Melting of Crosslinked DNA: VI. Comparison of Influence of Interstrand Crosslinks and Other Chemical Modifications Formed by Antitumor Compounds on DNA Stability

Abstract

A computer modeling of thermodynamic properties of a long DNA of N base pairs that includes omega interstrand crosslinks (ICLs), or omega chemical modifications involving one strand (monofunctional adducts, intrastrand crosslinks) has been carried out. It is supposed in our calculation that both types of chemical modifications change the free energy of the helix-coil transition at sites of their location by deltaF. The value deltaF>0 corresponds to stabilization, i.e., to the increase in melting temperature. It is also taken into account that ICLs form additional loops in melted regions and prohibit strand dissociation after full DNA melting. It is shown that the main effect of interstrand crosslinks on the stability of long DNA's is caused by the formation of additional loops in melted regions. This formation increases DNA melting temperature (Tm) much stronger than replacing omega base pairs of AT type with GC. A prohibition of strand dissociation after crosslinking, which strongly elevates the melting temperature of oligonucleotide duplexes, does not influence melting behavior of long DNA's (N>or=1000 bp). As was demonstrated earlier for the modifications involving one or the other strand, the dependence of the shift of melting temperature deltaTm on the relative number of modifications r=omega/(2N) is a linear function for any deltaF, and deltaTm(r) identical with 0 for the ideal modifications (deltaF=0). We have shown that deltaTm(r) is the same for periodical and random distribution if the absolute value of deltaF is less 2 kcal. The absolute value of deltaTm(r) at deltaF>2 kcal and deltaF<-2 kcal is higher for periodical distribution. For interstrand crosslinks, the character of the dependence deltaTm(r) is quite different. It is nonlinear, and the shape of the corresponding curve is strongly dependent on deltaF. For "ideal" interstrand crosslinks (deltaF=0), the function deltaTm(r) is not zero. It is monotone positive nonlinear, and its slope decreases with r. If r<0.004, then the entropy stabilizing effect of interstrand crosslinking itself exceeds the influence of a distortion of the double helix at sites of their location. The resulting deltaTm(r) is positive even in the case of the infinite destabilization at sites of the ICLs (deltaF-->-infinity). In general, stabilizing influence of interstrand crosslinks is almost fully compensated for by local structural distortions caused by them if 0<r<0.01 and -infinity<deltaF< approximately -5 kcal per mole of ICLs. The absolute value of deltaTm(r) in this case is approximately 10 times lower than for ideal ICLs as well as for local destabilization without crosslinking. Interstrand crosslinks formed by cisplatin do not change the melting temperature of long DNA's because of this compensation effect.

DNA‐Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences

“…In comparison, nitrogen mustards induce 1 to 5% of inter-strand crosslinks, whereas nitrosourea and mitomycin C induce 2 to 8% and 5 to 13%, respectively, [93–95]. C isplatin -induced intra-strand crosslinks at GpG base pairs result in (i) bending of the DNA axis toward the major groove with an angle of 55–78°, and (ii) DNA distortion, enabling local denaturation of the double helix via destabilization of the Watson-Crick base pairing [96–102]. In comparison, the bending angle for inter-strand crosslinks is 45° and is associated with DNA unwinding of 79 ± 4°.…”

Temporal behavior of DNA thermal stability in the presence of platinum compounds. Role of monofunctional and bifunctional adducts

“…At the r = 0.05 value used in this study, their per nucleotide number is 0.003 and 0.006. As follows from our recent calculations [49,66,77], interstrand crosslinks of the relative concentration 0.003 increase melting temperature of long DNA by 1.3°C if they do not cause distortions at sites of their location and by 1.6°C in the case of strong local stabilization. This corresponds to approximately 10% of the total change in δT m caused by all final modifications of cisplatin in alkaline medium (~12°C, Fig.…”

“…For [Pt(dien)Cl]Cl and transplatin, the value of δT m is positive at low [Na + ] and tends to zero at [Na + ]= 0.1-0.2 M. Even more surprising is the observation that [Pt(dien)Cl]Cl and transplatin complexes with long DNAs demonstrate the same melting behavior in neutral medium in spite of different final adducts [23,35]. The absence or low value of a decrease in thermal stability under platination of long DNAs can be caused by two effects that compensate thermal destabilization originating from structural distortions [35,49,66]. First, all modifications decrease DNA charge density, and therefore they stabilize the double helix [35,49,67].…”

“…Therefore, the thermal stabilization is also stronger for long molecules. Second, as shown from our studies [49,66], interstrand crosslinking can increase thermal stability of long DNAs under some conditions. As a result, the total thermal destabilizing effect of cisplatin is not large in neutral medium in spite of the strong structural distortions it causes in DNA (see [49,66] and Fig.…”

“…From the data on melting of oligonucleotide duplexes [39], one can obtain that local distortions formed by cisplatin and transplatin interstrand crosslinks give rise to the following change in the free energy (kcal/mol duplexes) of the helix-coil transition: δG=-18+0.037⋅T K and δG =-2-0.015⋅T K, respectively. Our calculations [49,66,78] demonstrate that, in long DNA, such interstrand crosslinks cause a very small change in thermal stability (less than 0.3°C). These estimations are valid for alkaline medium where a stabilizing electrostatic effect is eliminated that makes the situation similar to the case of oligonucleotide duplexes.…”