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Krupová M, Kessler J, Bouř P. Recent Trends in Chiroptical Spectroscopy: Theory and Applications of Vibrational Circular Dichroism and Raman Optical Activity. Chempluschem 2020; 85:561-575. [DOI: 10.1002/cplu.202000014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and PhysicsCharles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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2
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Kessler J, Andrushchenko V, Kapitán J, Bouř P. Insight into vibrational circular dichroism of proteins by density functional modeling. Phys Chem Chem Phys 2018; 20:4926-4935. [PMID: 29384537 DOI: 10.1039/c7cp08016f] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is an excellent method to determine the secondary structure of proteins in solution. Comparison of experimental spectra with quantum-chemical simulations represents a convenient and objective way to extract information on the structure. This has been difficult for such large molecules where approximate theoretical models have to be used. In the present study we applied the Cartesian-coordinate based tensor transfer (CCT) making it possible to extend the density functional theory (DFT) and model spectral intensities of large globular proteins nearly at quantum-chemical precision. Indeed, comparison with experiment provided a better understanding of the dependence of VCD spectral shapes on the geometry, their sensitivity to fine structural details and interactions with the environment. On a model set of globular proteins the simulated spectra correlated well with experimental data and revealed which structural information can (and cannot) be obtained from this kind of spectroscopy. Although the VCD technique has been regarded as being rather insensitive to side-chain variations, we found that the spectra of human and hen lysozyme differing by a few amino acids only are quite distinct. This has been explained by long-distance coupling of the amide vibrations. Likewise, the modeling reproduced some spectral changes caused by protein deuteration even when the protein structure was conserved.
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Affiliation(s)
- Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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3
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Jähnigen S, Scherrer A, Vuilleumier R, Sebastiani D. VCD‐Verstärkung durch chirale Packungseffekte in molekularen Kristallen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sascha Jähnigen
- Martin-Luther-Universität Halle-Wittenberg Institut für Chemie von-Danckelmann-Platz 4 Halle 06120 Deutschland
| | - Arne Scherrer
- Martin-Luther-Universität Halle-Wittenberg Institut für Chemie von-Danckelmann-Platz 4 Halle 06120 Deutschland
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS 75005 Paris Frankreich
| | - Daniel Sebastiani
- Martin-Luther-Universität Halle-Wittenberg Institut für Chemie von-Danckelmann-Platz 4 Halle 06120 Deutschland
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Jähnigen S, Scherrer A, Vuilleumier R, Sebastiani D. Chiral Crystal Packing Induces Enhancement of Vibrational Circular Dichroism. Angew Chem Int Ed Engl 2018; 57:13344-13348. [DOI: 10.1002/anie.201805671] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/25/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Sascha Jähnigen
- Martin-Luther-Universität Halle-WittenbergInstitut für Chemie von-Danckelmann-Platz 4 Halle 06120 Germany
| | - Arne Scherrer
- Martin-Luther-Universität Halle-WittenbergInstitut für Chemie von-Danckelmann-Platz 4 Halle 06120 Germany
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS 75005 Paris France
| | - Daniel Sebastiani
- Martin-Luther-Universität Halle-WittenbergInstitut für Chemie von-Danckelmann-Platz 4 Halle 06120 Germany
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5
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Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments. Molecules 2018; 23:molecules23092404. [PMID: 30235902 PMCID: PMC6225159 DOI: 10.3390/molecules23092404] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 08/25/2018] [Accepted: 09/07/2018] [Indexed: 01/10/2023] Open
Abstract
Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.
