The Study of the Stability of Watson-Crick Nucleic Acid Base Pairs in Water and Dimethyl Sulfoxide: Computer Simulation by the Monte Carlo Method

Danilov, V.I.; Zheltovsky, N. V.; Slyusarchuk, Oleg N.; Poltev, V. I.; Alderfer, James L.

doi:10.1080/07391102.1997.10508947

Cited by 18 publications

(8 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most of the experimental findings described above have been confirmed by classical molecular dynamics, Monte Carlo simulations [21][22][23][24][25][26][27][28][29][30][31][32] and free energy calculations of nucleobase pairs in systems containing explicit solvent molecules by using nonpolarizable molecular mechanics force fields, and this kind of treatment has also been used to study the hydration patterns in the first solvation shell of DNA nucleobase dimers. [28][29][30][31][32] Florian et al studied the interactions of nucleobases in water by using a modified Langevin dipoles solvation model 33,34 that included empirically scaled entropies of binding so that the computed free energies of association would agree with equilibrium constants obtained experimentally for substituted nucleosides of DNA and RNA.…”

Section: Introductionmentioning

confidence: 90%

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

Ribeiro

Marenich

Cramer

et al. 2011

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and π-π stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform-water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4-1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.

show abstract

Section: Introductionmentioning

confidence: 90%

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

Ribeiro

Marenich

Cramer

et al. 2011

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

show abstract

“…It was ascertained experimentally (using IR, NMR and calorimetric titration techniques) that isolated nucleic acid bases in nonpolar solvents, such as carbon tetrachloride (CCl 4 ) and chloroform (CHCl 3 ), associate by hydrogen bonding, [136][137][138][139] whereas in an aqueous solution, bases form stacked complexes. 140,141 Katz and Penman, 142 Shoup et al 143 and 147,148 in CCl 4 by Pohorille et al, 149,150 in dimethylsulfoxide by Danilov et al, 151,152 and in water by a series of papers by Poltev et al [153][154][155][156][157][158][159] and most recently by Canuto et al 160 Whereas all the above-mentioned theoretical papers are dedicated to the behavior of nucleic acid bases or base pairs in the bulk solvent, much less interest has been devoted to the exact description of the solvation pattern around the base pairs in the microhydrated environment. The hydrated H-bonded base pairs were studied in the references.…”

Section: Hydration Of Nucleic Acid Base Pairsmentioning

confidence: 99%

Hydration and stability of nucleic acid bases and base pairs

Kabeláč

Hobza

2007

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

show abstract

“…The stacking and hydrogen-bonding interactions between nucleobases are important forces stabilizing DNA double helix. − The nature of these forces has been examined by a wide range of computational approaches. The hydrophobic and electrostatic solute−solvent interactions were found to play a significant role in the semiempirical and classical − simulations. In addition, recent ab initio quantum mechanical studies − as well as some earlier experimental works , stressed the importance of the electron correlation (dispersion) contribution to the interaction energy for nucleobase stacking in the gas phase.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study

1999

View full text Add to dashboard Cite

The potentials of mean force (PMF) for the association of purine, adenine, thymine, guanine, cytosine, and uracil in aqueous solution are investigated using ab initio MP2/6-31G(d-0.25) calculations (diffuse d-polarization functions were used) and Langevin dipoles solvation model. The entropy contributions to the free energies for stacking and hydrogen bonding are approximated using the linear relationship between binding enthalpies and entropies determined here from the available experimental data. This methodology is used to evaluate the dependence of PMF, and the gas-phase and solvation energies on the twist angle (Ω) in a number of undisplaced face-to-back stacking complexes. Further, we characterized the vertical association of the parallel (Ω ) 0°) and antiparallel (Ω ) 180°) stacked cytosine dimers. The results show large compensation between the gas-phase and solvation energetics and an overall preference of the bases in the undisplaced face-to-back stacked complexes for the twist angles near 30°. An important exception from this trend involves the GC and CG complexes, for which the largest stabilization occurs for the twist angle near 180°. In addition, free energies for the formation of 27 hydrogen-bonded base pairs were determined and compared with their stacking counterparts. The calculated standard free energies for the formation of stacked and hydrogen-bonded complexes at 298 K and neutral pH fell in a narrow region between 0.3 and -1.9 kcal/mol. Here, the hydrogen-bonded Watson-Crick guanine‚cytosine base pair was found to be the most stable of all studied complexes. In agreement with the previous experimental findings, complexes containing purine bases were calculated to be more stable than their pyrimidine-containing counterparts.

show abstract

The Study of the Stability of Watson-Crick Nucleic Acid Base Pairs in Water and Dimethyl Sulfoxide: Computer Simulation by the Monte Carlo Method

Cited by 18 publications

References 51 publications

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

Hydration and stability of nucleic acid bases and base pairs

Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study

Contact Info

Product

Resources

About