A Raman scattering study of the interactions of DNA with its water of hydration

Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The ～ 3450?cm^?1 molecular O–H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for these water molecules. These hydrogen bonds appear to be about 0.3?Å shorter than the hydrogen bonds in bulk water. The linewidth of this mode shows no significant changes above water contents of about 15 water molecules per base pair. This technique of using a vibrational spectroscopy to obtain structural information about the hydration shells of DNA could be used to study the hydration shells of other biomolecules.     

Changes of hydration during conformational transitions of DNA

Fiber X-ray diffraction and measurement of fiber dimensions yields information about the hydration of DNA in fibers. The results obtained give us the fraction of nucleotides in the B form for the A-B transition or the rate of progression for the B-C transition as functions of the number of water molecules per nucleotide. The present experimental results confirm the importance of cooperativity in the A-B transition and the progressive change of the DNA double helix conformation during the C-B transition. At least twenty additional water molecules per nucleotide are necessary to stabilize the B form for DNA molecules in fibers following the A to B transition whereas only ten are sufficient when the B conformation is obtained starting from the C form. Offprint requests to: S. Premilat     

Temperature dependence of dielectric constant at 10 GHz of Na-DNA gels

Permittivity ε′ and dielectric loss ε″ of aqueous Na-DNA gels have been measured at 10 GHz in the temperature interval ?15 to + 45°C. The experimental results are analyzed in terms of a three-component equation (Na-DNA, interfacial water, bulk water) and yield a value of 35 water molecules/nucleotide interacting with DNA. According to theoretical and experimental data the presence of strongly bonded and weakly bonded water is considered. The modified water exhibits a mean dielectric relaxation time two-or threefold greater than that of bulk water.     

Ultrafast interfacial solvation dynamics in specific protein DNA recognition

An overwhelming number of structural and functional studies on specific protein–DNA complexes reveal the existence of water molecules at the interaction interface. What role does the interfacial water molecules play in determining the specificity of association is thus a critical question. Herein, we have explored the dynamical role of minor groove water molecules and DNA side chain flexibility in lambda repressor–operator DNA interaction using well-characterized DNA minor groove binder dye, Hoechst 33258. The most striking finding of our studies reveals that the solvation time scale corresponding to the minor groove water molecules (∼50 ps) and DNA side chain flexibility (∼10 ns) remain unaltered even in protein–DNA complex in comparison to unbound operator DNA. The temperature dependent study further reveals the slower exchange of minor grove water molecules with bulk water in DNA–protein complex in comparison to the unbound DNA. Detailed structural studies including circular dichroism (CD) and Förster resonance energy transfer (FRET) have also been performed to elucidate the interaction between protein and DNA.     

Concentration-dependent effects on fully hydrated DNA at terahertz frequencies

Using terahertz time-domain spectroscopy (THz-TDS), the frequency-dependent dielectric constant of deoxyribonucleic acid (DNA) in solution was measured. The response of the buffer solution is dominated by two Debye modes in this frequency range, and, from an analysis of the concentration dependence, the presence of the DNA increases the main relaxation time and dielectric constant. This reflects the fact that the water in the hydration layer is more tightly bound under the influence of the DNA molecule in comparison to bulk water. This dynamical slowing down with increasing DNA concentration is similar to what is observed with purine nucleotides, but opposite to the behavior of pyrimidine nucleotides. In addition, a suspension model was used with the concentration-dependent data to isolate the dielectric response of the hydrated DNA molecule. The data for the hydrated DNA molecule is still dominated by a Debye response. It is also possible to determine the thickness of the hydration layer, and the DNA molecule influences the surrounding water out to 16 or 17 Å, which corresponds to about six effective hydration layers.     