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6
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Polavarapu PL. Structural Analysis Using Chiroptical Spectroscopy: Insights and Cautions. Chirality 2016; 28:445-52. [DOI: 10.1002/chir.22601] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 11/09/2022]
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7
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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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Marty R, Frauenrath H, Helbing J. Aggregates from Perylene Bisimide Oligopeptides as a Test Case for Giant Vibrational Circular Dichroism. J Phys Chem B 2014; 118:11152-60. [DOI: 10.1021/jp506837c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Roman Marty
- Institute
of Materials, Ecole Polytechnique Federale de Lausanne (EPFL), EPFL - STI - IMX - LMOM, MXG 037, Station 12, 1015 Lausanne, Switzerland
| | - Holger Frauenrath
- Institute
of Materials, Ecole Polytechnique Federale de Lausanne (EPFL), EPFL - STI - IMX - LMOM, MXG 037, Station 12, 1015 Lausanne, Switzerland
| | - Jan Helbing
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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9
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Merten C, Reuther JF, DeSousa JD, Novak BM. Identification of the specific, shutter-like conformational reorientation in a chiroptical switching polycarbodiimide by VCD spectroscopy. Phys Chem Chem Phys 2014; 16:11456-60. [DOI: 10.1039/c4cp01226g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Xi H, Davis E, Ranjan N, Xue L, Hyde-Volpe D, Arya DP. Thermodynamics of nucleic acid "shape readout" by an aminosugar. Biochemistry 2011; 50:9088-113. [PMID: 21863895 PMCID: PMC3673541 DOI: 10.1021/bi201077h] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized as playing an equally important role in DNA recognition. Competition dialysis, UV, flourescent intercalator displacement (FID), computational docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, the results suggest the following. (1) Neomycin binds three RNA structures [16S A site rRNA, poly(rA)·poly(rA), and poly(rA)·poly(rU)] with high affinities (K(a) ~ 10(7) M(-1)). (2) The binding of neomycin to A-form GC-rich oligomer d(A(2)G(15)C(15)T(2))(2) has an affinity comparable to those of RNA structures. (3) The binding of neomycin to DNA·RNA hybrids shows a 3-fold variance that can be attributed to their structural differences [for poly(dA)·poly(rU), K(a) = 9.4 × 10(6) M(-1), and for poly(rA)·poly(dT), K(a) = 3.1 × 10(6) M(-1)]. (4) The interaction of neomycin with DNA triplex poly(dA)·2poly(dT) yields a binding affinity (K(a)) of 2.4 × 10(5) M(-1). (5) Poly(dA-dT)(2) shows the lowest association constant for all nucleic acids studied (K(a) < 10(5)). (6) Neomycin binds to G-quadruplexes with K(a) values of ~10(4)-10(5) M(-1). (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin's affinity for various nucleic acid structures can be ranked as follows: RNAs and GC-rich d(A(2)G(15)C(15)T(2))(2) structures > poly(dA)·poly(rU) > poly(rA)·poly(dT) > T·A-T triplex, G-quadruplex, B-form AT-rich, or GC-rich DNA sequences. The results illustrate the first example of a small molecule-based "shape readout" of different nucleic acid conformations.
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Affiliation(s)
- Hongjuan Xi
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Erik Davis
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Liang Xue
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - David Hyde-Volpe
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
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11
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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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12
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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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13
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Jiang N, Tan RX, Ma J. Simulations of Solid-State Vibrational Circular Dichroism Spectroscopy of (S)-Alternarlactam by Using Fragmentation Quantum Chemical Calculations. J Phys Chem B 2011; 115:2801-13. [DOI: 10.1021/jp110152q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nan Jiang
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
| | - Ren Xiang Tan
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
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14
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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15
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Petrovic AG, Polavarapu PL, Mahalakshmi R, Balaram P. Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism. Chirality 2009; 21 Suppl 1:E76-85. [DOI: 10.1002/chir.20779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Bour P, Andrushchenko V, Kabelác M, Maharaj V, Wieser H. Simulations of structure and vibrational spectra of deoxyoctanucleotides. J Phys Chem B 2007; 109:20579-87. [PMID: 16853664 DOI: 10.1021/jp051218g] [Citation(s) in RCA: 26] [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
Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG)(2) nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.
