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Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes (Basel) 2024; 15:113. [PMID: 38255005 PMCID: PMC10815195 DOI: 10.3390/genes15010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.
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Affiliation(s)
- Erica C. Silva
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Carlos A. Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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Stanković B, Ostojić B, Gruden M, Popović A, Đorđević D. Substituted naphthalenes: Stability, conformational flexibility and description of bonding based on ETS-NOCV method. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.08.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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El-Sayed AA, Tamara Molina A, Álvarez-Ros M, Alcolea Palafox M. Conformational analysis of the anti-HIV Nikavir prodrug: comparisons with AZT and Thymidine, and establishment of structure–activity relationships/tendencies in other 6′-derivatives. J Biomol Struct Dyn 2014; 33:723-48. [DOI: 10.1080/07391102.2014.909743] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - A. Tamara Molina
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
| | - M.C. Álvarez-Ros
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
| | - M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
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Brovarets' OO, Zhurakivsky RO, Hovorun DM. Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question. J Comput Chem 2013; 35:451-66. [PMID: 24382756 DOI: 10.1002/jcc.23515] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/12/2013] [Accepted: 11/30/2013] [Indexed: 02/04/2023]
Abstract
Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form.
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Affiliation(s)
- Ol'ha O Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str., 03680, Kyiv, Ukraine ; Research and Educational Center "State Key Laboratory of Molecular and Cell Biology", 150 Akademika Zabolotnoho Str., 03680, Kyiv, Ukraine; Department of Molecular Biology, Biotechnology and Biophysics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave., 03022, Kyiv, Ukraine
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Alcolea Palafox M. Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour. J Biomol Struct Dyn 2013; 32:831-51. [DOI: 10.1080/07391102.2013.789402] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lopes RP, Valero R, Tomkinson J, Marques MPM, Batista de Carvalho LAE. Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study. NEW J CHEM 2013. [DOI: 10.1039/c3nj00445g] [Citation(s) in RCA: 24] [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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9
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Xiao S, Liang H. The conformational flexibility of nucleic acid bases paired in gas phase: A Car-Parrinello molecular dynamics study. J Chem Phys 2012; 136:205102. [DOI: 10.1063/1.4720352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Omelchenko IV, Shishkin OV, Gorb L, Hill FC, Leszczynski J. Properties, aromaticity, and substituents effects in poly nitro- and amino-substituted benzenes. Struct Chem 2012. [DOI: 10.1007/s11224-012-9971-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Cyclic α-amino acids as precursors for synthesis of 2-amino-3-hetarylpyrrolin-4-ones and their spiro derivatives. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-012-0727-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Nikolaienko TY, Bulavin LA, Hovorun DM. Structural flexibility of DNA-like conformers of canonical 2′-deoxyribonucleosides. Phys Chem Chem Phys 2012; 14:15554-61. [DOI: 10.1039/c2cp43120c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Omelchenko IV, Shishkin OV, Gorb L, Leszczynski J, Fias S, Bultinck P. Aromaticity in heterocyclic analogues of benzene: comprehensive analysis of structural aspects, electron delocalization and magnetic characteristics. Phys Chem Chem Phys 2011; 13:20536-48. [DOI: 10.1039/c1cp20905a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sychrovsky V, Foldynova-Trantirkova S, Spackova N, Robeyns K, Van Meervelt L, Blankenfeldt W, Vokacova Z, Sponer J, Trantirek L. Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion. Nucleic Acids Res 2010; 37:7321-31. [PMID: 19786496 PMCID: PMC2790901 DOI: 10.1093/nar/gkp783] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.
