1
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Nakagawa O, Fujii A, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. 2'-O,4'-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. Chembiochem 2018; 19:2372-2379. [PMID: 30168891 DOI: 10.1002/cbic.201800448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 11/08/2022]
Abstract
The 2'-O,4'-C-methylene-bridged or locked nucleic acid (2',4'-BNA/LNA), with an N-type sugar conformation, effectively improves duplex-forming ability. 2',4'-BNA/LNA is widely used to improve gene knockdown in nucleic acid based therapies and is used in gene diagnosis. Metal-mediated base pairs (MMBPs), such as thymine (T)-HgII -T and cytosine (C)-AgI -C have been developed and used as attractive tools in DNA nanotechnology studies. This study aimed to investigate the application of 2',4'-BNA/LNA in the field of MMBPs. 2',4'-BNA/LNA with 5-methylcytosine stabilized the MMBP of C with AgI ions. Moreover, the 2',4'-BNA/LNA sugar significantly improved the duplex-forming ability of the DNA/DNA complex, relative to that by the unmodified sugar. These results suggest that the sugar conformation is important for improving the stability of duplex-containing MMBPs. The results indicate that 2',4'-BNA/LNA can be applied not only to nucleic acid based therapies, but also to MMBP technologies.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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2
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Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV. Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 2018; 13:1235-1242. [PMID: 29562136 DOI: 10.1021/acschembio.8b00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective base pairing is the foundation of DNA recognition. Here, we elucidate the molecular and structural details of a FRET-based two-component molecular beacon relying on steady-state fluorescence spectroscopy, small-angle X-ray scattering (SAXS), microscale thermophoresis (MST), and differential electrophoretic mobility. This molecular beacon was designed to detect the most common fusion sequences causing chronic myeloid leukemia, e14a2 and e13a2. The emission spectra indicate that the self-assembly of the different components of the biosensor occurs sequentially, triggered by the fully complementary target. We further assessed the structural alterations leading to the specific fluorescence FRET signature by SAXS, MST, and the differential electrophoretic mobility, where the size range observed is consistent with hybridization and formation of a 1:1:1 complex for the probe in the presence of the complementary target and revelator. These results highlight the importance of different techniques to explore conformational DNA changes in solution and its potential to design and characterize molecular biosensors for genetic disease diagnosis.
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Affiliation(s)
- Mílton Cordeiro
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
| | - Petr V. Konarev
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russia
- National Research Centre “Kurchatov Institute”, pl. Kurchatova 1, 123182 Moscow, Russia
| | - João Carlos Lima
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
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3
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Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:63-73. [DOI: 10.1016/j.pbiomolbio.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 04/16/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
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4
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Sedova A, Banavali NK. Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands. Biochemistry 2017; 56:1426-1443. [PMID: 28187685 DOI: 10.1021/acs.biochem.6b01101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.
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Affiliation(s)
- Ada Sedova
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , Albany, New York 12222, United States
| | - Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, Wadsworth Center, New York State Department of Health, CMS 2008, Biggs Laboratory, Empire State Plaza, P.O. Box 509, Albany, New York 12201-0509, United States.,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , Albany, New York 12222, United States
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5
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Elder RM, Pfaendtner J, Jayaraman A. Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA. Biomacromolecules 2015; 16:1862-9. [DOI: 10.1021/acs.biomac.5b00469] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Robert M. Elder
- U.S. Army Research
Laboratory, Aberdeen Proving
Ground, MD 21005, United States
- Department
of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- Departments
of Chemical and Biomolecular Engineering and Materials Science and
Engineering, University of Delaware, Newark, Delaware 19716, United States
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6
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Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Brancolini G, Migliore A, Corni S, Fuentes-Cabrera M, Luque FJ, Di Felice R. Dynamical treatment of charge transfer through duplex nucleic acids containing modified adenines. ACS NANO 2013; 7:9396-406. [PMID: 24060008 PMCID: PMC3903158 DOI: 10.1021/nn404165y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We address the issue of whether chemical alterations of nucleobases are an effective tool to modulate charge transfer through DNA molecules. Our investigation uses a multilevel computational approach based on classical molecular dynamics and quantum chemistry. We find yet another piece of evidence that structural fluctuations are a key factor to determine the electronic structure of double-stranded DNA. We argue that the electronic structure and charge transfer ability of flexible polymers is the result of a complex intertwining of various structural, dynamical and chemical factors. Chemical intuition may be used to design molecular wires, but this is not the sole component in the complex charge transfer mechanism through DNA.