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Setnicka V, Urbanová M, Volka K, Nampally S, Lehn JM. Investigation of guanosine-quartet assemblies by vibrational and electronic circular dichroism spectroscopy, a novel approach for studying supramolecular entities. Chemistry 2007; 12:8735-43. [PMID: 16983706 DOI: 10.1002/chem.200500973] [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: 11/12/2022]
Abstract
The self-assembly of guanosine-5'-hydrazide G-1 in D(2)O, in the presence and absence of sodium cations, has been investigated by chiroptical techniques: electronic (ECD) and the newly introduced vibrational (VCD) circular dichroism spectroscopy. Using a combination of ECD and VCD with other methods such as IR, electron microscopy, and electrospray ionization mass spectrometry (ESI-MS) it was found that G-1 produces long-range chiral aggregates consisting of G-quartets, (G-1)(4), subsequently stacked into columns, [(G-1)(4)](n), induced by binding of metal cations between the (G-1)(4) species. This process, accompanied by gelation of the sample, is highly efficient in the presence of an excess of sodium cations, leading to aggregates with strong quartet-quartet interaction. Thermally induced conformational changes and conformational stability of guanosine-5'-hydrazide assemblies were studied by chiroptical techniques and the melting temperature of the hydrogels formed was obtained. The temperature-dependent experiments indicate that the long-range supramolecular aggregates are dissociated by increasing temperature into less ordered species, monomers, or other intermediates in equilibrium, as indicated by MS experiments.
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Affiliation(s)
- Vladimír Setnicka
- Institute of Chemical Technology, Technická 5, 166 28 Prague 6, Czech Republic.
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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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Tandon P, Gupta VD, Mehrotra C, Gupta DC. Phase transition and specific heat anomaly in B⇌Z and other conformational transitions in poly(dG-dC). J MACROMOL SCI B 2006. [DOI: 10.1080/00222349208215463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- P. Tandon
- a Department of Physics , University of Lucknow Lucknow , 226 007, India
| | - V. D. Gupta
- a Department of Physics , University of Lucknow Lucknow , 226 007, India
| | - C. Mehrotra
- a Department of Physics , University of Lucknow Lucknow , 226 007, India
| | - D. C. Gupta
- a Department of Physics , University of Lucknow Lucknow , 226 007, India
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Pandyra A, Tsankov D, Andrushchenko V, van de Sande JH, Wieser H. Intercalation of daunomycin into d(CG)4 oligomer duplex containing G x T mismatches by vibrational circular dichroism and infrared absorption spectroscopy. Biopolymers 2006; 82:189-98. [PMID: 16312022 DOI: 10.1002/bip.20416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The vibrational circular dichroism (VCD) and infrared absorption (IR) spectra of the mismatched octamer oligonucleotides d(CGTGCGCG)(2) (CGT) and d(CGCGTGCG)(2) (CGC) and their complexes with the antitumor drug daunomycin were measured in D(2)O, interpreted, and compared to the octamer d(CGCGCGCG)(2) (CG). The IR spectra of the mismatched octamers in the carbonyl-stretching region are similar to those of the parent CG, whereas the VCD spectra differ in several respects between each other. The main VCD feature due to carbonyl stretching is informative for the mismatches and CG. Vibrational modes in the sugar-phosphate region remain essentially unchanged especially for PO(2) (-) symmetric stretching. Differences between the free and complexed mismatch octamers occurred mainly in the carbonyl-stretching region (1,700-1,600 cm(-1)). The absorption intensity of the C==O peak of G is more prominent for CGC than CGT and resembles CG in this respect. The detailed composition of this doublet is clearly visible, indicating the geometric rearrangement of the base pairs in the presence of the mismatch and upon forming the daunomycin complex.
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Affiliation(s)
- A Pandyra
- Department of Chemistry, Faculty of Science, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Krummel AT, Zanni MT. DNA Vibrational Coupling Revealed with Two-Dimensional Infrared Spectroscopy: Insight into Why Vibrational Spectroscopy Is Sensitive to DNA Structure. J Phys Chem B 2006; 110:13991-4000. [PMID: 16836352 DOI: 10.1021/jp062597w] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.
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Affiliation(s)
- Amber T Krummel
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, USA
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Palivec L, Urbanová M, Volka K. Circular dichroism spectroscopic study of non-covalent interactions of poly-L-glutamic acid with a porphyrin derivative in aqueous solutions. J Pept Sci 2005; 11:536-45. [PMID: 15880603 DOI: 10.1002/psc.672] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The interactions of poly-L-glutamic acid and a cationic porphyrin derivative in aqueous solutions were studied by the combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopies. It was found that non-covalent interactions between both agents influence the structure of the polymeric matrix and the guest porphyrins and vice versa, but the physico-chemical properties of the solutions, especially the pH and the relative permittivity of the solvent, play a key role in the structure of the polypeptide part of the formed complexes. It was shown that the interaction with porphyrins prevents the precipitation of poly-L-glutamic acid in aqueous solution at acidic pH. In special conditions, the porphyrins attached to the polypeptide probably possess face-to-face interaction as demonstrated by the enhancement of the characteristic ECD signal and the appearance of sidebands on its short and long wavelength sides.
