1
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Park G, Kang B, Park SV, Lee D, Oh SS. A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions. Nucleic Acids Res 2021; 49:4919-4933. [PMID: 33893806 PMCID: PMC8136788 DOI: 10.1093/nar/gkab285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
DNA can assume various structures as a result of interactions at atomic and molecular levels (e.g., hydrogen bonds, π–π stacking interactions, and electrostatic potentials), so understanding of the consequences of these interactions could guide development of ways to produce elaborate programmable DNA for applications in bio- and nanotechnology. We conducted advanced ab initio calculations to investigate nucleobase model structures by componentizing their donor-acceptor interactions. By unifying computational conditions, we compared the independent interactions of DNA duplexes, triplexes, and quadruplexes, which led us to evaluate a stability trend among Watson–Crick and Hoogsteen base pairing, stacking, and even ion binding. For a realistic solution-like environment, the influence of water molecules was carefully considered, and the potassium-ion preference of G-quadruplex was first analyzed at an ab initio level by considering both base-base and ion-water interactions. We devised new structure factors including hydrogen bond length, glycosidic vector angle, and twist angle, which were highly effective for comparison between computationally-predicted and experimentally-determined structures; we clarified the function of phosphate backbone during nucleobase ordering. The simulated tendency of net interaction energies agreed well with that of real world, and this agreement validates the potential of ab initio study to guide programming of complicated DNA constructs.
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Affiliation(s)
- Gyuri Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Donghwa Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
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2
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Norouzi P, Ghiasi R, Fazaeli R. Effects of External Electric Field on the Hydrolysis of Cisplatin: A Density Functional Theory Approach. RUSS J INORG CHEM+ 2021. [DOI: 10.1134/s0036023620140041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Daneshdoost V, Ghiasi R, Marjani A. INVESTIGATING THE EFFECTS OF THE EXTERNAL ELECTRIC FIELD ON OSMABENZYNE IN THE GROUND (S0) AND FIRST EXCITED SINGLET (S1) STATES: INSIGHT INTO STRUCTURES, ENERGY, AND PROPERTIES. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620110037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Norouzi P, Ghiasi R. Theoretical understanding the effects of external electric field on the hydrolysis of anticancer drug titanocene dichloride. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1781272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Parva Norouzi
- Department of Chemistry, Faculty of Basic Science, Arak Branch, Islamic Azad University, Arak, Iran
| | - Reza Ghiasi
- Department of Chemistry, Faculty of Basic Science, East Tehran Branch, Islamic Azad University, Tehran, Iran
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5
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Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
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6
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Ghiasi R, Sadeghi N. Effect of External Electric Field on the Electronic Structure and Aromaticity of Cr(CO)3(η6-C6H6) Complex. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s0036023619080114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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The interaction of 5-fluorouracil with graphene in presence of external electric field: a theoretical investigation. ADSORPTION 2019. [DOI: 10.1007/s10450-019-00140-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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8
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Porter JE, Chapagain P, Fernandez-Lima F. Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 2:60-65. [PMID: 30506977 DOI: 10.1002/rcm.8367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE DNA quadruplex structures have emerged as novel drug targets due to their role in preventing abnormal gene transcription and maintaining telomere stability. Trapped Ion Mobility Spectrometry-Mass Spectrometry (TIMS-MS), combined with theoretical modeling, is a powerful tool for studying the kinetic intermediates of DNA complexes formed in solution and interrogated in the gas phase after desolvation. METHODS A TAGGGT ssDNA sequence was purchased and studied in 10 mM ammonium acetate using nanospray electrospray ionization (nESI)-TIMS-MS in positive and negative ion mode. Collisional cross section (CCS) profiles were measured using internal calibration (Tune Mix). Theoretical structures were proposed based on molecular dynamics, charge location and geometry optimization for the most intense IMS bands based on the number of TAGGGT units, adduct form and charge states. RESULTS A distribution of monomeric, dimeric and tetrameric TAGGGT structures were formed in solution and separated in the gas phase based on their mobility and m/z value (e.g., [M + 2H]+2 , [2M + 3H]+3 , [M - 2H]-2 , [2M - 3H]-3 , [4M + 4H]+4 , [4M + 3H + NH4 ]+4 , [4M + 2H + 2NH4 ]+4 and [4M + H + 3NH4 ]+4 ). The high mobility resolution of the TIMS-MS analyzer permitted the observation of multiple CCS bands per molecular ion form. Comparison with theoretical candidate structures suggests that monomeric TAGGGT species are stabilized by A-T and G+ -G interactions, with the size of the conformer influenced by the proton location. In the case of the TAGGGT quadruplex, the protonated species displayed a broad CCS distribution, while six discrete conformers were stabilized by the presence of ammonium ions (n = 1-3). CONCLUSIONS This is the first observation of multiple conformations of TAGGGT complexes (n = 1, 2 and 4) in 10 mM ammonium acetate. Candidate structures with intramolecular interactions of the form of G+ -G and traditional A-T base pairing agreed with the experimental trends. Our results demonstrate the structural diversity of TAGGGT monomers, dimers and tetramers in the gas phase beyond the previously reported solution structure, using 10 mM ammonium acetate to replicate biological conditions.