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Affiliation(s)
- Giorgia Brancolini
- CNR Institute of Nanoscience, S3 Center, Via Campi 213/A, 41125 Modena, Italy
- (GB); (RDF). Phone: +39-059-205-5320. Fax: +39-059-205-5651
| | - Agostino Migliore
- School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Stefano Corni
- CNR Institute of Nanoscience, S3 Center, Via Campi 213/A, 41125 Modena, Italy
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, Tennessee 37831 6494, USA
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avenida Diagonal 643, Barcelona 08028, Spain
| | - Rosa Di Felice
- CNR Institute of Nanoscience, S3 Center, Via Campi 213/A, 41125 Modena, Italy
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089 USA
- (GB); (RDF). Phone: +39-059-205-5320. Fax: +39-059-205-5651
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8
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Villani G. Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers. Chemphyschem 2013; 14:1256-63. [PMID: 23494877 DOI: 10.1002/cphc.201200971] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/07/2013] [Indexed: 12/13/2022]
Abstract
Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM-UOS Pisa, Area della Ricerca del CNR, Via G. Moruzzi 1, 56124 Pisa, Italy.
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9
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McDonald AR, Denning EJ, MacKerell AD. Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA. J Phys Chem A 2013; 117:1560-8. [PMID: 23343365 DOI: 10.1021/jp308364d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Base stacking is known to make an important contribution to the stability of DNA and RNA, and accordingly, significant efforts are ongoing to calculate stacking energies using ab initio quantum mechanical methods. To date, impressive improvements have been made in the model chemistries used to perform stacking energy calculations, including extensions that include robust treatments of electron correlation with extended basis sets, as required to treat interactions where dispersion makes a significant contribution. However, those efforts typically use rigid monomer geometries when calculating the interaction energies. To overcome this, in the present work, we describe a novel internal coordinate definition that allows the relative, intermolecular orientation of stacked base monomers to be constrained during geometry optimizations while allowing full optimization of the intramolecular degrees of freedom. Use of the novel reference frame to calculate the impact of full geometry optimization versus constraining the bases to be planar on base monomer stacking energies, combined with density-fitted, spin-component scaling MP2 treatment of electron correlation, shows that full optimization makes the average stacking energy more favorable by -3.4 and -1.5 kcal/mol for the canonical A and B conformations of the 16 5' to 3' base stacked monomers. Thus, treatment of geometry optimization impacts the stacking energies to an extent similar to or greater than the impact of current state of the art increases in the rigor of the model chemistry itself used to treat base stacking. Results also indicate that stacking favors the B-form of DNA, though the average difference versus the A-form decreases from -2.6 to -0.6 kcal/mol when the intramolecular geometry is allowed to fully relax. However, stacking involving cytosine is shown to favor the A-form of DNA, with that contribution generally larger in the fully optimized bases. The present results show the importance of allowing geometry optimization, as well as properly treating the appropriate model chemistry, in studies of nucleic acid base stacking.
