Interaction energies in stacked DNA bases? How important are electrostatics?

Hill, Glake; Forde, Gareth K.; Hill, Nicholas; Lester, William A.; Sokalski, W. Andrzej; Leszczyński, Jerzy

doi:10.1016/j.cplett.2003.09.076

Cited by 42 publications

(48 citation statements)

References 29 publications

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“…Nucleotide stacking can be thought to be composed of multiple components, including electrostatics (dipole-dipole interactions) and electrodynamics (induced dipoles, van der Waals interactions, etc.) (Hill et al 2003). It is particularly revealing to compare the electrostatic maps of uridine and Ψ, which were generated using atomic substitution in conjunction with previously optimized geometries for U (Johnson et al 2011), operating under the assumption that Ψ assumes the same geometry as the parent U residue (Fig.…”

Section: Helix To Coil Transition Of ψ-A Oligoribonucleotidesmentioning

confidence: 99%

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

Hudson

Bloomingdale

Znosko

2013

RNA

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Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearestneighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs.

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Section: Helix To Coil Transition Of ψ-A Oligoribonucleotidesmentioning

confidence: 99%

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

Hudson

Bloomingdale

Znosko

2013

RNA

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“…The analysis of the nature of interactions in base pairs, however, has been settled on quantitative ground only quite recently [23][24][25][26][27][28][29][30][31]. Hill and collaborators analyzed the importance of electrostatics for stabilization of DNA bases [24]. Sedlak et al performed analysis for hydrogen bonded and stacked nucleic acid bases in configurations appearing in crystals using DFT-SAPT approach [32].…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

Theoretical insights into the nature of intermolecular interactions in cytosine dimer

Czyżnikowska¹,

Zaleśny²

2009

Biophysical Chemistry

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In this study we discuss stacking interactions in cytosine dimer in conformations appearing in B-DNA crystals. The variational-perturbational scheme was applied for decomposition of the intermolecular interaction energy at the MP2 level of theory. The significant influence of the mutual orientation of cytosine monomers was observed not only on the total intermolecular interaction energy but also on its components: Different components of intermolecular interaction energy depend in different manner on parameters describing mutual orientation of cytosine monomers.

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“…This approach using new model brings more accuracy in database minimizing simulation time [1][2][3][4][5][6][7][8]. In the present study a conventional type molecule Naphthol, having tetralin like structure and lot of biological and pharmaceutical activities [9][10][11], has been chosen.…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic investigations on Naphthol and Tetrahydronaphthol. A theoretical approach

De¹,

Ganguly

2011

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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Interaction energies in stacked DNA bases? How important are electrostatics?

Cited by 42 publications

References 29 publications

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

Theoretical insights into the nature of intermolecular interactions in cytosine dimer

Spectroscopic investigations on Naphthol and Tetrahydronaphthol. A theoretical approach

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