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Affiliation(s)
- Vladimir Sychrovsky
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo namesti 2, CZ, 16610 Prague, Czech Republic
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Furmanchuk A, Shishkin OV, Isayev O, Gorb L, Leszczynski J. New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics. Phys Chem Chem Phys 2010; 12:9945-54. [DOI: 10.1039/c002934c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Mohamed TA, Shabaan IA, Zoghaib WM, Husband J, Farag RS, Alajhaz AENM. Tautomerism, normal coordinate analysis, vibrational assignments, calculated IR, Raman and NMR spectra of adenine. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.09.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Shukla M, Dubey M, Zakar E, Namburu R, Czyznikowska Z, Leszczynski J. Interaction of nucleic acid bases with single-walled carbon nanotube. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Shishkin OV, Gorb L, Leszczynski J. Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study. Struct Chem 2009. [DOI: 10.1007/s11224-009-9477-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dobrowolski MA, Cyrański MK, Merner BL, Bodwell GJ, Wu JI, Schleyer PVR. Interplay of pi-electron delocalization and strain in [n](2,7)pyrenophanes. J Org Chem 2008; 73:8001-9. [PMID: 18798674 DOI: 10.1021/jo8014159] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The geometries of a series of [n](2,7)pyrenophanes (n = 6-12) were optimized at the B3LYP/6-311G** DFT level. The X-ray crystal structures determined for the [9](2,7)- and [10](2,7)pyrenophanes agreed excellently with the computed structures. The degree of nonplanarity of the pyrene moiety depends on the number of CH2 groups in the aliphatic bridge and, as analyzed theoretically, influences the strain energy and the extent of pi-electron delocalization in the pyrene fragment. Various indices, e.g., the relative aromatic stabilization energies (DeltaASE), magnetic susceptibility exaltations (Lambda), nucleus-independent chemical shifts (NICS), and the harmonic oscillator model of aromaticity (HOMA) were used to quantify the change in aromatic character of the pyrene fragment. DeltaASE and relative Lambda values (with respect to planar pyrene) were evaluated by homodesmotic equations comparing the bent pyrene unit with its bent quinoid dimethylene-substituted analog. The bend angle, alpha, DeltaASE, and Lambda were linearly related. The aromaticity decreases smoothly and regularly over a wide range of bending, but the magnitude of the change is not large. The differences between planar pyrene (alpha = 0 degrees) and the most distorted pyrene unit (alpha = 39.7 degrees in [6](2,7)pyrenophane) are only 15.8 kcal/mol (DeltaASE) and 18.8 cgs-ppm (Lambda). Also, the geometry-based HOMA descriptor changes by only 0.07 unit. The local NICS descriptors of aromatic character also correlate very well with the global indices of aromaticity. In line with the known reactivity of pyrenophanes, the variations of NICS(1), a measure of pi-electron delocalization, were largest for the outer, biphenyl-type rings. The strain energies of the pyrene fragments were much larger and varied more than those evaluated for the bridge. Both strain energies were interrelated (correlation coefficient R = 0.979) and depend on the bend angle, alpha.
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Affiliation(s)
- Michał A Dobrowolski
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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Shukla MK, Leszczynski J. Electronic Spectra, Excited State Structures and Interactions of Nucleic Acid Bases and Base Assemblies: A Review. J Biomol Struct Dyn 2007; 25:93-118. [PMID: 17676942 DOI: 10.1080/07391102.2007.10507159] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A comprehensive review of recent theoretical and experimental advances in the singlet electronic transitions, excited state structures and dynamics of nucleic acid bases (NABs) and base assemblies are presented. It is well known that NABs absorb ultraviolet radiation, but the absorbed energy is efficiently dissipated in the form of ultrafast internal conversion processes believed to occur in the subpicosecond time scale and, therefore, enabling NABs highly photostable. It is not known how much evolutionary role was played in evolving these molecules and the ultimate selection by nature as genetic materials, but it is well accepted that survival-of-fittest prevails. Recently, significant efforts have been continuously paid to understand the mechanism of electronic excitation deactivation, but universally acceptable mechanism is still elusive. However, recent investigations reveal that electronic excited state geometries of DNA bases are usually nonplanar and this structural nonplanarity may facilitate nonradiative deactivation. Investigation of excited state structures is challenging and, therefore, it is not surprising that despite the impressive theoretical and computational advances, this research area is still hampered by the methodological and computational limitations. Further, stacking has significant influence on the emission properties of molecules. The 2-aminopurine, a fluorescent adenine derivative frequently used in studying DNA dynamics, shows significant attenuations in fluorescence quantum yield when incorporated in the DNA. Theoretical and computational bottlenecks limit a thorough theoretical understanding of effect of stacking interactions on the excited state dynamics of NABs. Despite these limitations the investigations of excited state properties are progressing in the right direction and our better understanding of excited state structure and dynamics of NABs and nucleic acids may help to design preventive strategy for radiation induced illness and photostable materials.