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Affiliation(s)
- Ashley Ringer McDonald
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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10
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Sharma P, Lait LA, Wetmore SD. yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar-base orientation, hydrogen-bonding interactions and stacking abilities. Phys Chem Chem Phys 2013; 15:2435-48. [PMID: 23303174 DOI: 10.1039/c2cp43910g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti orientation with respect to the 2'-deoxyribose moiety, the expanded analogues will likely display (anti/syn) conformational heterogeneity, which may lead to alternate hydrogen-bonding modes in double-stranded duplexes. Nevertheless, the A:T Watson-Crick hydrogen-bond strengths do not significantly change upon base expansion, while the G:C interaction energy is slightly strengthened upon incorporation of either expanded pyrimidine. The largest effect of base expansion occurs in the stacking energies. Specifically, the maximum (most negative) stacking energies in isolated dimers formed by aligning the nucleobase centers of mass can be increased up to 45% by inclusion of a single y-pyrimidine and up to 55% by consideration of a yy-pyrimidine. Similar increases in the stacking interactions are found when a simplified duplex model composed of two stacked (hydrogen-bonded) base pairs is considered, where both the intrastrand and interstrand stacking interactions can be increased and the effects are more pronounced for the yy-pyrimidines. Moreover, the total stability (sum of all hydrogen-bonding and stacking interactions) is greater for duplexes containing expanded yy-pyrimidines compared to y-pyrimidines, which is mainly due to enhanced stacking interactions. Thus, our calculations suggest that multiple unidirectional increases in the size of the nucleobase spacer can continuously enhance the stability of expanded duplexes.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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11
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Villani G. Theoretical investigation of the coupling between hydrogen atoms transfer and stacking interaction in guanine–cytosine dimers. Phys Chem Chem Phys 2013; 15:19242-52. [DOI: 10.1039/c3cp52855c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Sharma P, Lait LA, Wetmore SD. Exploring the limits of nucleobase expansion: computational design of naphthohomologated (xx-) purines and comparison to the natural and xDNA purines. Phys Chem Chem Phys 2013; 15:15538-49. [DOI: 10.1039/c3cp52656a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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13
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Rutledge LR, Wetmore SD. A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase. Phys Chem Chem Phys 2012; 14:2743-53. [PMID: 22270716 DOI: 10.1039/c2cp23600a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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14
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FAN WENJIE, ZHANG RUIQIN. COMPUTATION OF LARGE SYSTEMS WITH AN ECONOMIC BASIS SET: AB INITIO CALCULATIONS OF BIOLOGICAL NUCLEIC ACID BASE PAIRS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.
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Affiliation(s)
- WENJIE FAN
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, P. R. China
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R. China
| | - RUIQIN ZHANG
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, P. R. China
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R. China
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15
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RIAHI SIAVASH, EYNOLLAHI SOLMAZ, GANJALI MOHAMMADREZA. INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610006055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.
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Affiliation(s)
- SIAVASH RIAHI
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, P. O. Box 11365-4563, Tehran, Iran
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - SOLMAZ EYNOLLAHI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - MOHAMMAD REZA GANJALI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
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16
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Parthasarathi R, Bellesia G, Chundawat SPS, Dale BE, Langan P, Gnanakaran S. Insights into Hydrogen Bonding and Stacking Interactions in Cellulose. J Phys Chem A 2011; 115:14191-202. [DOI: 10.1021/jp203620x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - S. P. S. Chundawat
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - B. E. Dale
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - P. Langan
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
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17
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Johnson CA, Bloomingdale RJ, Ponnusamy VE, Tillinghast CA, Znosko BM, Lewis M. Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings. J Phys Chem B 2011; 115:9244-51. [PMID: 21619071 DOI: 10.1021/jp2012733] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hydrogen-bonding, intrastrand base-stacking, and interstrand base-stacking energies were calculated for RNA and DNA dimers at the MP2(full)/6-311G** level of theory. Standard A-form RNA and B-form DNA geometries from average fiber diffraction data were employed for all base monomer and dimer geometries, and all dimer binding energies were obtained via single-point calculations. The effects of water solvation were considered using the PCM model. The resulting dimer binding energies were used to calculate the 10 unique RNA and 10 unique DNA computational nearest-neighbor energies, and the ranking of these computational nearest neighbor energies are in excellent agreement with the ranking of the experimental nearest-neighbor free energies. These results dispel the notion that average fiber diffraction geometries are insufficient for calculating RNA and DNA stacking energies.
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Affiliation(s)
- Charles A Johnson
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, USA
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18
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Svozil D, Hobza P, Sponer J. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? J Phys Chem B 2010; 114:1191-203. [PMID: 20000584 DOI: 10.1021/jp910788e] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal x mol(-1), which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the GC/GC [corrected] step that is well separated from the second most stable step CG/CG. [corrected] Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal x mol(-1) per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of DeltaG degrees(37) free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.
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Affiliation(s)
- Daniel Svozil
- Faculty of Chemical Technology, Laboratory of Informatics and Chemistry, Institute of Chemical Technology, Technická 3, 166 28, Prague 6, Czech Republic.