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Affiliation(s)
- Jacob E Porter
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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9
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Zoherh Zandiyeh, Reza Ghiasi. A Theoretical Approach towards Identification of External Electric Field Effect on (η5-C5H5)Me2Ta(η2-C6H4). RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024419030294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Ghobadi H, Ghiasi R, Jamehbozorgi S. Effect of the External Electric Field on the Electronic Structure and Aromaticity of Iridabenzene: A DFT Study. J STRUCT CHEM+ 2019. [DOI: 10.1134/s002247661904005x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Arya N, Mishra SK, Suryaprakash N. Intramolecular hydrogen bond directed distribution of conformational populations in the derivatives of N′-benzylidenebenzohydrazide. NEW J CHEM 2019. [DOI: 10.1039/c9nj03071a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The extensive NMR investigations reveal the presence of E-isomers in the derivative of N′-benzylidenebenzohydrazide. The different conformer populations are controlled by the strength of intramolecular hydrogen bonds.
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Affiliation(s)
- Neeru Arya
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - Sandeep Kumar Mishra
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - N. Suryaprakash
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
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12
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Gordon CKL, Eisenstein M, Soh HT. Direct Selection Strategy for Isolating Aptamers with pH-Sensitive Binding Activity. ACS Sens 2018; 3:2574-2580. [PMID: 30520292 PMCID: PMC6312627 DOI: 10.1021/acssensors.8b00945] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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An
aptamer reagent that can switch its binding affinity in a pH-responsive
manner would be highly valuable for many biomedical applications including
imaging and drug delivery. Unfortunately, the discovery of such aptamers
is difficult and only a few have been reported to date. Here we report
the first experimental strategy for generating pH-responsive aptamers
through direct selection. As an exemplar, we report streptavidin-binding
aptamers that retain nanomolar affinity at pH 7.4 but exhibit a ∼100-fold
decrease in affinity at pH 5.2. These aptamers were generated by incorporating
a known streptavidin-binding DNA motif into an aptamer library and
performing FACS-based screening at multiple pH conditions. Upon structural
analysis, we found that one aptamer’s affinity-switching behavior
is driven by a noncanonical G-A base-pair that controls its folding
in a highly pH-dependent manner. We believe our strategy could be
readily extended to other aptamer-target systems because it does not
require a priori structural knowledge of the aptamer or the target.
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Affiliation(s)
| | | | - Hyongsok Tom Soh
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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13
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Srinivasadesikan V, Chen YC, Lee SL. On the misincorporation of nucleotides opposite mutagenic cyclic 1,N 2-propanoguanine: A computational investigation. J Mol Graph Model 2018; 85:270-280. [PMID: 30253282 DOI: 10.1016/j.jmgm.2018.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/22/2018] [Accepted: 08/30/2018] [Indexed: 11/30/2022]
Abstract
The misincorporation properties of exocyclic DNA adduct, cyclic 1,N2-propanoguanine with nucleobases have been investigated using DFT and DFT-D methods. Number of possible and stable mispairing conformations of cyclic 1,N2-propanoguanine with A,T,G and C have been considered for our investigation. The single point energy calculations have been carried out at the M06/6-311++G**, ωB97XD/6-311++G** and MP2/6-311++G** levels on corresponding optimized geometries. The reaction enthalpy values were employed at the M06/6-31 + G* and ωB97XD/6-31 + G* levels. The energies have been compared among the cyclic 1,N2-propanoguanine adduct with nucleobases to find the most stable conformer. The CPCM model was utilized on account of solvent phase and overall polarizability. The computed binding energies follow the order as CPr-Gua-G(2)(-23.2 kcal/mol) > CPr-Gua-C(1) (-16.1 kcal/mol) > CPr-Gua-A(2)(-10.6 kcal/mol) > CPr-Gua-T(2)(-9.6 kcal/mol) in the gas phase at M06 level, which indicates the guanine and cytosine are favorable for mispairing with the cyclic 1,N2-propanoguanine adduct. The obtained results using computational tools are in good agreement with the experimental observation.
