Nucleic Acid G-quartets: Insights into Diverse Patterns and Optical Properties

Jissy, A. K.; Ashik, U.P.M.; Datta, Ayan

doi:10.1021/jp202401b

Cited by 65 publications

(77 citation statements)

References 147 publications

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“…It should be mentioned that dispersion interactions play a major role in the stabilities of large biomolecules, such as DNA, in which these interactions are abundant. For example, Datta and coworkers investigated the nucleic acid G‐quartets38 and various conformations of different DNA‐base mispairs39 and found that dispersion interactions play an important role in the stabilities of the studied complexes. Therefore, it could be anticipated that dispersion interactions also have influences on the stabilities of the base pairs studied in this work.…”

Section: Resultsmentioning

confidence: 99%

Survival in pulmonary hypertension associated with the scleroderma spectrum of diseases: Impact of interstitial lung disease

Mathai¹,

Hummers²,

Champion³

et al. 2009

Arthritis & Rheumatism

229

174

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Objective. Pulmonary hypertension (PH) is an important cause of mortality in systemic sclerosis (SSc), where it can be isolated (pulmonary arterial hypertension [PAH]) or associated with interstitial lung disease (ILD). This study was undertaken to characterize determinants of survival among SSc patients with either type of PH who received PAH-specific therapy.Methods. Consecutive SSc patients with PAH or ILD-associated PH confirmed by right heart catheterization were included in the study. Kaplan-Meier and Cox proportional hazards models were used to compare survival between SSc patients with PAH and those with ILD-associated PH and to identify predictors of survival.Results. Fifty-nine patients (39 with PAH and 20 with ILD-associated PH) were identified. The majority (15 of 20 with ILD-associated PH and 27 of 39 with PAH) received an endothelin receptor antagonist as initial therapy. Median followup time was 4.4 years (range 2.7-7.4 years). Survival was significantly worse in SSc patients with ILD-associated PH than in those with PAH (1-, 2-, and 3-year survival rates 82%, 46%, and 39% versus 87%, 79%, and 64%, respectively; P < 0.01 by log rank test). In a multivariable analysis, ILD-associated PH was associated with a 5-fold increase in risk of death compared with PAH. Pulmonary vascular resistance index was also an independent predictor of mortality in the overall cohort (hazard ratio 1.05, P < 0.01) and was a significant univariable risk factor in each group separately. Type of initial PAH therapy and the use of warfarin were not related to survival.Conclusion. Survival in SSc complicated by PH remains poor despite currently available treatment options. While therapy may be associated with improved survival in PAH compared with historical controls, the prognosis for patients with ILD-associated PH is particularly grim. Early diagnosis and treatment may improve outcomes since worsening hemodynamic factors were associated with reduced survival.

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Section: Resultsmentioning

confidence: 99%

Survival in pulmonary hypertension associated with the scleroderma spectrum of diseases: Impact of interstitial lung disease

Mathai¹,

Hummers²,

Champion³

et al. 2009

Arthritis & Rheumatism

229

174

View full text Add to dashboard Cite

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“…Close proximity of Truhlar's M06-2X meta-GGA-hybrid functional with benchmark databases has been previously reported in literature for a wide variety of molecular complexes. 13,14 According to previous benchmarks we expect the M06-2X and ωB97XD functional to give the most accurate DFT binding energies. 15,16 For the ONIOM calculations, the high layer consisting of the UBP along with the linked sugars and phosphates was performed at the M06-2X/6-31+(d) level, while the low layer consisting of the four natural base pairs above and below the UBP inclusive of their link sugars and phosphates was performed at the semiempirical PM3 level.…”

