In solutions of hydrated SO 2 it is well-known that both the bisulfite ion HOSO 2 -and the sulfonate ion HSO 3 -are present whereas the sulfonate form prevails in some salts. Here we show by ab initio and transition state theory considerations how the mechanism of sulfonate formation works. In aqueous solution, dissolved SO 2 first forms a bisulfite ion which is in a next step converted into the sulfonate ion. Direct formation of the sulfonate ion is kinetically hindered due to a very high reaction barrier for this process. Tautomerization of the bisulfite ion into the sulfonate ion is catalyzed by water molecules. Insight into this process is vital in understanding the formation of sulfonate salts upon crystallization from aqueous solution.

We have examined the backbone dynamics of two alternating purine-pyrimidine dodecamers. One sequence consists of "pure" GC bases; the other one contains 5-methylcytosines. The effect of the methyl groups on the backbone substates BI/BII was investigated by means of molecular dynamics. The methylation influences, on one hand, the transition barrier between BI and BII and, on the other hand, the state of equilibrium. The kinetic consequences are an increase of the DeltaG of Gp5mC steps by 1.5 kcal/mol and a decrease of the DeltaG of 5mCpG steps by 0.8 kcal/mol (compared with the nonmethylated DNA). Thus, the additive group differentiates between the two occurring dinucleotide steps and renders the phosphate of the 5-methylcytosine more rigid, as proposed by experimental studies. The thermodynamic consequences are an increase of the DeltaG of Gp5mC steps by 1.1 kcal/mol and a decrease of the DeltaG of 5mCpG steps by 0.8 kcal/mol. The reason for this shift in equilibrium is still not completely clear on a molecular basis. But we can conclude that the indirect readout of DNA is influenced by methylation.

In the present study, we try to determine if the dynamics of the B-DNA backbone phosphates (and especially their interconversions between their two distinct conformations B I and B II ) are fast enough to be sufficiently sampled in the course of molecular dynamics simulations in the nanosecond time range. For this purpose, we performed twelve 10-ns simulations of the Drew-Dickerson dodecamer d(CGCGAATTCGCG) 2 to investigate the dynamics of B I /B II interconversion. We forced the DNA backbone angles and with restraints to values that are characteristic for B I and B II , resulting in DNA double helices with all phosphates in the B I or B II substate. These restraints were removed after 10 ns, and unrestrained simulations at temperatures of 250, 275, 287.5, 300, and 325 K were performed for another 10 ns, which allowed us to analyze the dynamics of relaxation in detail. These simulations were compared to simulations of the undisturbed dodecamer at 250 and 300 K, as a reference for the equilibrated state. We found that the relaxation from the B II state is considerably fast, with high rate constants, and is dependent on temperature. From this temperature dependence of the rate constants, we calculated the activation energy necessary for the B II to B I transition to be 2.5 kcal/mol. Half-life times of the B II state derived from the relaxation process are in the range of 110-370 ps, which indicates that a simulation time of 10 ns is sufficiently long to investigate conformational transitions of the DNA backbone. The structures of the all-B I DNA are more similar to structures found for the DrewDickerson dodecamer by X-ray crystallography than the all-B II DNA. This fact is not astonishing, because the B I conformation has been observed to be privileged. Nevertheless, both structures are quite different from canonical A-or B-DNA. That observation is revealing, because we expected the all-B II DNA to be the transition state to canonical A-DNA or at least structurally very similar. Furthermore, we find that the relaxation of our rather-distorted starting structures is fast and, despite the large difference at the beginning, leads to a similar equilibrium, which, again, is similar to the undisturbed simulation.

Ligands which are able to recognize DNA sequence specifically are of fundamental interest as transcription controlling drugs. Recently a polyamide ligand was developed (ImHpPyPy-beta-Dp) which differentiates in a dimeric arrangement between all four possible base pair steps in the minor groove. This is a landmark for the design of DNA binding drugs because it was believed that such a recognition could only be possible in the major groove of DNA. Although the OH groups of the hydroxypyrrole (Hp) moieties of the ligands are responsible for this sequence discrimination, experiments showed that this OH group also reduces the absolute binding constant. We performed a free energy calculation by means of thermodynamic integration in order to find out the influence of this single hydroxyl on DNA binding. In our simulation, we found that the hydroxyl group reduces binding by about 1.3 kcal/mol, which is in excellent agreement with the experimentally determined value of 1.2 kcal/mol. In further MD simulations, the structural reasons for this reduction was estimated. The results of these simulations qualitatively agree with the X-ray structures, but in contrast, in the simulations both (ImHpPyPy-beta-Dp and ImPyPyPy-beta-Dp) ligand-DNA (d(CCAGTACTGG)(2)) complexes exhibit only slight structural differences. This is consistent with a recently published second pair of similar polyamide DNA crystal structures. Thus, we believe that the explanations resulting from the X-ray structures must be modified. We attribute the large structural differences between the two polyamide DNA complexes to a buffer molecule which binds only in the case of the ImHpPyPy-beta-Dp-DNA complex at the region of interest. We propose that the differential hydration of both ligands in the unbound state is responsible for the reduction of the binding constant. Additionally, we suggest an indirect readout of DNA, because of a lengthening of the Watson-Crick base pairs, which possibly contributes to the differentiation between T.A, A.T from G.C, C.G base pairs.

Methylated DNA bases are natural modifications which play an important role in protein-DNA interactions. Recent experimental and theoretical results have shown an influence of the base modification on the conformational behavior of the DNA backbone. MD simulations of four different B-DNA dodecamers (d(GC)(6), d(AT)(6), d(G(5mCG)(5)C), and d(A(T6mA)(5)T)) have been performed with the aim to examine the influence of methyl groups on the B-DNA backbone behavior. An additional control simulation of d(AU)(6) has also been performed to examine the further influence of the C5-methyl group in thymine. Methyl groups in the major groove (as in C5-methylcytosine, thymine, or N6-methyladenine) decrease the BII substate population of RpY steps. Due to methylation a clearer distinction of the BI substate stability between YpR and RpY (CpG/GpC or TpA/ApT) steps arises. A positive correlation between the BII substate population and base stacking distances is seen only for poly(GC). A methyl group added into the major groove increases mean water residence times around the purine N7 atom, which may stabilize the BI substate by improving the hydration network between the DNA backbone and the major groove. The N6-methyl group also forms a water molecule bridge between the N6 and O4 atoms, and thus further stabilizes the BI substate.