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Affiliation(s)
- V Srinivasadesikan
- Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan; Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, 522 213, Andhra Pradesh, India
| | - Ya-Chi Chen
- Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan.
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14
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On the effect of external perturbation on amino acid salt bridge: a DFT study. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1266-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Shamami MK, Ghiasi R. The Analysis of Os≡C Bond and Electric Field Influence on the Properties in the Osmium Carbyne Complex OsCl3
(≡CCH2
CMe3
)(PH3
)2
: A Theoretical Insight. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201700020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Reza Ghiasi
- Department of Chemistry, East Tehran Branch; Islamic Azad University; Tehran Iran
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16
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Kosevich MV, Zobnina VG, Stepanian SG, Karachevtsev VA, Adamowicz L. The effect of protonation of cytosine and adenine on their interactions with carbon nanotubes. J Mol Graph Model 2016; 70:77-84. [DOI: 10.1016/j.jmgm.2016.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 01/12/2023]
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17
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McConnell EM, Bolzon R, Mezin P, Frahm G, Johnston M, DeRosa MC. pHAST (pH-Driven Aptamer Switch for Thrombin) Catch-and-Release of Target Protein. Bioconjug Chem 2016; 27:1493-9. [PMID: 27115292 DOI: 10.1021/acs.bioconjchem.6b00124] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A pH-driven DNA nanomachine based on the human α-thrombin binding aptamer was designed for the specific catch-and-release of human α-thrombin at neutral and acidic pH, respectively. In neutral conditions, the thrombin aptamer component of the nanomachine is exposed and exists in the G-quadruplex conformation required to bind to the target protein. At slightly acidic pH, the polyadenine tail of the nanomachine becomes partially protonated and A+(anti)•G(syn) mispairing results in a conformational change, causing the target protein to be released. Förster resonance energy transfer (FRET) was used to monitor conformational switching over multiple pH cycles. Electrophoretic mobility shift assay (EMSA) and fluorescence anisotropy were used to show pH dependent protein binding and release by the nanomachine. This approach could be applied generally to existing G-rich aptamers to develop novel biosensors, theranostics, and nanoswitches.
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Affiliation(s)
- E M McConnell
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - R Bolzon
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - P Mezin
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - G Frahm
- Centre for Biologics Evaluation, Health Canada , 251 Sir Frederick Banting, Ottawa, Ontario K1A 0K9, Canada
| | - M Johnston
- Centre for Biologics Evaluation, Health Canada , 251 Sir Frederick Banting, Ottawa, Ontario K1A 0K9, Canada
| | - M C DeRosa
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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18
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Dahlen O, van Erp TS. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison. J Chem Phys 2015; 142:235101. [DOI: 10.1063/1.4922519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Oda Dahlen
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim, Norway
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim, Norway
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19
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Guillaumes L, Simon S, Fonseca Guerra C. The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics. ChemistryOpen 2015; 4:318-27. [PMID: 26246994 PMCID: PMC4522182 DOI: 10.1002/open.201402132] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 11/09/2022] Open
Abstract
Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp (2) to sp (3), does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.
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Affiliation(s)
- L Guillaumes
- Institut de Química Computacional i Catàlisi, Departament de Química, Universitat de Girona17071, Girona, Spain)
| | - S Simon
- Institut de Química Computacional i Catàlisi, Departament de Química, Universitat de Girona17071, Girona, Spain)
| | - C Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University AmsterdamDe Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands)
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20
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Halder A, Halder S, Bhattacharyya D, Mitra A. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study. Phys Chem Chem Phys 2015; 16:18383-96. [PMID: 25070186 DOI: 10.1039/c4cp02541e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India.