Section: ■ Computational Detailsmentioning

confidence: 94%

What Sustains the Unnatural Base Pairs (UBPs) with No Hydrogen Bonds

Jahiruddin

Datta

2015

J. Phys. Chem. B

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The recent report of a hydrophobic unnatural base pair (UBP), d5SICS-dNaM, which replicated in DNA PCR and also sustained and synthesized a plasmid inside E. coli genome by Romesberg and coworkers, is intriguing. Quantum chemical calculations show that the UBPs prefer a slipped parallel configuration to facilitate weak dispersion interactions somewhat similar to the so-called π-stacking interaction. Nevertheless, within a natural DNA tract, classical molecular dynamics simulations show that the backbone and neighboring stacked bases together reorient the UBPs in natural base pair like planar environment. Our computed structure with an average end-end distance, dC1'-C1' = 10.7 Å for d5SICS-dNaM is in excellent agreement with available crystal structure (PDB ID: 3SV3 , planar UBP with dC1'-C1'(crystal) = 11.0 Å). Quantum mechanical calculations for the UBP flanked by two natural base-pairs (A-T) on top and on bottom on equilibrated MD structure found large binding energy (ΔE = -74.0 kcal/mol). The present calculations therefore establish the fact that the hydrophobic UBPs can be stabilized by dispersion interactions with other base pairs in the DNA tract even in the absence of any hydrogen bonding between the UBPs themselves.

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“…For geometry optimization and subsequent interaction energy calculations, we have selected Truhlar's M05-2X 39 functional and the 6-31G++(2d,2p) basis set 40 . M05-2X is a hybrid meta GGA functional with 56% Hartree-Fock exchange component and is known to perform remarkably well for noncovalently bonded molecules of biological relevance, 41 including nucleobases [42][43][44][45][46][47][48][49] . 6-31G++(2d,2p) is a split valance double ζ type basis set, with two sets of d type polarization function for all non-hydrogen atoms and two sets of p type polarization function for hydrogen atoms, and also include s-p diffused orbitals for non-hydrogen atoms, was used for ground state geometry optimization.…”

Section: Tools and Methodsmentioning

confidence: 99%

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

Mittal¹,

Halder²,

Bhattacharya³

et al. 2017

Preprint

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Identification of static and/or dynamic roles of different noncanonical base pairs is essential for a comprehensive understanding of the sequence-structure-function space of RNA. In this context, reverse WatsonCrick purine-purine base pairs (A:A, G:G & A:G W:W Trans) constitute an interesting class of noncanonical base pairs in RNA due to their characteristic C1 -C1 distance (highest among all base pairing geometries) and parallel local strand orientation. Structural alignment of the RNA stretches containing these W:W Trans base pairs with their corresponding homologous sites in a non-redundant set of RNA crystal structures show that, as expected, these base pairs are associated with specific structural folds or functional roles. Detailed analysis of these contexts further revealed a bimodal distribution in the local backbone geometry parameters associated with these base pairs. One mode, populated by both A:A and G:G W:W Trans pairs, manifests itself as a characteristic backbone fold. We call this fold a 'Sharp-turn' motif. The other mode is exclusively associated with A:A W:W Trans pairs involved in mediating higher order interactions. The same trend is also observed in available solution NMR structures. We have also characterized the importance of recurrent hydrogen bonding interactions between adenine and guanine in W:W Trans geometry. Quantum chemical calculations performed at M05-2X/6-31++(2d,2p) level explain how the characteristic electronic properties of these W:W Trans base pairs facilitate their occurrence in such exclusive structural folds that are important for RNA functionalities.

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Nucleic Acid G-quartets: Insights into Diverse Patterns and Optical Properties

Abstract: We thank DST À Fast Track scheme, CSIR, and University Grants Commission (UGC) for partial funding. We thank Prof. M. Hariharan for fruitful discussions.

Cited by 65 publications

References 147 publications

Survival in pulmonary hypertension associated with the scleroderma spectrum of diseases: Impact of interstitial lung disease

Survival in pulmonary hypertension associated with the scleroderma spectrum of diseases: Impact of interstitial lung disease

What Sustains the Unnatural Base Pairs (UBPs) with No Hydrogen Bonds

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

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