Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps

Kailasam, Senthilkumar; Bhattacharyya, Dhananjay; Bansal, Manju

doi:10.1186/1756-0500-7-83

Cited by 13 publications

(17 citation statements)

References 55 publications

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“…The purine‐purine and purine‐pyrimidine sequences are seen to prefer small roll values while the pyrimidine‐purine sequences have their minimum energy for larger positive roll. Similar base sequence dependent variations in roll in the dinucleotides containing only Watson‐Crick base pairs was seen and characterized earlier . Such variability was explained by Calladine as effect of cross strand purine‐purine steric clash due to negative propeller twist in most of the Watson‐Crick base pairs.…”

Section: Resultssupporting

confidence: 72%

“…Similarly six dinucleotide step parameters (tilt, roll, twist, shift, slide, and rise) were suggested by IUPAC‐IUB to describe relative orientation of the two stacked base pair with respect to each other. Previous analysis indicate these values for the G:U W:WC base pair containing steps are also quite similar to those for canonical steps . The sequence‐dependent preferred geometry of dinucleotide sequences are mostly reflected from the dinucleotide step parameters roll, twist and slide .…”

Section: Introductionmentioning

confidence: 52%

“…It was seen that average twist values in RNA for most dinucleotide sequences containing only Watson‐Crick base pairs are very close to 30 o . We have therefore first studied the energy contours in roll ‐ slide space for 30 o twist for the eleven dinucleotide steps containing G:U W:WC base pair.…”

Section: Resultsmentioning

confidence: 99%

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Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

et al. 2015

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Emergence of thousands of crystal structures of noncoding RNA molecules indicates its structural and functional diversity. RNA function is based upon a large variety of structural elements which are specifically assembled in the folded molecules. Along with the canonical Watson-Crick base pairs, different orientations of the bases to form hydrogen-bonded non-canonical base pairs have also been observed in the available RNA structures. Frequencies of occurrences of different non-canonical base pairs in RNA indicate their important role to maintain overall structure and functions of RNA. There are several reports on geometry and energetic stabilities of these non-canonical base pairs. However, their stacking geometry and stacking stability with the neighboring base pairs are not well studied. Among the different non-canonical base pairs, the G:U wobble base pair (G:U W:WC) is most frequently observed in the RNA double helices. Using quantum chemical method and available experimental data set we have studied the stacking geometry of G:U W:WC base pair containing dinucleotide sequences in roll-slide parameters hyperspace for different values of twist. This study indicates that the G:U W:WC base pair can stack well with the canonical base pairs giving rise to large interaction energy. The overall preferred stacking geometry in terms of roll, twist and slide for the eleven possible dinucleotide sequences is seen to be quite dependent on their sequences.

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Section: Resultssupporting

confidence: 72%

Section: Introductionmentioning

confidence: 52%

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Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

et al. 2015

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“…The dinucleotide sequences are recognized to have specific mean values for each dinucleotide parameters. Along with the various analyses of the B‐DNA parameters, it is shown recently that characteristic sequence dependent geometries are also observed for the RR, RY, and YR type of dinucleotide steps in RNA. It was shown from experimentally determined structures (both crystallography and NMR spectroscopy) that dinucleotide step parameters in RNA helices show mean values as well as correlated variations that are different from those observed in B‐DNA .…”

Section: Resultsmentioning

confidence: 99%

Stacking interactions in RNA and DNA: Roll‐slide energy hyperspace for ten unique dinucleotide steps

et al. 2014

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Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by ωB97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality.

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“…Crystal structure database analysis reflects the sequence‐dependent preferences of some of these parameters . For instance, in A‐DNA conformation, which is stable in low water activity environments, slide adopts large negative value along with large positive roll.…”

Section: Introductionmentioning

confidence: 99%

Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs

et al. 2016

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Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non-canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte-Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER-parm99bsc0 and CHARMM-36 force-fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte-Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson-Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non-canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse-grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson-Crick base pairs, as found often in the non-coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212-226, 2016.

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Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps

Cited by 13 publications

References 55 publications

Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

Stacking interactions in RNA and DNA: Roll‐slide energy hyperspace for ten unique dinucleotide steps

Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs

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