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21
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Jahiruddin S, Datta A. What Sustains the Unnatural Base Pairs (UBPs) with No Hydrogen Bonds. J Phys Chem B 2015; 119:5839-45. [DOI: 10.1021/acs.jpcb.5b03293] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sk Jahiruddin
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road,
Jadavpur, 700032 Kolkata, West Bengal, India
| | - Ayan Datta
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road,
Jadavpur, 700032 Kolkata, West Bengal, India
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22
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Ganguly M, Mondal C, Pal A, Pratik SM, Pal J, Pal T. Aggregation of nitroaniline in tetrahydrofuran through intriguing H-bond formation by sodium borohydride. Phys Chem Chem Phys 2015; 16:12865-74. [PMID: 24845227 DOI: 10.1039/c4cp00497c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The participation of sodium borohydride (NaBH4) in hydrogen bonding interactions and transient anion radical formation has been proved. Thus, the properties of NaBH4 are extended beyond the purview of its normal reducing capability and nucleophilic property. It is reported that ortho- and para-nitroanilines (NAs) form stable aggregates only in tetrahydrofuran (THF) in the presence of NaBH4 and unprecedented orange/red colorations are observed. The same recipe with nitrobenzene instead of nitroanilines (NAs) in the presence of NaBH4 evolves a transient rose red solution due to the formation of a highly fluorescent anion radical. Spectroscopic studies (UV-vis, fluorescence, RLS, Raman, NMR etc.) as well as theoretical calculations supplement the J-aggregate formation of NAs due to extensive hydrogen bonding. This is the first report where BH4(-) in THF has been shown to support such an aggregation process through H-bonding. It is further confirmed that stable intermolecular hydrogen bond-induced aggregation requires a geometrical match in both the nitro- and amino-functionalities attached to the phenyl ring with proper geometry. On the contrary, meta-nitroaniline remains as the odd man out and does not take part in such aggregation. Surprisingly, Au nanoparticles dismantle the J-aggregates of NA in THF. Explicit hydrogen bond formation in NA has been confirmed experimentally considering its promising applications in different fields including non-linear optics.
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Affiliation(s)
- Mainak Ganguly
- Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India.
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23
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Bhattacharyya PK. Effect of external electric field on ground and singlet excited states of phenylalanine: A theoretical study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.01.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Halder A, Bhattacharya S, Datta A, Bhattacharyya D, Mitra A. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs. Phys Chem Chem Phys 2015; 17:26249-63. [DOI: 10.1039/c5cp04894j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ab initio computations and bioinformatics studies reveal that stabilization of some important RNA structural motifs might involve N7 protonation of guanine.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | | | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
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Jacquemin D, Zúñiga J, Requena A, Céron-Carrasco JP. Assessing the importance of proton transfer reactions in DNA. Acc Chem Res 2014; 47:2467-74. [PMID: 24849375 DOI: 10.1021/ar500148c] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.
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Affiliation(s)
- Denis Jacquemin
- CEISAM, UMR CNRS 6230, Université de Nantes, 2, Rue de la Houssinière, Nantes 44322 Cedex 3, France
- Institut Universitaire de France, 103 bd St Michel, Paris 75005 Cedex 5, France
| | - José Zúñiga
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - José Pedro Céron-Carrasco
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
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26
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Dutta BJ, Bhattacharyya PK. Reactivity and Aromaticity of Nucleobases are Sensitive Toward External Electric Field. J Phys Chem B 2014; 118:9573-82. [DOI: 10.1021/jp5047535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Biswa Jyoti Dutta
- Department of Chemistry, Arya Vidyapeeth College, Guwahati, Assam 781016, India
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27
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Majhi D, Das SK, Sahu PK, Pratik SM, Kumar A, Sarkar M. Probing the aggregation behavior of 4-aminophthalimide and 4-(N,N-dimethyl) amino-N-methylphthalimide: a combined photophysical, crystallographic, microscopic and theoretical (DFT) study. Phys Chem Chem Phys 2014; 16:18349-59. [DOI: 10.1039/c4cp01912a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Abstract
While the Watson-Crick base pairs are known to stabilize the DNA double helix and play a vital role in storage/replication of genetic information, their replacement with non-Watson-Crick base pairs has recently been shown to have interesting practical applications. Nowadays, theoretical calculations are routinely performed on very complex systems to gain a better understanding of how molecules interact with each other. We not only bring together some of the basic concepts of how mispaired or unnatural nucleobases interact with each other but also look at how such an understanding influences the prediction of novel properties and development of new materials. We highlight the recent developments in this field of research. In this Perspective, we discuss the success of DFT methods, particularly, dispersion-corrected DFT, for applications such as pH-controlled molecular switching, electric-field-induced stacking of disk-like molecules with guanine quartets, and optical birefringence of alkali-metal-coordinated guanine quartets. The synergy between theoretical models and real applications is highlighted.
