Influence of the  -  interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

Mignon, Pierre; Loverix, Stefan; Steyaert, Jan; Geerlings, Pau̧l

doi:10.1093/nar/gki317

Cited by 225 publications

(172 citation statements)

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“…[40] Der größte Beitrag zur Stabilisierung der Komplexe stammt von dispersiven und nicht von elektrostatischen Wechselwirkungen. Stapelungen zwischen aromatischen Seitenketten von Aminosäuren und Nukleobasen wurden intensiv mit computergestützten Verfahren untersucht.…”

Section: Rechnungenunclassified

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

2011

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Dieser Aufsatz beschreibt Phänomene der molekularen Erkennung von aromatischen Ringen in chemischen und biologischen Systemen in einem multidimensionalen Ansatz. Neue Ergebnisse aus der Wirt‐Gast‐Chemie, biologischen Affinitätsassays und Biostrukturanalysen, Datenbanksuchen in der Cambridge Structural Database (CSD) und der Protein Data Bank (PDB) und hochentwickelten Rechnungen, die seit dem Erscheinen eines früheren Aufsatzes in 2003 veröffentlicht wurden, sind hier zusammengefasst. Die Themen Aren‐Aren‐, Perfluoraren‐Aren‐, Schwefel‐Aren‐, Kation‐π‐ und Anion‐π‐Wechselwirkungen sowie Wasserstoffbrücken zu aromatischen Systemen werden behandelt. Das gewonnene Wissen kommt besonders der strukturbasierten Hit‐zur‐Leitstruktur‐Entwicklung und der Leitstrukturoptimierung sowohl in der pharmazeutischen als auch in der Pflanzenschutzindustrie zugute. Zudem erleichtert es die Entwicklung neuer Materialien und supramolekularer Systeme und soll zu weiteren Anwendungen von Wechselwirkungen mit aromatischen Ringen zur Kontrolle des stereochemischen Verlaufs chemischer Umsetzungen inspirieren.

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Section: Rechnungenunclassified

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

2011

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“…The aromatic p-p interactions play pivotal role in determining crystal structures, stabilization of protein structures, DNA base-pair stacking, controlling the intercalation of certain drugs into DNA, encapsulation of linear carbon chain molecules inside single-walled carbon nanotubes, and molecular recognition process in biological, and artificial systems [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23]. Very recently, benzene-triphenylene and triphenylene-triphenylene interactions have been studied using MP2 method with a suitably modified double-f basis set.…”

Section: Introductionmentioning

confidence: 99%

Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed

Dinadayalane

Leszczyński

2009

Struct Chem

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Benzene dimer configurations namely T-shaped, parallel-displaced, sandwich, and V-shaped that were proposed by experimental studies are investigated using second-and fourth-order Møller-Plesset perturbation theory. The MP2 method with aug-cc-pVDZ and aug-cc-pVTZ basis sets unequivocally shows that the parallel-displaced configuration is considerably more stable than T-shaped structure. On the other hand, the MP4(SDTQ)/aug-cc-pVDZ level predicts that the T-shaped and parallel-displaced configurations are nearly isoenergetic, which is parallel to the previous results of estimated CCSD(T)/CBS level reported recently. The lowest energy T-shaped configuration is stabilized by 0.17 kcal/mol over the parallel-displaced configuration at the MP4(SDTQ)/aug-cc-pVDZ level. Although the structures of all the four different types of configurations are found to be stable at both MP2 and full MP4 methods, the V-shaped configuration is the least stable among them. The calculated interaction energy of -2.3 kcal/mol for the lowest energy T-shaped structure at the MP4(SDTQ)/aug-cc-pVDZ level is in good agreement with the experimental value of -2.4 ± 0.4 kcal/mol. We conclude that the MP4(SDTQ) with a reasonably good basis set can be used for systems involving p-p interactions to obtain qualitative and quantitative results.

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“…The d-polarization functions are capable of filling the gap between the interacting monomers, which significantly improves the description of base stacking interactions compared with the standard 6-31G* basis set. The MP2/6-31G*(0.25) method has been the most widely used ab initio technique to study aromatic stacking in the past literature 31,35,50,51,60,85,100,101,[107][108][109][110][111][112][113][114][115][116][117][118][119][120] and has only recently been replaced by CBS(T). The MP2/6-31G*(0.25) method is entirely sufficient to capture the nature of base stacking, and therefore all conclusions reported with this method remain qualitatively valid.…”

mentioning

confidence: 99%

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal · mol, which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal · mol -1 per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of ∆G°3 7 free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.

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Influence of the - interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

Cited by 225 publications

References 58 publications

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

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