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Interaction of psoralens with DNA-bases (II): An ab initio quantum chemical, density functional theory and second-order MØller-Plesset perturbational study. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Ode H, Matsuo Y, Neya S, Hoshino T. Force field parameters for rotation around chi torsion axis in nucleic acids. J Comput Chem 2008; 29:2531-42. [PMID: 18470965 DOI: 10.1002/jcc.21006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.
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Affiliation(s)
- Hirotaka Ode
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
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The post-SCF quantum chemistry characteristics of the energetic heterogeneity of stacked guanine–guanine pairs found in B-DNA and A-DNA crystals. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Riahi S, Reza Ganjali M, Dinarvand R, Karamdoust S, Bagherzadeh K, Norouzi P. A theoretical study on interactions between mitoxantrone as an anticancer drug and DNA: application in drug design. Chem Biol Drug Des 2008; 71:474-482. [PMID: 18384527 DOI: 10.1111/j.1747-0285.2008.00653.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This research is an effort to further understand the physicochemical interaction between the novel drug, mitoxantrone (MTX) and its biologic receptor, DNA. The ultimate goal is to design drugs that interact more with DNA. Understanding the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA, it should ultimately allow the rational design of novel anti-cancer or anti-viral drugs. Molecular modelling on the complex formed between MTX and DNA presented that this complex was indeed fully capable of participating in the formation of a stable intercalation site. Furthermore, the molecular geometries of MTX and the DNA bases (adenine, guanine, cytosine and thymine) were optimized with the aid of the B3LYP/6-31G* method. The properties of the isolated intercalator and its stacking interactions with the adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were studied with the DFTB method (density functional tight-binding), an approximate version of the DFT method, that was extended to cover the London dispersion energy. The B3LYP/6-31G* stabilization energies of the intercalator...base pair complexes were found 10.06 kcal/mol and 21.64 kcal/mol for AT...MTX and GC...MTX, respectively. It was concluded that the dispersion energy and the electrostatic interaction contributed to the stability of the intercalator.DNA base pair complexes. The results concluded from the comparison of the DFTB method and the Hartree-fock method point out that these methods show close results and support each other.
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Affiliation(s)
- Siavash Riahi
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Mohammad Reza Ganjali
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Rassoul Dinarvand
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Sanaz Karamdoust
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Kowsar Bagherzadeh
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Parviz Norouzi
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
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23
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Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 2007; 92:3817-29. [PMID: 17351000 PMCID: PMC1868997 DOI: 10.1529/biophysj.106.097782] [Citation(s) in RCA: 1751] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 02/05/2007] [Indexed: 11/18/2022] Open
Abstract
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution.
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Affiliation(s)
- Alberto Pérez
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica & Instituto Nacional de Bioinformática, Parc Científic de Barcelona, Barcelona 08028, Spain
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El-Gogary TM, Koehler G. Interaction of psoralens with DNA-bases (I). An ab initio quantum chemical, density functional theory and second-order Møller–Plesset perturbational study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.12.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Abstract
A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.
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Affiliation(s)
- Setsuko Nakagawa
- Department of Human Life and Environment, Kinjo Gakuin University, Omori, Moriyama-ku, Nagoya 463-8521, Japan
- Department of Theoretical Chemistry, Royal Institute of Technology, S-106 91 Stockholm, Sweden
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26
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McConnell TL, Wetmore SD. How Do Size-Expanded DNA Nucleobases Enhance Duplex Stability? Computational Analysis of the Hydrogen-Bonding and Stacking Ability of xDNA Bases. J Phys Chem B 2007; 111:2999-3009. [PMID: 17388411 DOI: 10.1021/jp0670079] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Computational chemistry (B3LYP, MP2) is used to study the properties of size-expanded DNA nucleobases generated by inserting a benzene spacer into the natural nucleobases. Although the addition of the spacer does not significantly affect the hydrogen-bonding properties of natural nucleobases, the orientation of the base about the glycosidic bond necessary for Watson-Crick binding is destabilized, which could have implications for the selectivity of expanded bases, as well as the stability of expanded duplexes. Consideration of the (stacked) binding energies in the preferred relative orientation of natural and expanded nucleobases aligned according to their centers of mass reveals that the stacking within natural dimers can be increased by up to 50% upon expansion of one nucleobase and up to 90% upon expansion of two nucleobases. The implications of these findings to the stability of expanded duplexes were revealed by considering simplified models of natural and mixed duplexes composed of four nucleobases. Although intra- and interstrand interactions within double helices are typically less than those predicted when nucleobases are stacked according to their centers of mass, some nucleobases utilize their full stacking potential within double helices, where both intra- and interstrand interactions can be significant. Most importantly, increasing the size of nucleobases within the duplex significantly increases both intra- and interstrand stacking interactions. Specifically, some interactions are double the magnitude of the corresponding intrastrand interactions in natural helices, and even greater increases in interstrand interactions are sometimes found. Thus, our work suggests that mixed duplexes composed of natural bases hydrogen bound to expanded bases may exploit the increase in the inherent stacking ability of the expanded bases in more than one way and thereby afford duplexes with greater stability than natural DNA.
