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Sychrovský V, Sochorová Vokáčová Z, Trantírek L. Guanine bases in DNA G-quadruplex adopt nonplanar geometries owing to solvation and base pairing. J Phys Chem A 2012; 116:4144-51. [PMID: 22471881 DOI: 10.1021/jp2110049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The effect of base pairing and solvation on pyramidalization of the glycosidic nitrogen found in the residues of parallel G-quadruplex with NDB ID UDF062 is analyzed and explained with theoretical calculations. The extent of the pyramidalization depends on the local geometry of the 2'-deoxyguanosine residues, namely on their glycosidic torsion and sugar pucker, which are predetermined by the 3D-architecture of G-quadruplex. Pyramidal inversion of the glycosidic nitrogen found in 2'-deoxyguanosines of G-quadruplex is induced owing to site-specifically coordinated solvent. Different adiabatic structural constraints used for fixing the base-to-sugar orientation of 2'-deoxyguanosine in geometry optimizations result in different extents of pyramidalization and induce pyramidal inversion of the glycosidic nitrogen. These model geometry constraints helped us analyze the effect of real constraints represented by explicit molecular environment of selected residues of the G-quadruplex. The maximal extent of the glycosidic nitrogen pyramidalization found in the high-resolution crystal structure corresponds to the calculation to deformation energy of only 1 kcal mol(-1). The out-of-plane deformations of nucleobases thus provide a way for compensating the site-specific external environmental stress on the G-quadruplex.
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Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo square 2, 166 10 Prague 6, Czech Republic.
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9
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Giuliano BM, Feyer V, Prince KC, Coreno M, Evangelisti L, Melandri S, Caminati W. Tautomerism in 4-Hydroxypyrimidine, S-Methyl-2-thiouracil, and 2-Thiouracil. J Phys Chem A 2010; 114:12725-30. [DOI: 10.1021/jp106883s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Barbara M. Giuliano
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Vitaliy Feyer
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Kevin C. Prince
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Marcello Coreno
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Luca Evangelisti
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Sonia Melandri
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Walther Caminati
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
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10
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Li XQ, Fan P. A duplex DNA model with regular inter-base-pair hydrogen bonds. J Theor Biol 2010; 266:374-9. [PMID: 20621103 DOI: 10.1016/j.jtbi.2010.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 04/15/2010] [Accepted: 07/04/2010] [Indexed: 10/19/2022]
Abstract
It is well known that base-pair stacking is the main factor in stabilizing DNA duplex and plays an important role in determining DNA sequence-dependence. What is the dominant force in base-pair stacking? This fundamental biological question remains a challenging problem. Here, based on recent studies about the non-planarity of amino groups on DNA bases, we propose a new duplex DNA model, in which all base amino groups are non-planar and participate in forming regular inter-base-pair hydrogen bonds (IBP H-bonds). This model implies that IBP H-bonds are the dominant force stabilizing base-pair stacking and play a crucial role in determining the geometry and physical properties of sequence-dependent twisted stacking between adjacent base pairs. The model presents a new insight into the link, through regular IBP H-bonds, between base-sequence, fine structure and physical properties at dinucleotide step level, and provides an attractively concise, uniform and quantitative interpretation for various experimentally observed DNA sequence-dependent properties in terms of regular IBP H-bonds. It would provide a new approach to understanding the dynamics and underlying mechanisms of DNA sequence-dependent biological processes, sequence-structure-property relationships, DNA strand separation during replication and transcriptions, etc.
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Affiliation(s)
- Xu-Qing Li
- Department of Biomedical Engineering, Kunming University of Science and Technology, Kunming 650051, China.
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13
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Vogt N, Dorofeeva OV, Sipachev VA, Rykov AN. Molecular Structure of 9H-Adenine Tautomer: Gas-Phase Electron Diffraction and Quantum-Chemical Studies. J Phys Chem A 2009; 113:13816-23. [DOI: 10.1021/jp905755u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalja Vogt
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
| | - Olga V. Dorofeeva
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
| | - Victor A. Sipachev
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
| | - Anatolii N. Rykov
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
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14
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Conti I, Garavelli M, Orlandi G. Deciphering Low Energy Deactivation Channels in Adenine. J Am Chem Soc 2009; 131:16108-18. [DOI: 10.1021/ja902311y] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irene Conti
- Dipartimento di Chimica ‘G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica ‘G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Giorgio Orlandi
- Dipartimento di Chimica ‘G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
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15
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Conti I, Di Donato E, Negri F, Orlandi G. Revealing Excited State Interactions by Quantum-Chemical Modeling of Vibronic Activities: The R2PI Spectrum of Adenine. J Phys Chem A 2009; 113:15265-75. [DOI: 10.1021/jp905795n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irene Conti
- Dipartimento di Chimica “G. Ciamician”, Universitá di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Eugenio Di Donato
- Dipartimento di Chimica “G. Ciamician”, Universitá di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Fabrizia Negri
- Dipartimento di Chimica “G. Ciamician”, Universitá di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Giorgio Orlandi
- Dipartimento di Chimica “G. Ciamician”, Universitá di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
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