Melting of Cross-Linked DNA: II. Influence of Interstrand Linking on DNA Stability

Abstract

In the previous paper (D.Y. Lando, J. Biomol. Struct. Dynam, 15, 129-140 (1997)) the melting of cross-linked DNA with N base pairs and omega interstrand cross-links has been considered theoretically. In the present study on the basis of these results, two simple schemes are developed for the computation of melting curves of cross-linked DNA. The investigation of influence of interstrand linking on DNA stability has been carried out by computer simulation. It is shown that the relative concentration of cross-links, CCT = omega/N, their distribution along a DNA molecule, and particular values of the entropy factors of small loops formed by cross-links in melted regions strongly affect the DNA melting temperature, Tm. On the contrary, for DNA without cross-links, a ten-fold increase or decrease in the entropy factors of small loops does not cause the Tm variation. The comparison of the results of calculation with experimental data suggests that the majority of types of cross-link neither maintain ordered parallel orientation of bases in melted regions nor increase considerably the thermostability of cross-linked base pairs. Four different ways of influence of interstrand cross-linking on the DNA double helix stability are considered. It is shown that cross-linking significantly enhances the influence of single strand stiffness in melted regions on DNA melting behavior.

DNA Damage Induced by Gamma-Radiation Revealed from UV Absorption Spectroscopy

“…The helix-coil transition of DNA is very sensitive to the state of secondary structure of the macromolecule, to its interaction with biologically active agents, and also to defects of the primary structure of DNA [21][22][23][24] Table 3. An example of DNA melting curves and their first derivatives in the control solution (before irradiation) and after the expose to γ-radiation with the dose of 30 Gy at the different dose rates are presented in the Figure 2.One can see that at this dose the melting temperatures T m of irradiated DNA are equal with the accuracy of the experimental error ( Table 3).As it was expected T m in the solutions of μ=0.15 M are larger than T m in the solutions of μ=0.005 M, which indicates the stabilization of DNA secondary structure by counterions.…”

“…But the radiation effect on T m does not repeat the pattern observed in our previous results. At μ=0.15 M the relative decrease of T m after the irradiation is slightly bigger than at μ=0.005 M. Considering the possible DNA lesions in irradiated solutions we can divide them on two groups: 1) the lesions which decrease T m (SSB, DSB, destruction, modification and release of nucleobases) and 2) the lesions which increase T m (inter-or intramolecular crosslinks) [19,23]. We suppose that we observe the combined influence of these two groups of lesions on the DNA melting temperature.…”

Role of small loops in DNA melting

“…This representation we have already used for consideration of melting of cross-linked DNA. 1,2,31,32 Let us a DNA chain contains N units (base pairs) that are numbered from left to right by m ϭ 1, . .…”

“…(1) for ␣ ϭ 1.7 were determined earlier. 1 DNA sequences for X GC ϭ 50% are produced with a random number generator.…”

“…1,2 However in the absence of cross-links, the probability of formation of melted regions of length less than 100 base pairs is usually low for natural DNA for which base pair distribution is uniform. 3,4 Therefore, peaks corresponding to this size are rarely found in differential melting curves (DMCs).…”