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Krupová M, Leszczenko P, Sierka E, Emma Hamplová S, Pelc R, Andrushchenko V. Vibrational Circular Dichroism Unravels Supramolecular Chirality and Hydration Polymorphism of Nucleoside Crystals. Chemistry 2022; 28:e202201922. [DOI: 10.1002/chem.202201922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Hylleraas Centre for Quantum Molecular Sciences Department of Chemistry UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Patrycja Leszczenko
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
| | - Ewa Sierka
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
| | - Sára Emma Hamplová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Department of Biology and Biochemistry University of Bath Claverton Down Bath BA2 7AY United Kingdom
| | - Radek Pelc
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Third Faculty of Medicine Charles University Ruská 87 10000 Prague Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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2
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Polavarapu PL, Santoro E, Covington CL, Johnson JL, Puente AR, Schley ND, Kallingathodi Z, Prakasan PC, Haleema S, Thomas AA, Ibnusaud I. How important are the intermolecular hydrogen bonding interactions in methanol solvent for interpreting the chiroptical properties? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119094. [PMID: 33142265 DOI: 10.1016/j.saa.2020.119094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Two crispine A analogs and tetrahydrofuro[2,3-b]furan-3,3a(6aH)-diol, endowed with hydroxyl groups that can participate in intramolecular hydrogen bonding, have been synthesized and experimental vibrational circular dichroism (VCD) spectra and optical rotatory dispersion (ORD) data have been measured in CD3OD/CH3OH solvents. The absolute configurations (ACs) of these compounds have been determined using their synthetic schemes, supplemented wherever possible with X-ray diffraction data. The ACs are also analyzed with quantum chemical (QC) calculations of VCD and ORD utilizing implicit solvation as well as explicit solvation models, with the later employing classical molecular dynamics (MD) simulations. It is found that VCD calculations with implicit solvation model are adequate for determining the ACs, despite propensity of studied compounds for intermolecular hydrogen bonding between solute and solvent molecules. This observation is important because time-consuming MD simulations may not be necessary in the type of situations studied here. Additionally, it is found that the QC predicted VCD spectra provided enough diastereomer discrimination for determining the correct AC of studied compounds independently. The same observation did not apply to ORD.
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Affiliation(s)
| | - Ernesto Santoro
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Cody L Covington
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Austin Peay State University, Clarksville, TN 37044, USA
| | - Jordan L Johnson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Nathan D Schley
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
| | - Zabeera Kallingathodi
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Prasanth C Prakasan
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Simimole Haleema
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Annu Anna Thomas
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India
| | - Ibrahim Ibnusaud
- Institute for Integrated Programmes and Research in Basic Sciences, Mahatma Gandhi University, Kottayam 686560, India.
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3
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Bonsaii M, Gholivand K, Khosravi M, Abdi K. Negative hyperconjugation effect on the reactivity of phosphoramide mustard derivatives as a DNA alkylating agent: theoretical and experimental insights. NEW J CHEM 2017. [DOI: 10.1039/c7nj01402c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we suggest new factors affecting the reactivity of compounds similar to cyclophosphamide; as their reactivity mainly relies on the frontier molecular orbitals, the factors causing changes in the frontier molecular orbitals, alter the reactivity of these compounds too.
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Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- North Tehran Branch
- Tehran
- Iran
| | | | - Morteza Khosravi
- Department of Chemistry
- Islamic Azad University
- North Tehran Branch
- Tehran
- Iran
| | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
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4
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Bonsaii M, Gholivand K, Abdi K, Valmoozi AAE, Khosravi M. A combined experimental and computational study on the interaction of nitrogen mustards with DNA. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00264a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present work, we suggest that the role of water in the reaction of nitrogen mustards with DNA is more than what was thought before. Nitrogen mustards become activated when they are hydrated by water.