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Affiliation(s)
- M K Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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Shishkin OV, Omelchenko IV, Krasovska MV, Zubatyuk RI, Gorb L, Leszczynski J. Aromaticity of monosubstituted derivatives of benzene. The application of out-of-plane ring deformation energy for a quantitative description of aromaticity. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.01.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Shukla MK, Leszczynski J. Effect of Hydration on the Lowest Singlet ππ* Excited-State Geometry of Guanine: A Theoretical Study. J Phys Chem B 2005; 109:17333-9. [PMID: 16853213 DOI: 10.1021/jp0520751] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An ab-initio computational study was performed to investigate the effect of explicit hydration on the ground and lowest singlet PiPi* excited-state geometry and on the selected stretching vibrational frequencies corresponding to the different NH sites of the guanine acting as hydrogen-bond donors. The studied systems consisted of guanine interacting with one, three, five, six, and seven water molecules. Ground-state geometries were optimized at the HF level, while excited-state geometries were optimized at the CIS level. The 6-311G(d,p) basis set was used in all calculations. The nature of potential energy surfaces was ascertained via the harmonic vibrational frequency analysis; all structures were found minima at the respective potential energy surfaces. The changes in the geometry and the stretching vibrational frequencies of hydrogen-bond-donating sites of the guanine in the ground and excited state consequent to the hydration are discussed. It was found that the first solvation shell of the guanine can accommodate up to six water molecules. The addition of the another water molecule distorts the hydrogen-bonding network by displacing other neighboring water molecules away from the guanine plane.
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Affiliation(s)
- M K Shukla
- Computational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA
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Fernández-Quejo M, de la Fuente M, Navarro R. Theoretical calculations and vibrational study of hypoxanthine in aqueous solution. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Shishkin OV, Gorb L, Zhikol OA, Leszczynski J. Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides. J Biomol Struct Dyn 2005; 22:227-44. [PMID: 15317483 DOI: 10.1080/07391102.2004.10506998] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The molecular structure of different conformers of isolated canonical purine 2'-deoxyribonucleotides 2-deoxyadenosine-5'-phosphate (pdA) and 2'-deoxyguanosine-5'-phosphate (pdG) was optimized using the B3LYP/6-31G(d) method. The results of the calculations reveal that the geometrical parameters and relative stability of the conformers significantly depend on the nature of the nucleobase, its orientation, the conformation of the furanose ring, the charge of the phosphate group and the character of the intramolecular hydrogen bonds. Analysis of the electron density distribution in purine nucleotides reveals the existence of a number of intramolecular hydrogen bonds. In general, the south conformer has a lower energy at the anti orientation of the base, and both conformers occur as the most stable for the syn orientation of the nucleobases. The results of the calculations reveal that the geometry and relative energy of the conformers of purine DNTs may be easily tuned by the charge of the phosphate group.
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Affiliation(s)
- Oleg V Shishkin
- Institute for Scintillation Materials, National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv 61001, Ukraine.
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Shishkin OV, Gorb L, Zhikol OA, Leszczynski J. Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides. J Biomol Struct Dyn 2004; 21:537-54. [PMID: 14692798 DOI: 10.1080/07391102.2004.10506947] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The molecular structure and relative stability of north and south conformers of 2'-deoxyribonucleotides containing pyrimidine nucleic acid bases ( 2'-deoxythymidilic (pdT), 2'-deoxycytidilic (pdC) acids and their mono- and dianions) have been obtained and analyzed at the DFT/B3LYP level using the standard 6-31G(d) basis set. We have revealed that, when the nucleobase moiety is incorporated into the nucleotides, it maintains a nonplanar and nonrigid conformation due to out-of-plane deformation of the amino group and pyrimidine ring. It has been demonstrated that an increase of negative charge of the phosphate group results in increase of amino group pyramidalization, discrimination between conformers with syn and anti orientation of base with respect to sugar, strengthening of intramolecular C-H.O hydrogen bonds leading to deformation and fixation of geometry of nucleotides, and weakening of phosphodiester bond. These results allow to make suggestions about sources of twist and buckle deformations of base pairs, mechanisms of repaire of DNA via change of base orientation, and conditions for breakage of the P-O bonds during hydrolysis.
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Affiliation(s)
- Oleg V Shishkin
- Institute for Scintillation Materials, National Academy of Science of Ukraine, 60 Lenina Ave, Kharkiv 61001, Ukraine.