Interaction of Topotecan,DNA Topoisomerase I Inhibitor,with Double-Stranded Polydeoxyribonucleotides. 2. Formation of Topotecan–DNA Complex Containing Several DNA Molecules

This study is a continuation of a series of papers dealing with topotecan interaction with double-stranded polydeoxyribonucleotides. We showed earlier that topotecan molecules form dimers in solution at concentration above 10^–5(per base pair). Topotecan interaction with calf thymus DNA in solutions of low ionic strength was studied by fluorescence, circular dichroism, and linear flow dichroism. The data obtained indicate that topotecan forms two types of complex with DNA, DNA molecules combining with each other during formation of one of these complexes. The association constant of two topotecan-filled DNA molecules with each other was estimated at 10⁴M^–1(per base pair) in 1 mM sodium cacodylate buffer, pH 6.8, at 20°C. A possibility of modulation of DNA topoisomerase I activity by topotecan due to complexation with several sites of a supercoiled DNA molecule is discussed.     

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure

Molecular dynamics (MD) computer simulations have been carried out on four systems that correspond to an infinite array of parallel ordered B-DNA, mimicking the state in oriented DNA fibers and also being relevant for crystals of B-DNA oligonucleotides. The systems were all comprised of a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charges. The sequence of the double helical DNA decamer was d(5'-ATGCAGTCAG)xd(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine(3+) (Spd(3+)) and putrescine(2+) (Put(2+)), the synthetic polyamine diaminopropane(2+) (DAP(2+)), and the simple monovalent cation Na(+). This work compares the specific structures of the polyamine- and Na-DNA systems and how they are affected by counterion interactions. It also describes sequence-specific hydration and interaction of the cations with DNA. The local DNA structure is dependent on the nature of the counterion. Even the very similar polyamines, Put(2+) and DAP(2+), show clear differences in binding to DNA and in effect on hydration and local structure. Generally, the polyamines disorder the hydration of the DNA around their binding sites whereas Na(+) being bound to DNA attracts and organizes water in its vicinity. Cation binding at the selected sites in the minor and in the major groove is compared for the different polyamines and Na(+). We conclude that the synthetic polyamine (DAP(2+)) binds specifically to several structural and sequence-specific motifs on B-DNA, unlike the natural polyamines, Spd(3+) and Put(2+). This specificity of DAP(2+) compared to the more dynamic behavior of Spd(3+) and Put(2+) may explain why the latter polyamines are naturally occurring in cells.     

Effect of a mechanical tension on the hydration of DNA in fibres.

Fiber X-ray diffraction and measurement of fibre dimensions yield information about the effects of a mechanical tension on hydration of DNA in fibres. At a given relative humidity, the mechanical tension changes the DNA conformation but does not modify the number of water molecules associated to a nucleotide. The number of water molecules per nucleotide necessary to maintain B form decreases for increasing tensions applied to the DNA fibre. Form transitions can be opposed by mechanical tensions; an energy of 1 Kcal per mole of nucleotide pairs is sufficient to prevent the B to A transition.     

Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model

When proteins bind to their DNA target sites, ordered water molecules are often present at the protein–DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein–DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA‐bound water molecules, while treating the majority of the solvent implicitly. Comparing the performance of this model with that of its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein side‐chain placement and DNA sequence recovery. Base‐by‐base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large‐scale statistical evidence for the role of ordered water for protein–DNA recognition, together with detailed examination of several well‐characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems. Proteins 2013; 81:1318–1329. © 2013 Wiley Periodicals, Inc.     

Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration.