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Affiliation(s)
- Lukás Palivec
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28 Praha 6, Czech Republic
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Schweitzer-Stenner R. Secondary Structure Analysis of Polypeptides Based on an Excitonic Coupling Model to Describe the Band Profile of Amide I‘ of IR, Raman, and Vibrational Circular Dichroism Spectra. J Phys Chem B 2004. [DOI: 10.1021/jp0477654] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Andrushchenko V, Wieser H, Bouř P. RNA Structural Forms Studied by Vibrational Circular Dichroism: Ab Initio Interpretation of the Spectra. J Phys Chem B 2004. [DOI: 10.1021/jp037106b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valery Andrushchenko
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary AB, T2N 1N4, Canada, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Hal Wieser
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary AB, T2N 1N4, Canada, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Petr Bouř
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary AB, T2N 1N4, Canada, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
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25
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Andrushchenko V, van de Sande JH, Wieser H. Vibrational circular dichroism and IR absorption of DNA complexes with Cu2+ ions. Biopolymers 2003; 72:374-90. [PMID: 12949828 DOI: 10.1002/bip.10439] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu2+ ions at room temperature in a Cu2+ concentration range of 0-0.4M (a Cu2+/phosphate molar ratio [Cu]/[P] of 0-0.7). In some important instances, VCD provides more detailed insights than previous IR investigations whereas in several others it leads to the same interpretations. The Cu2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu2+ binds to the N7 of guanine (G) and a phosphate group. Detectable only by VCD, significant distortion of most guanine-cytosine (GC) base pairs occurs at a [Cu]/[P] ratio of 0.5 with only a minor affect on adenine-thymine (AT) base pairs, which favors a "sandwich" complex in which a Cu2+ ion is inserted between two adjacent guanines in a GpG sequence. The AT base pairs become significantly distorted when the metal concentration is increased to 0.7 [Cu]/[P]. A number of GC base pairs, which are possibly involved in sandwich complexes, remain stacked and paired even at 0.7 [Cu]/[P], preventing complete strand separation. The DNA secondary structure changes considerably from the standard B-form geometry at a [Cu]/[P] ratio of 0.4 and higher. A further transition to some intermediate conformation that is inconsistent with either the A- or Z-form or a completely denatured state is suggested in agreement with other works. In general, VCD proves to be a reliable indicator of the 3-dimensional structure of the DNA-metal ion complexes, which reveals structural details that cannot be deduced from the IR absorption spectra alone.
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Affiliation(s)
- V Andrushchenko
- Department of Chemistry, Faculty of Science, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
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Andrushchenko V, Tsankov D, Wieser H. Vibrational circular dichroism spectroscopy and the effects of metal ions on DNA structure. J Mol Struct 2003. [DOI: 10.1016/j.molstruc.2003.08.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Wang F, Polavarapu PL. Conformational analysis of melittin in solution phase: Vibrational circular dichroism study. Biopolymers 2003; 70:614-9. [PMID: 14648771 DOI: 10.1002/bip.10504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The vibrational absorption and vibrational circular dichroism (VCD) spectra of melittin in D(2)O solutions at different pH values, different salt concentrations, or different 2,2,2-trifluoroethanol (TFE) concentrations are recorded in the amide I' (1850-1600 cm(-1)) region. Two models are used to simulate this peptide in different conditions, and a coupled oscillator program is used to obtain the calculated absorption and VCD spectra. This study indicates that melittin adopts a mixed structure in D(2)O solution at low pH, low salt concentration, or low TFE concentration. With an increase in pH, salt concentration, or TFE concentration, the structure changes to alpha-helix and further increases lead to aggregation. These results demonstrate the versatility of VCD in probing the conformations of peptides under different environmental perturbations.