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Affiliation(s)
- Tom L McConnell
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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27
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Hunter KC, Millen AL, Wetmore SD. Effects of Hydrogen-Bonding and Stacking Interactions with Amino Acids on the Acidity of Uracil. J Phys Chem B 2007; 111:1858-71. [PMID: 17256895 DOI: 10.1021/jp066902p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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28
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Rutledge LR, Wheaton CA, Wetmore SD. A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 2007; 9:497-509. [PMID: 17216066 DOI: 10.1039/b606388h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
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29
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Fan WJ, Zhang RQ, Liu S. Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory. J Comput Chem 2007; 28:967-74. [PMID: 17269120 DOI: 10.1002/jcc.20670] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.
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Affiliation(s)
- W J Fan
- Center of Super-Diamond and Advanced Films (COSDAF) & Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People's Republic of China
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30
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Schmidt A, Lindner A, Nieger M, Ruiz-Delgado MDC, Ramirez FJ. Syntheses, pi-stacking interactions and base-pairings of uracil pyridinium salts and uracilyl betaines with nucleobases. Org Biomol Chem 2006; 4:3056-66. [PMID: 16886072 DOI: 10.1039/b606249k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reaction of 6-chlorouracil with 4-(dimethylamino)pyridine, 4-methylpyridine, and pyridin-4-yl-morpholine yielded pyridinium-substituted uracils as chlorides which were converted into pyridinium uracilates by deprotonation. These heterocyclic mesomeric betaines are cross-conjugated and thus possess separate cationic (pyridinium) and anionic (uracilate) moieties. Calculations and X-ray single crystal analyses were performed in order to characterize these systems and to compare the salts with the betaines. (1)H NMR experiments in D(2)O proved pi-interactions between the uracilyl betaines and adenine, adenosine, as well as adeninium. No pi-stacking interactions were detected between the betaines and guanosine. The acidic N8-H group of the uracil pyridinium salts caused acid-base reactions which were observed in parallel to pi-stacking interactions. Self-complementarity of the modified uracils was detected by (1)H NMR experiments in DMSO-d(6) and electrospray ionisation mass spectrometry (ESIMS). Ab initio calculations predicted base-pairings of the modified uracils with adeninium, cytosine, and guanine. Several geometries of hydrogen-bonded associates were calculated. Hoogsteen pairings between the uracil-4-(dimethylamino)pyridinium salt and adeninium, as well as associates between the corresponding betaine plus cytosine, and the betaine plus guanine were calculated, and the most stable conformations were determined. In the ESI mass spectra, prominent peaks of associates between the modified uracils and adeninium, cytosine, cytidine, guanosine and d(CpGp) were detected.
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Affiliation(s)
- Andreas Schmidt
- Clausthal University of Technology, Institute of Organic Chemistry, Leibnizstrasse 6, D-38678, Clausthal-Zellerfeld, Germany.
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31
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Fukuzawa K, Komeiji Y, Mochizuki Y, Kato A, Nakano T, Tanaka S. Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA:Ab initio fragment molecular orbital study. J Comput Chem 2006; 27:948-60. [PMID: 16586530 DOI: 10.1002/jcc.20399] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP, and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding.
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Affiliation(s)
- Kaori Fukuzawa
- Mizuho Information & Research Institute, Inc., Chiyoda-ku, Tokyo 101-8443, Japan.