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Affiliation(s)
- A K Jissy
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur 700032 West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur 700032 West Bengal, India
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29
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Ghosh R, K. S. A, Pratik SM, Datta A, Nath R, Mandal S. Synthesis, structure, photocatalytic and magnetic properties of an oxo-bridged copper dimer. RSC Adv 2014. [DOI: 10.1039/c4ra01886a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A new paramagnetic and semiconductor copper citrate dimer exhibits photocatalytic behaviour towards organic dye degradation.
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Affiliation(s)
- Raja Ghosh
- School of Chemistry Indian Institute of Science Education and Research
- Thiruvananthapuram, India-695016
| | - Asha K. S.
- School of Chemistry Indian Institute of Science Education and Research
- Thiruvananthapuram, India-695016
| | - Saied Md. Pratik
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata, India-700032
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata, India-700032
| | - Ramesh Nath
- School of Physics
- Indian Institute of Science Education and Research
- Thiruvananthapuram, India-695016
| | - Sukhendu Mandal
- School of Chemistry Indian Institute of Science Education and Research
- Thiruvananthapuram, India-695016
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30
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Cerón-Carrasco JP, Cerezo J, Jacquemin D. How DNA is damaged by external electric fields: selective mutation vs. random degradation. Phys Chem Chem Phys 2014; 16:8243-6. [DOI: 10.1039/c3cp54518k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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31
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TIWARY AMITS, MUKHERJEE ASOKK. Inductive effect of methyl group in a series of methylated indoles: A graph theoretical analysis in the light of density functional theory and correlation with experimental charge transfer transition energies. J CHEM SCI 2013. [DOI: 10.1007/s12039-013-0436-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Mandal TK, Samanta S, Chakraborty S, Datta A. An Interplay of Cooperativity between Cation⋅⋅⋅π, Anion⋅⋅⋅π and CH⋅⋅⋅Anion Interactions. Chemphyschem 2013; 14:1149-54. [DOI: 10.1002/cphc.201300128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Indexed: 01/20/2023]
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33
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Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J. Nucleic acid bases in anionic 2'-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities. J Phys Chem B 2013; 117:2841-9. [PMID: 23425497 DOI: 10.1021/jp311363c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protonation of nucleobases in anions of canonical 2'-deoxyribonucleotides has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz level of theory. It is demonstrated that the protonation leads to a significant decrease of conformational space of purine nucleotides while almost all conformers found for non-protonated molecules correspond to minima of the potential energy surface for protonated mdTMP and mdCMP. However, in all nucleotides, only one conformer is populated. This applies to all tautomers of protonated molecules except the mdTMP and mdCMP with the proton attached to the carbonyl group where a minor population of second conformer is observed. Protonation of nucleobase leads to significant elongation of the N-glycosidic bond. These findings agree well with suggestions that protonation of nucleobase is a first step in cleavage of the glycosidic bond. The oxygen atoms of both carbonyl groups of thymine and the N3 atom of the pyrimidine ring of cytosine, guanine, and adenine represent the most preferable sites for protonation of anions of 2'-deoxyrobonucleotides. The highest proton affinity is observed for the base in mdGMP and the lowest for the thymine moiety in mdTMP. It should be noted that calculated values of the proton affinities in anionic nucleotides are significantly higher (by 2-3 eV) than for nucleosides and neutral nucleotides. This allows assuming that the proton affinity of the base in DNA macromolecule may be tuned by changing the extent of shielding or neutralization of negative charge of the phosphate group.
