths (from 10 to 10 6 base pairs) calculated with a program based on the algorithms underlying MELTSIM. Using the embedded loop exponent we find that the cooperativity parameter is one order of magnitude bigger than current estimates. We argue that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.

Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation

“…With all other factors being equal, adding loop entropy and strand sliding increases the stability of the closed state, resulting in sharper melting curves and higher values of T m (N ) (see Figs. 9 and 10 of [4] and [40]). The importance of this loop entropy contribution would change with chain length N and may lead to an increase in T m (N ) with increasing N [14] at least for a certain range of chain sizes .…”

“…9 of [4], effective Ising models without loop entropy, like ours, can be considered to account implicitly (and approximately) for loop entropy, provided that one allows for loop entropy contributions to both J and K. This loop entropy renormalization of the Ising model parameters will depend on the value of the loop entropy exponent k and the chain length N and could allow for a simple approximate way of accounting for the influence of loop entropy within the framework of an effective Ising model (cf. [40]). This renormalization probably explains why our the model value for σ LI is at the low end of the accepted spectrum.…”

“…The matrix elements appearing in the above expressions can be found explicitly using Eqs. (11), (39), and (40). The Pauli matrixσ z , which can be interpreted as a quantum mechanical dipole moment operator, is diagonal in the canonical basis, |U = | + 1 and |B = | − 1 [see Eq.…”

Dynamic Approach to DNA Breathing

“…2 To interrupt the double helix to initiate a bubble, that is bordered by helical domains (compare Figure 2), co-operative interactions have to be overcome, to release base-stacked and paired nucleotides. This is expressed by an additional weight σ 0 ≡ exp(−γ 0 ), and varies between a few 10 −2 to 10 −5 , for different temperatures [11,12,17,18]. Finally, the formation of a flexible bubble includes an entropy loss corresponding to the returning probability of a random walk [3,[11][12].…”

Renewal Sequences, Disordered Potentials, and Pinning Phenomena

“…We note that inhomogeneous or disordered modeling is really required in this context, because the pinning strength does depend on the type of base pair, see Figure 2. The renewal pinning model with inhomogeneous charges has been and is extensively used for the study of DNA denaturation [11,17]: appropriate values of α are close to 1.15. Figure 2.…”