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Latypov S, Fakhfakh MA, Jullian JC, Franck X, Hocquemiller R, Figadère B. Self-Associative Properties of Quinoline Derivatives in Solution. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2005. [DOI: 10.1246/bcsj.78.1296] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Schweiger S, Hartke B, Rauhut G. Double proton transfer reactions at the transition from a concerted to a stepwise mechanism: a comparative ab initio study. Phys Chem Chem Phys 2005. [DOI: 10.1039/b415528a] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nakatani K, Kobori A, Kumasawa H, Goto Y, Saito I. The binding of guanine–guanine mismatched DNA to naphthyridine dimer immobilized sensor surfaces: kinetic aspects. Bioorg Med Chem 2004; 12:3117-23. [PMID: 15158779 DOI: 10.1016/j.bmc.2004.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 04/08/2004] [Accepted: 04/08/2004] [Indexed: 10/26/2022]
Abstract
Naphthyridine dimer composed of two naphthyridine chromophores and a linker connecting them strongly, and selectively, binds to the guanine-guanine mismatch in duplex DNA. The kinetics for the binding of the G-G mismatch to the naphthyridine dimer was investigated by surface plasmon resonance assay. The sensor surface was prepared by immobilizing naphthyridine dimer through a long poly(ethylene oxide) linker with the ligand density of 9.1 x 10(-12) fmolnm(-2). The kinetic analyses revealed that the binding of the G-G mismatch was sequence dependent on the flanking base pairs, and the G-G mismatches flanking at least one G-C base pair bound to the surface via a two-step process with a 1:1 DNA-ligand stoichiometry. The first association rate constant for the binding of the G-G mismatch in the 5'-CGG-3'/3'-GGC-5' sequence to the naphthyridine dimer-immobilized sensor surface was 3.2 x 10(3)M(-1)s(-1) and the first dissociation rate constant was 1.4 x 10(-2)s(-1). The association and dissociation rate constants for the second step were insensitive to the flanking sequences, and were almost of the same order of magnitude as the first dissociation rate constant. This indicates that the second step had only a small energetic contribution to the binding. The association constant calculated from kinetic parameters was 2.7 x 10(5)M(-1), which is significantly smaller than the apparent association constants obtained from experiments in solution. Electrospray ionization time-of-flight (ESI-TOF) mass spectrometry on the complex produced from the G-G mismatch and naphthyridine dimer showed the formation of the 1:1 complex and a 1:2 DNA-ligand complex in solution. The latter complex became the dominant complex when a six-fold excess of naphthyridine dimer was added to DNA.
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Affiliation(s)
- Kazuhiko Nakatani
- PRESTO, Japan Science and Technology Agency (JST), Kyoto 615-8510, Japan.
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Kobori A, Horie S, Suda H, Saito I, Nakatani K. The SPR sensor detecting cytosine[bond]cytosine mismatches. J Am Chem Soc 2004; 126:557-62. [PMID: 14719953 DOI: 10.1021/ja037947w] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have synthesized the first surface plasmon resonance (SPR) sensor that detects cytosine-cytosine (C[bond]C) mismatches in duplex DNA by immobilizing aminonaphthyridine dimer on the gold surface. The ligand consisting of two 2-aminonaphthyridine chromophores and an alkyl linker connecting them strongly stabilized the C[bond]C mismatches regardless of the flanking sequences. The fully matched duplexes were not stabilized at all under the same conditions. The C[bond]T, C[bond]A, and T[bond]T mismatches were also stabilized with a reduced efficiency. SPR analyses of mismatch-containing 27-mer duplexes were performed with the sensor surface on which the aminonaphthyridine dimer was immobilized. The response for the C[bond]C mismatch in 5'-GCC-3'/3'-CCG-5' was about 83 times stronger than that obtained for the fully matched duplex. The sensor successfully detects the C[bond]C mismatch at the concentration of 10 nM. SPR responses are proportional to the concentration of the C[bond]C mismatch in a range up to 200 nM. Aminonaphthyridine dimer could bind strongly to the C[bond]C mismatches having 10 possible flanking sequences with association constants in the order of 10(6) M(-1). The facile protonation of 2-aminonaphthyridine chromophore at pH 7 producing the hydrogen-bonding surface complementary to that of cytosine was most likely due to the remarkably high selectivity of 1 to the C[bond]C mismatch.