The data and approach reported in paper I (Hanlon et al., 1975, preceding paper) have been used to calculate the fractional changes in secondary structure of calf thymus deoxyribonucleic acid which occur in aqueous solutions as a function of the concentration of NaCl, KCl, LiCl, CsCl, and NH4Cl. There is a continuous loss in the "B" character of the nucleic acid with concomitant production of the C and, in some instances, an A form, as well, as the salt concentration increases. Sedimentation velocity studies suggest that there is an accompanying change in the hydrodynamic characteristics of the DNA molecules, as well. Utilizing the existing hydration data in the literature (Hearst and Vinograd, 1961a,b; Hearst, 1965; Tunis and Hearst, 1968a; Cohen and Eisenberg, 1968; Falk et al., 1962, 1963a,b), we have found that a gradual loss of "B" character and a decrease in the frictional coefficient of DNA occur as the net hydration of DNA is reduced from the fully hydrated from (60-80 mol of H2O/mol of nucleotide) to values of ca. 12-14 mol of H2O/mol of nucleotide. Below that value, a more precipitous decrease in these properties occurs. Extrapolation of the linear relationship observed between the fractional B content and the net hydration in the latter regions yield values of ca. 18 mol of H2O/mol of nucleotide at 100% B and ca. 4 mol of H2O/mol of nucleotide at 0% B (i.e., 100% C or C + A) for the alkali metal salts of DNA. The ammonium salt retains somewhat more H2O in the C and A forms (ca. 7). These results together with the hydration site assignments of Falk et al. (1962, 1963a,b) are interpreted in terms of a hydration model for DNA in aqueous solution in which an intact primary hydration shell of ca. 18 mol of H2O/mol of nucleotide is required for the maintenance of the "B" conformation. Removal of all but those water molecules solvating the phosphate groups results in the conversion to the C forms, predominantly, with a small amount of A structure formed as well in some salts. The accompanying changes in the sedimentation coefficients suggest that the DNA molecule assumes a more compact and/or flexible form under these conditions in which it is mainly in the C and A structures. The combination of these two events which ensue upon dehydration create a polymeric structure which can be more easily packaged in biological systems.     

Radiation-induced DNA damage as a function of hydration. I. Release of unaltered bases.

The release of unaltered bases from irradiated DNA, hydrated between 2.5 and 32.7 mol of water per mole of nucleotide (gamma), was investigated using HPLC. The objective of this study was to elucidate the yield of the four DNA bases as a function of dose, extent of hydration, and the presence or absence of oxygen. The increase in the yield of radiation-induced free bases was linear with dose up to 90 kGy, except for the DNA with gamma = 2.5, for which the increase was linear only to 10 kGy. The yield of free bases as a function of gamma was not constant in either the absence or the presence of oxygen over the range of hydration examined. For DNA with gamma between 2.5 and 15, the yield of free bases was nearly constant under nitrogen, but decreased under oxygen. However, for DNA with gamma greater than 15, the yield increased rapidly under both nitrogen and oxygen. The yield of free bases was described by a model that depended on two factors: 1) a change in the DNA conformation from a mixture of the A and C conformers in vacuum-dried DNA to predominantly the B conformer in the fully hydrated DNA, and 2) the proximity of the water molecules to the DNA. Irradiation of the inner water molecules (gamma less than 15) was less efficient than irradiation of the outer water molecules (gamma greater than 15), by a factor of approximately 3.3, in forming DNA lesions that resulted in the release of an unaltered base. This factor is similar to the previously published relative efficiency of 2.8 with which hydroxyl radicals and base cations induce DNA strand breaks. Our irradiation results are consistent with the hypothesis that the G value for the first 12-15 water molecules of the DNA hydration layer is the same as the G value for the form of DNA to which it is bound (i.e., the pseudo-C or the B form). Thus we suggest that the release of bases originating from irradiation of the hydration water is obtained predominantly: (1) by charge transfer from the direct ionization of the first 12-15 water molecules of the primary hydration layer and (2) by the attack of hydroxyl radicals generated in the outer, more loosely bound water molecules.     

Structure of DNA hydration shells studied by Raman spectroscopy

We have used Raman scattering to study the water O-H stretching modes at approximately 3450 and approximately 3220 cm-1 in DNA films as a function of relative humidity (r.h.). The intensity of the 3220-cm-1 band vanishes as the r.h. is decreased from 98% to around 80%, which indicates that the hydrogen-bond network of water is disrupted in the primary hydration shell (which therefore cannot have an "ice-like" structure). The number of water molecules in the primary hydration shell was determined from the intensity of the approximately 3200-cm-1 band as about 30 water molecules per nucleotide pair. The approximately 3400-cm-1 O-H stretch band was used for determining the total water content, and this band persists at 0% r.h., implying that 5-6 tightly bound water molecules per nucleotide pair remain. The frequency of the approximately 3400-cm-1 O-H stretch mode is lower by 30 to 45 cm-1 in the primary hydration shell compared to free water. The water content as a function of r.h. obtained from these experiments agrees with gravimetric measurements. The disappearance of the approximately 3200-cm-1 band and the shift of the approximately 3400-cm-1 O-H stretch band provide a reliable way of measuring the hydration number of DNA.     

Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation

An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ～1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen–phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.     

Dependence of the hydration shell structure in the minor groove of the DNA double helix on the groove width as revealed by Monte Carlo simulation.

The hydration shell of several conformations of the polynucleotides poly(dA).poly(dT), poly(dA).poly(dU), and poly(dA-dI).poly(dT-dC) has been simulated using the Monte Carlo method (Metropolis sampling). Calculations have shown that the structure of the hydration shell of the minor groove greatly depends on its width. In conformations with a narrowed minor groove, the first layer of the hydration shell of this groove has only one molecule per nucleotide pair that forms H bonds with purine N3 of one pair and pyrimidine O2 of the next pair. The second layer of the hydration shell of such conformations contains molecules that form H bonds between two adjacent molecules of the first layer. The probability of formation of hydration spine is about 20% while the bridges of the first layer are formed with a probability of about 70%. In the first layer of the minor groove of the B-DNA conformation with wide minor groove there are approximately two water molecules per base pair that form H bonds with purine N3 or pyrimidine O2 and with the sugar ring oxygen of the adjacent nucleotide. The probability of simultaneous H bonding of a water molecule with N3 (or O2) and O of sugar ring is about 30%. The results of simulation suggest that hydration spine proposed for the narrowed minor groove of oligonucleotide crystals [H. R. Drew, and R. E. Dickerson (1981) Journal of Molecular Biology, Vol. 151, pp. 535-556] can be formed in fibers of poly(dA).poly(dT), poly(dA).poly(dU), and poly(dA-dI).poly(dT-dC) as well as in DNA fragments of these sequences in solution.(ABSTRACT TRUNCATED AT 250 WORDS)     

Thermotropic properties of bipolar lipids of Sulfolobus solfataricus and of their mixtures with dipalmitoylphosphatidylcholine

The thermotropic properties of the bipolar lipids, glycerol dialkylglycerol tetraether (GDGT) and glycerol dialkylnonitol tetraether (GDNT), were determined at different degrees of hydration and in mixtures with dipalmitoylphosphatidylcholine (DPPC). The number of water molecules rendered unfreezable by the GDNT molecule is 10+/-1.5 and that by the GDGT molecule 2.8+/-0.7 or about 1.1-1.5 H2O molecules per OH group. Binding of water molecules causes randomization of the two polar heads from the oriented form prevailing in the dry state. The hydration seems to be a cooperative process extending over a whole lipid domain. DPPC added in small amounts to GDNT interacts preferentially with the nonitol halves of the molecules separating them from the glycerol half molecules. In the cooperative interaction domain each DPPC molecule is surrounded by up to six GDNT molecules. Cooperative domains formed during the interaction of DPPC with GDGT are less pronounced. In both cases they affect the thermotropic properties of the system.     

Hydration of B-DNA: comparison between the water network around poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) on the basis of Monte Carlo computations

A computational method is elaborated for studying the water environment around regular polynucleotide duplexes; it allows rigorous structural information on the hydration shell of DNA to be obtained. The crucial aspect of this Monte Carlo simulation is the use of periodical boundary conditions. The output data consists of local maxima of water density in the space near the DNA molecule and the properties of one- and two-membered water bridges as function of pairs of polar groups of DNA. In the present paper the results for poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) are presented. The differences in their hydration shells are of a purely structural nature and are caused by the symmetry of the polar groups of the polymers under study, the symmetry being reflected by the hydration shell. The homopolymer duplex hydration shell mirrors the mononucleotide repeat. The water molecules contacting the polynucleotide in the minor groove are located nearly in the plane midway between the planes of successive base pairs. One water molecule per base pair forms a water bridge facing two polar groups of bases from adjacent base pairs and on different strands making a "spine"-like structure. In contrast, the major groove hydration is stabilized exclusively by two-membered water bridges; the water molecules deepest in the groove are concentrated near the plane of the corresponding base pair. The alternating polymer is characterized by a marked dyad symmetry of the hydration shell corresponding to the axis between two successive base pairs. The minor groove hydration of the dCpdG step resembles the characteristic features of the homopolymer, but the bridge between the O2 oxygens of the other base-stacking type is formed by two water molecules. The major groove hydration is characterized by high probability of one-membered water bridges and by localization of a water molecule on the dyad axis of the dGpdC step. The found structural elements are discussed as reasonable invariants of a dynamic hydration shell.     

