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Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments. J Mol Model 2018; 24:46. [DOI: 10.1007/s00894-018-3589-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
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2
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Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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3
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Poltev VI, Anisimov VM, Sanchez C, Deriabina A, Gonzalez E, Garcia D, Rivas F, Polteva NA. Analysis of the conformational features of Watson–Crick duplex fragments by molecular mechanics and quantum mechanics methods. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Anisimov VM, Bauer GH, Chadalavada K, Olson RM, Glenski JW, Kramer WTC, Aprà E, Kowalski K. Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures. J Chem Theory Comput 2014; 10:4307-16. [DOI: 10.1021/ct500404c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victor M. Anisimov
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Gregory H. Bauer
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Kalyana Chadalavada
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Ryan M. Olson
- Cray, Inc., 380 Jackson
Street, St.
Paul, Minnesota 55101, United States
| | - Joseph W. Glenski
- Cray, Inc., 380 Jackson
Street, St.
Paul, Minnesota 55101, United States
| | - William T. C. Kramer
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Edoardo Aprà
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, K8-91, Richland, Washington 99352, United States
| | - Karol Kowalski
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, K8-91, Richland, Washington 99352, United States
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Poltev V, Anisimov VM, Danilov VI, Garcia D, Sanchez C, Deriabina A, Gonzalez E, Rivas F, Polteva N. The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures. Biopolymers 2014; 101:640-50. [DOI: 10.1002/bip.22432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/23/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Valeri Poltev
- Autonomous University of Puebla; Puebla 72570 Mexico
| | | | | | | | | | | | | | | | - Nina Polteva
- Institute of Theoretical and Experimental Biophysics RAS; Pushchino 142290 Russia
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Lenz SAP, Kellie JL, Wetmore SD. Glycosidic bond cleavage in deoxynucleotides: effects of solvent and the DNA phosphate backbone in the computational model. J Phys Chem B 2012; 116:14275-84. [PMID: 23167947 DOI: 10.1021/jp3096677] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Density functional theory (B3LYP) was employed to examine the hydrolysis of the canonical 2'-deoxynucleotides in varied environments (gas phase or water) using different computational models for the sugar residue (methyl or phosphate group at C5') and nucleophile (water activated through full or partial proton abstraction). Regardless of the degree of nucleophile activation, our results show that key geometrical parameters along the reaction pathway are notably altered upon direct inclusion of solvent effects in the optimization routine, which leads to significant changes in the reaction energetics and better agreement with experiment. Therefore, despite the wide use of gas-phase calculations in the literature, small model computational work, as well as large-scale enzyme models, that strive to understand nucleotide deglycosylation must adequately describe the environment. Alternatively, although inclusion of the phosphate group at C5' also affects the geometries of important stationary points, the effects cancel to yield unchanged deglycosylation barriers, and therefore smaller computational models can be used to estimate the energy associated with nucleotide deglycosylation, with the 5' phosphate group included if full (geometric) details of the reaction are desired. Hydrogen-bonding interactions with the nucleobase can significantly reduce the barrier to deglycosylation, which supports suggestions that discrete hydrogen-bonding interactions with active-site amino acid residues can play a significant role in enzyme-catalyzed nucleobase excision. Taken together with previous studies, the present work provides vital clues about the components that must be included in future studies of the deglycosylation of isolated noncanonical nucleotides, as well as the corresponding enzyme-catalyzed reactions.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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7
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Samanta PK, Manna AK, Pati SK. Structural, Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight. Chem Asian J 2012; 7:2718-28. [DOI: 10.1002/asia.201200630] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Pralok K. Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
| | - Arun K. Manna
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
| | - Swapan K. Pati
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
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Millen AL, Kamenz BL, Leavens FMV, Manderville RA, Wetmore SD. Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates. J Phys Chem B 2011; 115:12993-3002. [PMID: 21942470 DOI: 10.1021/jp2057332] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.
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Affiliation(s)
- Andrea L Millen
- Department of Chemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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Churchill CDM, Wetmore SD. Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA. Phys Chem Chem Phys 2011; 13:16373-83. [PMID: 21842033 DOI: 10.1039/c1cp21689a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J. Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J Chem Theory Comput 2010. [DOI: 10.1021/ct1004593] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Petr Jurečka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Pavel Banáš
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Michal Otyepka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Daniel Svozil
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
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