CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Blanchet, Christophe; Pasi, Marco; Zakrzewska, K.; Lavery, Richard

doi:10.1093/nar/gkr316

Cited by 222 publications

(244 citation statements)

References 17 publications

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“…Initial structures of molecules were modelled by NAB and CHIMERAcode [19][20][21] assuming B-DNA conformation of the sequence by using the parameters from the Arnott fibre diffraction model [19]. The simulation was performed in the presence of 10 Å thickness of solvent (TIP3P water molecules) around duplex in an orthogonal box of density 0.739 g/cc at atmospheric pressure and room temperature.…”

Section: Methodsmentioning

confidence: 99%

“…The computed data was analysed by using the CPPTRAJ module of AMBER-14-code. Standard angles and helicoidal parameters were determined by using algorithm adapted by Babcok et al and reference-frame-coordinate was used from Olsen et al [27][28][29]. Similarly, the helical parameters of modified-base-pairs were defined by the set of atoms of modified base-pair corresponding to the natural base-pair A-T. Nucleic acid residue names are referred to in the text as one-letter codes with a residue number; residue numbers in the 5′ to 3′ directions are represented by 1-14 for the first strand and, 15-28 for the second strand of the duplex (14-mer sequence) respectively.…”

Section: Methodsmentioning

confidence: 99%

“…The average value of Y-displacement and Inclination angle is-0.11 Å and 9.5 ° respectively, which represents that bases are not perpendicular to the helix axis and total axisbending observed for of duplex is about 29 °. Major and Minor groove parameters which are superlative to phosphate-phosphate distance measurement, are calculated by the method given in X3DNA, which is compatible with the method of Lavery [27]. The time variation of Major and Minor groove parameters are shown in fig.…”

Section: Trajectory Analysismentioning

confidence: 99%

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MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

Tiwari

2018

Int J Pharm Pharm Sci

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Objective: The objective of the study was to elucidate the structural activity of a natural DNA sequence modified by a hydrophobic base-pair which didn't form Watson-Crick (W-C) hydrogen-bond. The modified unnatural base-pair (DNAM-D5SICS) was introduced in DNA sequences of 14-mer for molecular dynamics study in water solution. Methods:A 200 ns molecular-dynamics-simulation in orthogonal-box-water-solvent, using Particle-mesh-Ewald-method (PME) within periodicboundary-condition (PBC) was performed by using AMBER-14 code. The force-field-ff12SB-force-field was used during the simulation while the force-field-parameters of modified base-pair, compatible to ff12SB-force-field, were calculated by Gaussian-09-code using ab-inito/Hartree-Fockmethodology. The code CPPTRAJ, (a module of AMBER-14) CURVE and Chimera were used in the analysis of the data.Results: Root mean square deviation (RMSD) of heavy atoms of the trajectory revealed that the structure of the equilibrated duplex was stable, sequence-dependent and had mixed DNA-conformation. A little distortion near to the neighbor of the modified base-pair in the duplex strand was observed. However, we got a stabilized structure of such type of duplex if we placed modified base-pair after the third place in the strand. Conclusion:The study concluded that the distortion produced by modified-base-pair in the overall structure of duplex was local while the confirmation of such type of duplex was mixed and maintained the Watson-Crick (W-C) integrity of DNA. The study would help in the use of hydrophobic base-pair materials in biotechnological applications and the understanding of their structure-function relationship.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Trajectory Analysismentioning

confidence: 99%

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MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

Tiwari

2018

Int J Pharm Pharm Sci

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“…Analysis of the nucleic acid structure was performed using the program CurvesC 45,46 as well as on structures from the following PDB files: 3U2N, 1BNA, 137D, 240D, 1RNA, 4KYY, 4H8K, 1ZBI, 1G4Q, 1FIX, 1D87, and 3SSF. The parameters used for CurvesC were wback D 2 .9 A and wbase D 3 .5 A .…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding

et al. 2015

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“…For purposes of statistical analysis, sets of uncorrelated samples of DNA morphological parameters were obtained by setting the Curves+ [12] stride to g, the statistical inefficiency described earlier. Prior to statistical analysis, the sugar parameter values output by Curves+ were recast into the appropriate 2π interval so as to yield continuous distributions.…”