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Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | | | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
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5
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Andrushchenko V, Benda L, Páv O, Dračínský M, Bouř P. Vibrational Properties of the Phosphate Group Investigated by Molecular Dynamics and Density Functional Theory. J Phys Chem B 2015; 119:10682-92. [PMID: 26193890 DOI: 10.1021/acs.jpcb.5b05124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phosphate group (PO2(-)) is an important building block occurring in many components of living matter including nucleic acids. It provides distinct features in vibrational spectra and is useful as a local probe of NA conformation and interactions with the environment. For this purpose, it is desirable to explore in detail various factors influencing spectral shapes of characteristic phosphate vibrations. In the present study, effects of the solvent and conformational averaging are analyzed for simple model molecules, dimethylphosphate, ethylmethylphosphate, and ethylmethylthiophosphate. Infrared absorption (IR) and Raman spectra were measured and calculated using a combination of molecular dynamics (MD) and density functional theory (DFT). To fully understand the link between the structure and the spectra, the solvent has to be explicitly included in the computational modeling. The results indicate that vibrational properties of the phosphate moiety are very sensitive to its conformation and interactions with the aqueous environment indeed. Polarizable continuum solvent models without explicit water molecules provided significantly worse agreement with the experiment. The combined MD/DFT approach captures well spectral characteristics for the model systems and constitutes the most reliable basis for exploration of phosphate vibrational properties in biomolecular structural studies.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
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6
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Dračínský M, Procházková E, Kessler J, Šebestík J, Matějka P, Bouř P. Resolution of Organic Polymorphic Crystals by Raman Spectroscopy. J Phys Chem B 2013; 117:7297-307. [DOI: 10.1021/jp404382f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United
Kingdom
| | - Eliška Procházková
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Pavel Matějka
- Department of Physical
Chemistry, Institute of Chemical Technology, Technická
5, 166 28 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 166 10 Prague, Czech Republic
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FAN WENJIE, ZHANG RUIQIN. COMPUTATION OF LARGE SYSTEMS WITH AN ECONOMIC BASIS SET: AB INITIO CALCULATIONS OF BIOLOGICAL NUCLEIC ACID BASE PAIRS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.
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Affiliation(s)
- WENJIE FAN
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, P. R. China
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R. China
| | - RUIQIN ZHANG
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, P. R. China
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R. China
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8
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Andrushchenko V, Tsankov D, Krasteva M, Wieser H, Bour P. Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism. J Am Chem Soc 2011; 133:15055-64. [PMID: 21823674 DOI: 10.1021/ja204630k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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9
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Bieler NS, Haag MP, Jacob CR, Reiher M. Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. J Chem Theory Comput 2011; 7:1867-81. [DOI: 10.1021/ct2001478] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah S. Bieler
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Moritz P. Haag
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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10
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Magyarfalvi G, Tarczay G, Vass E. Vibrational circular dichroism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.39] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Andrushchenko V, Bouř P. Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides. Chirality 2011; 22 Suppl 1:E96-E114. [PMID: 21038400 DOI: 10.1002/chir.20872] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
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12
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Schwartz E, Domingos SR, Vdovin A, Koepf M, Buma WJ, Cornelissen JJLM, Rowan AE, Nolte RJM, Woutersen S. Direct Access to Polyisocyanide Screw Sense Using Vibrational Circular Dichroism. Macromolecules 2010. [DOI: 10.1021/ma101601e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Erik Schwartz
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Sérgio R. Domingos
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Alexander Vdovin
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Matthieu Koepf
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wybren Jan Buma
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Alan E. Rowan
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roeland J. M. Nolte
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Sander Woutersen
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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13
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Andrushchenko V, Bour P. Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: experimental and theoretical study. J Phys Chem B 2009; 113:283-91. [PMID: 19063657 DOI: 10.1021/jp8058678] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+) cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm(-1) band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region ( approximately 800-1200 cm(-1)), but also notable frequency shifts of the carbonyl vibrations. The Cu(2+) and Zn(2+) ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu(2+) binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Praha 6, Czech Republic
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14
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One-pot synthesis, structure, theoretical study and vibrational spectroscopy of 5-amino-4-cyano-3H-1,2-dithiole-3-thione. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.12.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Frenkel FE, Korotkov EV. Classification analysis of triplet periodicity in protein-coding regions of genes. Gene 2008; 421:52-60. [PMID: 18593596 DOI: 10.1016/j.gene.2008.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/14/2008] [Accepted: 06/06/2008] [Indexed: 11/16/2022]
Abstract
We introduce a new concept of triplet periodicity class (TPC) and a measure of similarity between such classes. We performed classification of 472288 triplet periodicity (TP) regions found in 578868 genes from 29th release of KEGG databank. Totally 2520 classes were obtained. They contain 94% of 472288 found cases of TP. For 92% of TP regions contained in classes the same linkage of TP to open reading frame (ORF) is observed. For 8% of TP cases we revealed a shift between ORF of a gene and ORF common for majority of genes contained in a TPC. For these 8% of periodic regions the hypothetical amino acid sequences corresponding to ORF built by TPC were made. BLAST program has shown that 2679 hypothetical amino acid sequences have statistically significant similarity with proteins from UniProt databank. We suppose that 8% of TP regions contained in classes possess a mutation originating from ORF shift. Obtained TPCs can be used for identification of genes' coding regions as well as for searching for mutations arisen arising from ORF shift.