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Affiliation(s)
- Feng Wang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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28
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Andrushchenko V, Van De Sande H, Wieser H. DNA interaction with Mn2+ ions at elevated temperatures: VCD evidence of DNA aggregation. Biopolymers 2003; 69:529-45. [PMID: 12879498 DOI: 10.1002/bip.10419] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Interaction of natural calf thymus DNA with Mn(2+) ions was studied at room temperature and at elevated temperatures in the range from 23 degrees C to 94 degrees C by means of IR absorption and vibrational circular dichroism (VCD) spectroscopy. The Mn(2+) concentration was varied between 0 and 1.3M (0 and 10 [Mn]/[P]). The secondary structure of DNA remained in the frame of the B-form family in the whole ion concentration range at room temperature. No significant DNA denaturation was revealed at room temperature even at the highest concentration of metal ions studied. However at elevated temperatures, DNA denaturation and a significant decrease of the melting temperature of DNA connected with a decrease of the stability of DNA induced by Mn(2+) ions occurred. VCD demonstrated sensitivity to DNA condensation and aggregation as well as an ability to distinguish between these two processes. No condensation or aggregation of DNA was observed at room temperature at any of the metal ion concentrations studied. DNA condensation was revealed in a very narrow range of experimental conditions at around 2.4 [Mn]/[P] and about 55 degrees C. DNA aggregation was observed in the presence of Mn(2+) ions at elevated temperatures during or after denaturation. VCD spectroscopy turned out to be useful for studying DNA condensation and aggregation due to its ability to distinguish between these two processes, and for providing information about DNA secondary structure in a condensed or aggregated state.
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Affiliation(s)
- Valery Andrushchenko
- Department of Chemistry, Faculty of Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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29
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Tsankov D, Kalisch B, van de Sande H, Wieser H. Cisplatin-DNA Adducts by Vibrational Circular Dichroism Spectroscopy: Structure and Isomerization of d(CCTG*G*TCC)·d(GGACCAGG) Intrastrand Cross-Linked by Cisplatin. J Phys Chem B 2003. [DOI: 10.1021/jp034246c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dimiter Tsankov
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Berndt Kalisch
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hans van de Sande
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hal Wieser
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
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30
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Andrushchenko V, Wieser H, Bouř P. B−Z Conformational Transition of DNA Monitored by Vibrational Circular Dichroism. Ab Initio Interpretation of the Experiment. J Phys Chem B 2002. [DOI: 10.1021/jp0262721] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Valery Andrushchenko
- Department of Chemistry, University of Calgary, 2500 University Dr., Calgary AB, T2N 1N4, Canada and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Helmut Wieser
- Department of Chemistry, University of Calgary, 2500 University Dr., Calgary AB, T2N 1N4, Canada and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Petr Bouř
- Department of Chemistry, University of Calgary, 2500 University Dr., Calgary AB, T2N 1N4, Canada and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
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31
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Andrushchenko V, Leonenko Z, Cramb D, van de Sande H, Wieser H. Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation. Biopolymers 2002; 61:243-60. [PMID: 12115140 DOI: 10.1002/bip.10159] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling electronic CD (ECD) spectra, which appear during psi-type DNA condensation, were observed. These spectra are characterized mainly by an anomalous, severalfold increase of VCD intensity. Such anomalous VCD spectra were assigned to DNA condensation with formation of large and dense particles of a size comparable to the wavelength of the probing ir beam and possessing large-scale helicity. Atomic force microscopy confirmed DNA condensation by Cr(3+) ions and the formation of tight DNA particles responsible for the psi-type VCD spectra. Upon increasing the Cr(3+) ion concentration the shape of the condensates changed from loose flower-like structures to highly packed dense spheres. No DNA denaturation was seen even at the highest concentration of Cr(3+) ions studied. The secondary structure of DNA remained in a B-form before and after the condensation. VCD and ir as well as AFM proved to be an effective combination for investigating DNA condensation. In addition to the ability of VCD to determine DNA condensation, VCD and ir can in the same experiment provide unambiguous information about the secondary structure of DNA contained in the condensed particles.