Section: Statistical Analysesmentioning

confidence: 99%

Comprehensive Comparative Analysis of the Morphological Changes in a 12-mer DNA Oligonucleotide upon Platination by Cisplatin, Oxaliplatin and BNP3029 (a Substituted Cyano ligand-based Platinum analogue) using Molecular Dynamics Simulation Studies

PNV¹,

Py²,

Ar³

et al. 2014

J Phys Chem Biophys

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and (vi) increased replicative bypass (or trans-lesion synthesis).In order to develop platinum analogues that overcome the aforementioned limitations, key characteristics were evaluated in studies reported herein, and a series of platinum analogues with substituted cyano groups as the carrier ligand were synthesized [5]. In an earlier study, ab initio computational studies on cisplatin, oxaliplatin and BNP3029 (Figure 1), a representative substituted cyano ligand from our novel platinum complexes [6], were reported. Herein, we present a comprehensive comparative computational study on the geometrical and morphological changes induced by cisplatin, oxaliplatin and BNP3029 upon binding to a 12-mer DNA oligonucleotide using molecular dynamics simulations with key findings described using Kolmogorov-Smirnov based statistical analyses [7]. Materials and Methods Molecular dynamics (MD) simulation: B-DNA and platinated-DNA with cisplatin, oxaliplatin and BNP3029MD simulations were carried out using the AMBER6.0 suite of programs [8] employing the parm99 forcefield. For a better description of α/γ backbone angle conformers in DNA, the parm99 forcefield was modified with the inclusion of parmbsc0 forcefield [9] AbstractCisplatin is an important anti-cancer agent widely used in the clinic; however, it has several notable limitations. To develop novel platinum analogues, key characteristics were considered that may result in more effective platinum analogues. In this study, we present comprehensive molecular dynamics simulation studies using a 12-mer DNA (5'-CCTCTggTCTCC-3', gg= the site of platination) oligonucleotide which was platinated with cisplatin (1), oxaliplatin_1R_2R (2), and BNP3029 (3, a novel substituted cyano platinum analogue, PtCl 2 [N≡C(CH 2 ) 3 (C 6 H 5 )] 2 ), and analyzed the large data output using the Kolmogorov-Smirnov statistical analyses. In summary, data indicated that BNP3029-DNA had less A-like DNA morphology in comparison to cisplatin-DNA and oxaliplatin-DNA thus maintaining a more B-like DNA form. BNP3029 demonstrated more potent cytotoxic activity, relative to cisplatin and oxaliplatin, in a variety of human cancer cell lines, including several platinum-resistant cell lines. 5'-TCTCCGGTCTCC-3' DNA sequence for B-DNA was used for each MD run. In the case of platinated-DNA, N7 atoms of the two guanines (gg) attach to platinum atom forming the platinum-DNA adduct (5'-TCTCCggTCTCC-3'). Published parameters for terms involving platinum with DNA bases (such as bond, angle and dihedral) were employed [10]. The only deviation from the published parameters was the use of 1.8 Å vdW radius for platinum in the current study based on the recommendation of smaller radius for platinum [11] compared to the 2.2 Å radius used in reference 10. J Phys Chem Total number of MD runsFor B-DNA, five separate runs were performed starting from the same topology and coordinates for the randomly generated initial velocities by using five different seeds. For four of the seeds, MD runs were performed for a period of 10 n...

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CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Cited by 222 publications

References 17 publications

MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding

Comprehensive Comparative Analysis of the Morphological Changes in a 12-mer DNA Oligonucleotide upon Platination by Cisplatin, Oxaliplatin and BNP3029 (a Substituted Cyano ligand-based Platinum analogue) using Molecular Dynamics Simulation Studies

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