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Affiliation(s)
- F E Frenkel
- Bioengineering Centre of RAS, Moscow, Russia.
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16
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Andrushchenko V, Wieser H, Bour P. DNA oligonucleotide-cis-platin binding: Ab initio interpretation of the vibrational spectra. J Phys Chem A 2007; 111:9714-23. [PMID: 17784739 DOI: 10.1021/jp074572i] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nAm. 2, 16610, Praha 6, Czech Republic
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17
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Ducasse L, Castet F, Fritsch A, Huc I, Buffeteau T. Density Functional Theory Calculations and Vibrational Circular Dichroism of Aromatic Foldamers. J Phys Chem A 2007; 111:5092-8. [PMID: 17506537 DOI: 10.1021/jp071645p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio calculations together with vibrational circular dichroism (VCD) have been used for studying the conformations of a quinoline-derived oligoamide bearing a terminal chiral residue. Three helically folded conformers of the dimer, trimer, and tetramer forms of the oligomer were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-31G* basis set. For each form, the three conformers differ in their helical handedness and in the conformation of the chiral end group. The calculated structures of the tetramer and also the proportions predicted between them based on their calculated Gibbs free energies differences match remarkably well with experimental data collected on an octamer. Specifically, a R-phenethyl terminal group gives rise to a 91:9 ratio between left handed and right handed helices. The predicted VCD spectrum calculated from the Boltzmann population of the individual conformer reproduces very well the experimental VCD spectrum of the tetramer in CDCl3 solution. The DFT calculations performed for the trimer also allow one to assess the preferred handedness of the helix and the conformation of the chiral end group, but the calculated relative populations differ slightly from experimental data. Finally, this study shows that the dimer fragment is not sufficient to obtain valuable information on the conformation of this aromatic oligoamide foldamer.
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Affiliation(s)
- Laurent Ducasse
- Institut des Sciences Moléculaires, UMR CNRS 5255, Université Bordeaux I, 351 Cours de la Libération, 33405 Talence, France.
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18
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Lee C, Cho M. Vibrational dynamics of DNA: IV. Vibrational spectroscopic characteristics of A-, B-, and Z-form DNA’s. J Chem Phys 2007; 126:145102. [PMID: 17444751 DOI: 10.1063/1.2715602] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Linear and nonlinear IR spectroscopic studies of nucleic acids can provide crucial information on solution conformations of DNA double helix and its complex with other molecules. Carrying out density functional theory calculations of A-, B-, and Z-form DNA's, the authors obtained vibrational spectroscopic properties as well as coupling constants between different basis modes. The vibrational couplings that determine the extent of exciton delocalization are strongly dependent on DNA conformation mainly because the interlayer distance between two neighboring base pairs changes with respect to the DNA conformation. The Z-DNA has comparatively small interlayer vibrational coupling constants so that its vibrational spectrum depends little on the number of base pairs, whereas the A-DNA shows a notable dependency on the size. Furthermore, it is shown that a few distinctively different line shape changes in both IR and two-dimensional IR spectra as the DNA conformation changes from B to A or from B to Z can be used as marker bands and characteristic features distinguishing different DNA conformations.