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Affiliation(s)
- V Andrushchenko
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
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32
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Zhao C, Polavarapu PL, Das C, Balaram P. Vibrational Circular Dichroism of β-Hairpin Peptides. J Am Chem Soc 2000. [DOI: 10.1021/ja000451j] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chunxia Zhao
- Contribution from the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Prasad L. Polavarapu
- Contribution from the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Chittaranjan Das
- Contribution from the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - P. Balaram
- Contribution from the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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33
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Andrushchenko VV, van de Sande JH, Wieser H, Kornilova SV, Blagoi YP. Complexes of (dG-dC)20 with Mn2+ ions: a study by vibrational circular dichroism and infrared absorption spectroscopy. J Biomol Struct Dyn 1999; 17:545-60. [PMID: 10636089 DOI: 10.1080/07391102.1999.10508385] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The B-Z transition of the synthetic oligonucleotide, (dG-dC)20, induced by Mn2+ ions at room temperature, was investigated by absorption and Vibrational Circular Dichroism (VCD) spectroscopy in the range of 1800-800 cm(-1). Metal ion concentration was varied from 0 to 0.73 M Mn2+ (0 to 8.5 moles of Mn2+ per mole of oligonucleotide phosphate, [Mn]/[P]). While both types of spectra showed considerable changes as the Mn2+ concentrations were raised, differences between the two were often complementary in their expression and extent, those displayed by VCD being more clearly evident due to the inversion of the opposite helical sense from the right-handed to the left-handed conformation. The main phase of the transition occurred in the metal ion concentration between 0.8-1.1 [Mn]/[P]. Gradual changes that took place in the spectra were interpreted in terms of simultaneous processes that depended on metal ion concentration, namely B-Z transformation, binding of Mn2+ to phosphates and to nitrogen bases, and partial denaturation. Below approximately 0.6 [Mn]/[P], only a small portion of the oligonucleotide adopted the Z conformation within a 3 hour period, whereas conversion was completed in the same time interval for concentrations between 0.9-1.2 [Mn]/[P]. At [Mn]/[P] >1.7, complete transition to the Z-form took place immediately on adding Mn2+. Applying VCD spectroscopy in combination with conventional infrared absorption proved most useful for corroborating changes in the absorption spectra, and for detecting in an unique manner, not attainable by absorption methods, conformational changes that lead to the inversion of the helical sense of the oligonucleotide.
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Affiliation(s)
- V V Andrushchenko
- Department of Chemistry, Faculty of Science, University of Calgary, AB, Canada
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34
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Acetate groups as probes of the stereochemistry of carbohydrates: a vibrational circular dichroism study. Carbohydr Res 1999. [DOI: 10.1016/s0008-6215(99)00211-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Ito H. Linear response polarizability bandshape calculations of vibrational circular dichroism, vibrational absorption, and electronic circular dichroism of cyclo(Gly-Pro-Gly-D-Ala-Pro): A small cyclic pentapeptide having β- and γ-turns. ACTA ACUST UNITED AC 1998. [DOI: 10.1002/(sici)1520-6343(1996)2:1<17::aid-bspy3>3.0.co;2-p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Koçak A, Luque R, Diem M. The solution structure of small peptides: An IR CD study of aqueous solutions of (L-Ala)n [n = 3, 4, 5, 6] at different temperatures and ionic strengths. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199812)46:7<455::aid-bip3>3.0.co;2-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Abstract
Advances in the field of vibrational optical activity (VOA) are reviewed over the past decade. Topics are surveyed with an emphasis on the theoretical and instrumental progress in both vibrational circular dichroism (VCD) and Raman optical activity (ROA). Applications of VOA to stereochemical and biological problems are reviewed, with a bias toward new kinds of experiments made possible by theoretical and instrumental advances. In the field of VCD, the most notable advances have taken place in the quality and size of ab initio calculations of VOA intensities and in the quality of step-scan Fourier transform instrumentation. For ROA, the most dramatic progress has occurred in the areas of theoretical formulation and high-throughput instrumentation. Applications of VOA now include all major classes of biological and pharmaceutical molecules. VOA's importance as a diagnostic tool will likely grow as the control of molecular chirality increases in research and industrial areas.
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Affiliation(s)
- L A Nafie
- Department of Chemistry, Syracuse University, New York 13244-4100, USA.