Molecular dynamics simulations of DNA in solutions with different counter-ions

Molecular dynamics simulations of the [d(ATGCAGTCAG]2 fragment of DNA, in water and in the presence of three different counter-ions (Li+, Na+ and Cs+) are reported. Three-dimensional hydration structure and ion distribution have been calculated using spatial distribution functions for a detailed picture of local concentrations of ions and water molecules around DNA. According to the simulations, Cs+ ions bind directly to the bases in the minor groove, Na+ ions bind prevailing to the bases in the minor groove through one water molecule, whereas Li+ ions bind directly to the phosphate oxygens. The different behavior of the counter-ions is explained by specific hydration structures around the DNA and the ions. It is proposed how the observed differences in the ion binding to DNA may explain different conformational behavior of DNA. Calculated self-diffusion coefficients for the ions agree well with the available NMR data.     

Hydration effects accompanying the formation of DNA complexes with some ligands

In the range of millimeter wavelengths the dielectric properties of aqueous solutions of some biologically active ligands (potential anticarcinogen chlorophyllin; pharmacological drug caffeine; polyamine putrescine; mutagens proflavine and ethidium bromide; actinocin derivative, an analogue of antitumor antibiotic actinomycin D) and DNA complexes with these substances were studied. It was shown that complex formation is accompanied by the change in dielectric properties of the solution. These changes during interaction of DNA with the first three compounds correspond to a decrease in hydration (compared with the total hydration of free components), and in other cases they cause an increase in hydration. The number of water molecules bound with both the ligand and DNA nucleotide in the complex was estimated. The results were compared with existing models of DNA interaction with the studied substances.     

Dynamic properties of water bound to matrices of natural DNA and model complexes

From experimental data on the hydration energetics of nucleic acids obtained by differential scanning calorimetry under isothermal conditions, dielectric relaxation time tau d and "free volume" Vf occupied by water molecules in hydration shells of natural DNA and model polyribonucleotides were calculated. In addition, systems consisting of dinucleotides ApA, TpT, UpU, TpU, UpT and water clusters of various sizes (from 20 to 400 water molecules) were studied by Monte Carlo computer simulation. It was shown that, as water content in systems increases, the dynamic characteristics of bound water obtained with both methods approached the values for bulk water.     

C60 binds to and deforms nucleotides

Atomistic molecular dynamics simulations are performed for up to 20 ns to monitor the formation and the stability of complexes composed of single- or double-strand DNA molecules and C60 in aqueous solution. Despite the hydrophobic nature of C60, our results show that fullerenes strongly bind to nucleotides. The binding energies are in the range -27 to -42 kcal/mol; by contrast, the binding energy of two fullerenes in aqueous solution is only -7.5 kcal/mol. We observe the displacement of water molecules from the region between the nucleotides and the fullerenes and we attribute the large favorable interaction energies to hydrophobic interactions. The features of the DNA-C60 complexes depend on the nature of the nucleotides: C60 binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C60 binds to single-strand DNA and deforms the nucleotides significantly. Unexpectedly, when the double-strand DNA is in the A-form, fullerenes penetrate into the double helix from the end, form stable hybrids, and frustrate the hydrogen bonds between end-group basepairs in the nucleotide. When the DNA molecule is damaged (specifically, a gap was created by removing a piece of the nucleotide from one helix), fullerenes can stably occupy the damaged site. We speculate that this strong association may negatively impact the self-repairing process of the double-strand DNA. Our results clearly indicate that the association between C60 and DNA is stronger and more favorable than that between two C60 molecules in water. Therefore, our simulation results suggest that C60 molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.