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Zhigalko MV, Shishkin OV, Gorb L, Leszczynski J. Out-of-plane deformability of aromatic systems in naphthalene, anthracene and phenanthrene. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.02.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Structure and conformational flexibility of uracil: A comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00032-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Chen Q, Richardson NV. Enantiomeric interactions between nucleic acid bases and amino acids on solid surfaces. NATURE MATERIALS 2003; 2:324-328. [PMID: 12692537 DOI: 10.1038/nmat878] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Accepted: 03/18/2003] [Indexed: 05/24/2023]
Abstract
Molecular interaction between nucleic acid bases and amino acids is a fundamental process in biology. The adsorption of the molecules on surfaces provides the opportunity to study such interactions in great detail by exploiting the high-resolution imaging capabilities of scanning tunnelling microscopy (STM). The chemisorption of prochiral molecules, such as adenine, on a metal surface causes the adsorbed species to become chiral. Subsequent interactions with inherently chiral molecules may then lead to the formation of diastereoisomers, if the enantiomeric interaction process is sufficiently strong. In the case of adenine adsorption on Cu[110], the chiral adsorbates form homochiral chains. Here, we show that the adenine chain direction is fully correlated with the chirality, and that the alpha-amino acid, phenylglycine, shows a strong chiral preference in its interaction with these chains. STM images clearly demonstrate that S-phenylglycine (R-phenylglycine) binds only to chains rotated 19.5 degrees (anti-) clockwise from the [001] direction. Closer examination reveals that the enantiomeric interaction involves double rows of phenylglycine molecules and the adenine chains. This is the first observation at the molecular level of diastereoisomeric interaction, and demonstrates that STM is a powerful method for studying the details of these interactions.
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Affiliation(s)
- Q Chen
- School of Chemistry, North Haugh, University of St Andrews, St Andrews, Fife KY16 9ST, UK.
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Munzarová ML, Sklenár V. DFT analysis of NMR scalar interactions across the glycosidic bond in DNA. J Am Chem Soc 2003; 125:3649-58. [PMID: 12643728 DOI: 10.1021/ja028931t] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relationship between the glycosidic torsion angle chi, the three-bond couplings (3)J(C2/4-H1') and (3)J(C6/8-H1'), and the one-bond coupling (1)J(C1'-H1') in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and chi depend strongly on the aromatic base. (3)J(C2/4-H1') reveals different behavior for deoxyadenosine, deoxyguanosine, and deoxycytidine as compared to deoxythymidine and deoxyuridine. In the case of (3)J(C6/8-H1'), an opposite trans to cis ratio of couplings is obtained for pyrimidine nucleosides in contrast to purine nucleosides. The extremes of the Karplus curves are shifted by ca. 10 degrees with respect to syn and anti-periplanar orientations of the coupled nuclei. The change in the sugar pucker from S to N decreases (3)J(C2/4-H1') and (3)J(C6/8-H1'), while increasing (1)J(C1'-H1') for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. The influence of the sugar pucker on (1)J(C1'-H1') is interpreted in terms of interactions between the n(O4'), sigma*(C1'-H1') orbitals. The (1)J(C1'-H1') are related to chi through a generalized Karplus relationship, which combines cos(chi) and cos(2)(chi) functions with mutually different phase shifts that implicitly accounts for a significant portion of the related sugar pucker effects. Most of theoretical (3)J(C2/4-H1') and (3)J(C6/8-H1') for uracil cyclo-nucleosides compare well with available experimental data. (3)J(C6/8-H1') couplings for all C2-bridged nucleosides are up to 3 Hz smaller than in the genuine nucleosides with the corresponding chi, revealing a nonlocal aspect of the spin-spin interactions across the glycosidic bond. Theoretical (1)J(C1'-H1') are underestimated with respect to the experiment by ca. 10% but reproduce the trends in (1)J(C1'-H1') vs chi.
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Affiliation(s)
- Markéta L Munzarová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, CZ-611 37 Brno, Czech Republic.
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Sukhanov OS, Shishkin OV, Gorb L, Podolyan Y, Leszczynski J. Molecular Structure and Hydrogen Bonding in Polyhydrated Complexes of Adenine: A DFT Study. J Phys Chem B 2003. [DOI: 10.1021/jp026487a] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oleg S. Sukhanov
- Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina Avenue, Kharkiv 61072, Ukraine, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217
| | - Oleg V. Shishkin
- Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina Avenue, Kharkiv 61072, Ukraine, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217
| | - Leonid Gorb
- Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina Avenue, Kharkiv 61072, Ukraine, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217
| | - Yeugen Podolyan
- Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina Avenue, Kharkiv 61072, Ukraine, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina Avenue, Kharkiv 61072, Ukraine, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217
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