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38
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Holmén A. Vibrational Transition Moments of Aminopurines: Stretched Film IR Linear Dichroism Measurements and DFT Calculations. J Phys Chem A 1997. [DOI: 10.1021/jp970381b] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anders Holmén
- Department of Physical Chemistry, Chalmers University of Technology, S-412 96 Göteborg, Sweden
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39
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Maharaj V, Rauk A, van de Sande J, Wieser H. Infrared absorption and vibrational circular dichroism spectra of selected deoxyoctanucleotides complexed with daunorubicin. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(96)09668-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Birke SS, Diem M. Conformational studies of the smallest structural motifs of DNA detectable via vibrational circular dichroism: cytidylyl-(3'-5')-guanosine and guanylyl-(3'-5')-cytidine. Biophys J 1995; 68:1045-9. [PMID: 7756524 PMCID: PMC1281827 DOI: 10.1016/s0006-3495(95)80279-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The infrared absorption and vibrational circular dichroism (VCD) spectra of buffered aqueous solutions of cytidylyl-(3'-5')-guanosine (5'(CG)3') and guanylyl-(3'-5')-cytidine (5'(GC)3') are reported. Under low ionic strength conditions, these dinucleotides exhibit VCD features that can be predicted qualitatively from structural data of (CG)2 and (GC)2 sequences of poly(dG-dC).poly(dG-dC), using the exciton model for infrared VCD intensities.
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Affiliation(s)
- S S Birke
- Department of Chemistry, City University of New York, Hunter College, New York 10021, USA
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42
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Abstract
Vibrational optical activity (VOA) is a relatively new spectroscopic technique, which has two principal manifestations, ir vibrational CD and vibrational Raman optical activity. Progress in the study of oligopeptides using both of these forms of VOA is reviewed from the perspective of theoretical and instrumental techniques, spectral results, and structural interpretations.
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Affiliation(s)
- T B Freedman
- Department of Chemistry, Syracuse University, New York 13244-4100, USA
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43
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Wang L, Yang L, Keiderling TA. Vibrational circular dichroism of A-, B-, and Z-form nucleic acids in the PO2-stretching region. Biophys J 1994; 67:2460-7. [PMID: 7535113 PMCID: PMC1225631 DOI: 10.1016/s0006-3495(94)80734-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Vibrational circular dichroism (VCD) spectra were measured for H2O solutions of several natural and model DNAs (single and double strands, oligomers and polymers) in the B-form, poly(dG-dC)-poly(dG-dC) in the Z-form, and various duplex RNAs in an A-form over the PO2-stretching region. Only the symmetric PO2 stretch at approximately 1075 cm-1 yields a significant intensity VCD signal. Differences of the PO2-stretching VCD spectra found for these conformational types are consistent with the spectral changes seen in the base region, but no sequence dependence was seen in contrast to VCD for base modes. The B to Z transition is accompanied by an inversion of the PO2- VCD spectra, which is characteristic of the change in the helical sense of the nucleic acid backbone. A-RNAs give rise to the same sense of couplet VCD as do B-DNAs but have a somewhat different shape because of overlapping ribose modes. These PO2- VCD spectral characteristics have been successfully modeled using simple dipole coupling calculations. The invariability of the symmetric PO2- stretching mode VCD spectra to the base sequence as opposed to that found for the C = O stretching and base deformation modes is evidence that this mode will provide a stable indication of the DNA helical sense.
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Affiliation(s)
- L Wang
- Department of Chemistry, University of Illinois at Chicago 60607-7061
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44
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Ito H, I’Haya YJ. Linear Response Polarizability Tensor Theory for Vibrational Circular Dichroism: VCD and IR Absorption Bandshape Calculations ofα-Helical andβ-Sheet Polypeptides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1994. [DOI: 10.1246/bcsj.67.1238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Chapter 4 Application of infrared CD to the analysis of the solution conformation of biological molecules. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s0167-9244(08)70177-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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46
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Xiang T, Goss DJ, Diem M. Strategies for the computation of infrared CD and absorption spectra of biological molecules: ribonucleic acids. Biophys J 1993; 65:1255-61. [PMID: 7694671 PMCID: PMC1225845 DOI: 10.1016/s0006-3495(93)81175-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We report observed and computed infrared (vibrational) circular dichroism spectra of a number of polyribonucleic acids in aqueous solutions in the 1600-1750 cm-1 spectral region, in which C = O and some nucleotide base ring stretching vibrations occur. The experimental data are compared with results calculated using different levels of sophistication within the exciton approach. We find that observed band shapes are generally well reproduced by these models, particularly if care is taken to determine the direction of the vibrational dipole transition moments accurately.