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Affiliation(s)
- Akio Kobori
- PRESTO, Japan Science and Technology Agency (JST), Kyoto 615-8510, Japan
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36
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Parthasarathi R, Amutha R, Subramanian V, Nair BU, Ramasami T. Bader's and Reactivity Descriptors' Analysis of DNA Base Pairs. J Phys Chem A 2004. [DOI: 10.1021/jp031285f] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R. Parthasarathi
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - R. Amutha
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | | | - T. Ramasami
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
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37
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Dračínský M, Castaño O. Calculations of interaction energies of ellipticine derivatives with DNA base pairs. Phys Chem Chem Phys 2004. [DOI: 10.1039/b400471j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Schweiger S, Rauhut G. Plateau Reactions: Double Proton-Transfer Processes with Structureless Transition States. J Phys Chem A 2003. [DOI: 10.1021/jp0350060] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Schweiger
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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39
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Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs. Int J Mol Sci 2003. [DOI: 10.3390/i4100537] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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40
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Šponer J, Hobza P. Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies. ACTA ACUST UNITED AC 2003. [DOI: 10.1135/cccc20032231] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.
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41
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Li X, Cai Z, Sevilla MD. Energetics of the Radical Ions of the AT and AU Base Pairs: A Density Functional Theory (DFT) Study. J Phys Chem A 2002. [DOI: 10.1021/jp021322n] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xifeng Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - Zhongli Cai
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - M. D. Sevilla
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
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42
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Rueda M, Luque FJ, López JM, Orozco M. Amino−Imino Tautomerism in Derivatives of Cytosine: Effect on Hydrogen-Bonding and Stacking Properties. J Phys Chem A 2001. [DOI: 10.1021/jp010838o] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manuel Rueda
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
| | - F. Javier Luque
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
| | - Josep Maria López
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
| | - Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
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43
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Abstract
It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.
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Affiliation(s)
- R Luo
- Center for Advanced Research in Biotechnology, Rockville, Maryland 20850-3479, USA
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44
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Rauhut G. Recent Advances in Computing Heteroatom-Rich Five- and Six-Membered Ring Systems. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)81010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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45
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Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
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46
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Barsky D, Colvin ME. Guanine−Cytosine Base Pairs in Parallel-Stranded DNA: An ab Initio Study of the Keto−Amino Wobble Pair versus the Enol−Imino Minor Tautomer Pair. J Phys Chem A 2000. [DOI: 10.1021/jp001420d] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Barsky
- Biology and Biotechnology Research Program, Lawrence Livermore National Lab, L-448, Livermore, California 94550
| | - Michael E. Colvin
- Biology and Biotechnology Research Program, Lawrence Livermore National Lab, L-448, Livermore, California 94550
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47
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Lamsabhi M, Alcamí M, Mó O, Bouab W, Esseffar M, Abboud JLM, Yáñez M. Are the Thiouracils Sulfur Bases in the Gas-phase? J Phys Chem A 2000. [DOI: 10.1021/jp000071k] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Lamsabhi
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
| | - M. Alcamí
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
| | - O. Mó
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
| | - W. Bouab
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
| | - M. Esseffar
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
| | - J. L.-M. Abboud
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
| | - M. Yáñez
- Departement de Chimie, Faculté des Sciences Semlalia Université Cadi Ayyad., Marrakech, Morocco, Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, and Instituto “Rocasolano”, C.S.I.C., Serrano, 119, 28006-Madrid, Spain
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48
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Šponer J, Hobza P. Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals. J Phys Chem A 2000. [DOI: 10.1021/jp9943880] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic
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49
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Fonseca Guerra C, Bickelhaupt FM, Snijders JG, Baerends EJ. Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment. J Am Chem Soc 2000. [DOI: 10.1021/ja993262d] [Citation(s) in RCA: 372] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Célia Fonseca Guerra
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
| | - F. Matthias Bickelhaupt
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
| | - Jaap G. Snijders
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
| | - Evert Jan Baerends
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
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50
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Saito I, Nakamura T, Nakatani K. Mapping of Highest Occupied Molecular Orbitals of Duplex DNA by Cobalt-Mediated Guanine Oxidation. J Am Chem Soc 2000. [DOI: 10.1021/ja993891n] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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