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Affiliation(s)
- Chewook Lee
- Department of Chemistry, Korea University, Seoul 136-701, Korea
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Abstract
The sequential addition of water molecules to protonated and deprotonated forms of the four mononucleotides dAMP, dCMP, dGMP, and dTMP was studied experimentally by equilibrium measurements using an electrospray mass spectrometer equipped with a drift cell and theoretically by computational methods including molecular modeling and density functional theory calculations. Experiments were carried out in positive and negative ion mode, and calculations included the protonated and deprotonated forms of the four nucleotides. For deprotonated anionic nucleotides the experimental enthalpies of hydration (DeltaH degrees n) were found to be similar for all four systems and varied between -10.1 and -11.5 kcal mol-1 for the first water molecule (n = 1) and -8.3 and -9.6 kcal mol-1 for additional water molecules (n = 2-4). Theory indicated that the first water molecule binds to the charge-carrying phosphate group. Simulations of deprotonated mononucleotides with four water molecules yielded a large number of structures with similar energies. In some of the structures all four water molecules cluster around the phosphate group, and in other structures the four water molecules each hydrate a different functional group of the nucleotide. These include the phosphate group, the deoxyribose hydroxyl group, and various functional groups on the nucleobases. Experimental DeltaH degrees 1 values for the protonated cationic mononucleotides ranged from -10.5 to -13.5 kcal mol-1 with more negative values (< or =-12 kcal mol-1) for dCMP, dGMP, and dTMP and the least negative value for dAMP. For n = 2-4 DeltaH degrees n values varied from -6.9 to -9.7 kcal/mol and were similar in value to the deprotonated nucleotides except for dAMP. Theory on the protonated nucleotides indicated that the first water molecule binds to the charge-carrying group for dCMP, dGMP, and dTMP. For protonated dAMP, on the other hand, the charge-carrying N3 group is well self-solvated by the phosphate group and not readily available for a hydrogen bond with the water molecule. The insight gained on nucleotide stabilization by individual water molecules is used to discuss the competition between hydration of individual nucleotides and Watson-Crick base pairing.
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Affiliation(s)
- Dengfeng Liu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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Fan WJ, Zhang RQ, Liu S. Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory. J Comput Chem 2007; 28:967-74. [PMID: 17269120 DOI: 10.1002/jcc.20670] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.
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Affiliation(s)
- W J Fan
- Center of Super-Diamond and Advanced Films (COSDAF) & Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People's Republic of China
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21
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Krummel AT, Zanni MT. Interpreting DNA Vibrational Circular Dichroism Spectra Using a Coupling Model from Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2006; 110:24720-7. [PMID: 17134235 DOI: 10.1021/jp063227a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.
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Affiliation(s)
- Amber T Krummel
- Department of Chemistry, University of Wisconsin at Madison, Madison, Wisconsin 53706-1396, USA
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22
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Liao B, He B, Chen S, Huang Y. The EB-DNA Liquid Crystalline Complex with High Concentration of Mg2+. Polym J 2006. [DOI: 10.1295/polymj.pj2005210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Polyanichko AM, Chikhirzhina EV, Andrushchenko VV, Vorob'ev VI, Wieser H. The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: Electronic and vibrational circular dichroism studies. Biopolymers 2006; 83:182-92. [PMID: 16732569 DOI: 10.1002/bip.20544] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The interactions were studied of DNA with the nonhistone chromatin protein HMGB1 and histone H1 in the presence of manganese(II) ions at different protein to DNA and manganese to DNA phosphate ratios by using absorption and optical activity spectroscopy in the electronic [ultraviolet (UV) and electronic circular dichroism ECD)] and vibrational [infrared (IR) and vibrational circular dichroism (VCD)] regions. In the presence of Mn2+, the protein-DNA interactions differ from those without the ions and cause prominent DNA compaction and formation of large intermolecular complexes. At the same time, the presence of HMGB1 and H1 also changed the mode of interaction of Mn2+ with DNA, which now takes place mostly in the major groove of DNA involving N7(G), whereas interactions between Mn2+ and DNA phosphate groups are weakened by histone molecules. Considerable interactions were also detected of Mn2+ ions with aspartic and glutamic amino acid residues of the proteins.
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Affiliation(s)
- A M Polyanichko
- Department of Chemistry, University of Calgary, Calgary, Canada.
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