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Affiliation(s)
- Gennady V Palamarchuk
- STC Institute for Single Crystals, National Academy of Sciences of Ukraine, 60 Lenina ave., Kharkiv 61001, Ukraine
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34
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Jissy AK, Konar S, Datta A. Molecular Switching Behavior in Isosteric DNA Base Pairs. Chemphyschem 2013; 14:1219-26. [DOI: 10.1002/cphc.201201083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 12/22/2022]
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35
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Jissy AK, Datta A. Effect of External Electric Field on H-Bonding and π-Stacking Interactions in Guanine Aggregates. Chemphyschem 2012; 13:4163-72. [DOI: 10.1002/cphc.201200690] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/07/2012] [Indexed: 01/19/2023]
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36
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Prabavathi N, Nilufer A, Krishnakumar V, Akilandeswari L. Spectroscopic, electronic structure and natural bond analysis of 2-aminopyrimidine and 4-aminopyrazolo[3,4-d]pyrimidine: a comparative study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 96:226-241. [PMID: 22683558 DOI: 10.1016/j.saa.2012.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/23/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
The FTIR and FT-Raman spectra of 2-aminopyrimidine (2-AP) and 4-aminopyrazolo[3,4-d]pyrimidine (4-APP) has been recorded in the region 4000-400 and 3500-100 cm(-1), respectively. The tautomeric stability, optimized geometry, frequency and intensity of the vibrational bands of 2-AP and 4-APP were obtained by the DFT level using 6-31G(d) and 6-31G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. A detailed interpretation of the infrared and Raman spectra of 2-AP and 4-APP are also reported based on total energy distribution (TED). The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically simulated spectra. The (1)H and (13)C NMR spectra have been simulated using the gauge independent atomic orbital (GIAO) method. The theoretical UV-Vis spectrum of the compound using CIS method and the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β(0)) of these novel molecular system and related properties (β, α(0) and Δα) of 2-AP and 4-APP are calculated using DFT/6-31G(d) method on the finite-field approach. The Mulliken charges, the values of electric dipole moment (μ) of the molecule were computed using DFT calculations. The change in electron density (ED) in the σ(∗) antibonding orbitals and stabilization energies E(2) have been calculated by natural bond (NBO) analysis to give clear evidence of stabilization originating in the hyper conjugation of hydrogen-bonded interactions.
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Affiliation(s)
- N Prabavathi
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India.
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37
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JISSY AK, RAMANA JHV, DATTA AYAN. π-Stacking interactions between G-quartets and circulenes: A computational study. J CHEM SCI 2011. [DOI: 10.1007/s12039-011-0155-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Scott D, Hamorsky KT, Ensor CM, Anderson KW, Daunert S. Cyclic AMP receptor protein-aequorin molecular switch for cyclic AMP. Bioconjug Chem 2011; 22:475-81. [PMID: 21329338 DOI: 10.1021/bc100486b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Molecular switches are designer molecules that combine the functionality of two individual proteins into one, capable of manifesting an "on/off" signal in response to a stimulus. These switches have unique properties and functionalities and thus, can be employed as nanosensors in a variety of applications. To that end, we have developed a bioluminescent molecular switch for cyclic AMP. Bioluminescence offers many advantages over fluorescence and other detection methods including the fact that there is essentially zero background signal in physiological fluids, allowing for more sensitive detection and monitoring. The switch was created by combining the properties of the cyclic AMP receptor protein (CRP), a transcriptional regulatory protein from E. Coli that binds selectively to cAMP with those of aequorin, a bioluminescent photoprotein native of the jellyfish Aequorea victoria . Genetic manipulation to split the genetic coding sequence of aequorin in two and genetically attach the fragments to the N and C termini of CRP resulted in a hybrid protein molecular switch. The conformational change experienced by CRP upon the binding of cyclic AMP is suspected to result in the observed loss of the bioluminescent signal from aequorin. The "on/off" bioluminescence can be modulated by cyclic AMP over a range of several orders of magnitude in a linear fashion in addition to the capacity to detect changes in cellular cyclic AMP of intact cells exposed to different external stimuli without the need to lyse the cells. We envision that the molecular switch could find applications in vitro as well as In Vivo cyclic AMP detection and/or imaging.
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Affiliation(s)
- Daniel Scott
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, USA
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39
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Asaduzzaman AM, Schreckenbach G. Interactions of the N3 dye with the iodide redox shuttle: quantum chemical mechanistic studies of the dye regeneration in the dye-sensitized solar cell. Phys Chem Chem Phys 2011; 13:15148-57. [DOI: 10.1039/c1cp21168d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Cerón-Carrasco JP, Zúñiga J, Requena A, Perpète EA, Michaux C, Jacquemin D. Combined effect of stacking and solvation on the spontaneous mutation in DNA. Phys Chem Chem Phys 2011; 13:14584-9. [DOI: 10.1039/c1cp20946a] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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