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Affiliation(s)
- T Xiang
- Department of Chemistry, City University of New York, Hunter College, New York 10021
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47
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Birke SS, Moses M, Kagalovsky B, Jano D, Gulotta M, Diem M. Infrared CD of deoxy oligonucleotides. Conformational studies of 5'd(GCGC)3', 5'd(CGCG)3', 5'd(CCGG)3', and 5'd(GGCC)3' in low and high salt aqueous solution. Biophys J 1993; 65:1262-71. [PMID: 8241406 PMCID: PMC1225846 DOI: 10.1016/s0006-3495(93)81176-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Infrared (vibrational) circular dichroism (VCD) spectra have been obtained for the self-complementary tetranucleotides, 5'd(CGCG)3', 5'd(GCGC)3', 5'd(CCGG)3', and 5'd(GGCC)3'. In buffered aqueous solution at low salt concentration, these tetramers exhibit spectra associated with right-handed polymers, although the spectra differ significantly for the four species. In high salt solution, a B-->Z transition occurs in 5'd(CGCG)3', while the other tetranucleotides appear only slightly altered. Temperature dependent studies of these oligonucleotides reveal a greater amount of thermal stability for the tetramers in low salt than for the high salt solutions. VCD intensities computed via the exciton formalism are compared with observed results.
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Affiliation(s)
- S S Birke
- Department of Chemistry and Biochemistry, City University of New York, Hunter College, New York 10021
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Wang L, Keiderling TA. Helical nature of poly(dI-dC).poly(dI-dC). Vibrational circular dichroism results. Nucleic Acids Res 1993; 21:4127-32. [PMID: 8371987 PMCID: PMC310019 DOI: 10.1093/nar/21.17.4127] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Poly(dI-dC).poly(dI-dC) was studied using vibrational circular dichroism and IR spectroscopy in both the base deformation C = O and symmetric PO2- stretching regions. VCD spectra of this duplex under low salt conditions are consistent with its having a B-form structure. Addition of 5 M NaCl leads to relatively uniform VCD intensity loss which is consistent with loss of helical structure rather than formation of an intermediate state between the B and Z forms. This duplex polymer under high salt conditions with added NiCl2 shows aggregation effects, but its IR and VCD spectra have characteristic features of the Z-form DNA conformation. The cooperative change of backbone and base pair structure upon thermal denaturation is indicated by the simultaneous collapse of the VCD at 65 degrees C in both the PO2- and C = O stretching regions. This study further demonstrates that the VCD bandshape of a specific localized nucleic acid vibrational transition can be a useful indicator of the helical handedness. The empirical conformational interpretations are supported by simulated VCD spectra, which are in excellent agreement with the experimental results, based on dipole coupling calculations.
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Affiliation(s)
- L Wang
- Department of Chemistry, University of Illinois at Chicago 60680
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49
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Abstract
The vibrational cd (VCD) of a double-stranded RNA, poly(rA).poly(rU), at pH 7 and moderate added salt concentration (0.1 M) has been measured in both the base-stretching and phosphate-stretching regions of the ir as a function of temperature. The data in both cases show two distinct phase transitions. The first is from double- to a triple-stranded form, and the second is from triple- to single-stranded forms, which still retain substantial local order even up to 80 degrees C. The nature of these transitions has been identified by comparison of the VCD and ir absorption spectra of the initially double-stranded samples with those of single-stranded poly(rA) and poly(rU) and with triple-stranded poly-(rA).poly-(rU).poly(rU). The large differences in the VCD band shapes allows positive identification of the intermediate and final states. Thus under VCD-concentration conditions, a simple helix-to-coil transition can be eliminated for poly(rA).poly(rU) while such a two-step transition can be seen at low salt conditions. All of these observations are consistent with previous studies of the phase transitions of poly(rA).poly(rU) under various salt conditions. Additionally, the VCD is indicative of premelting for all the triple-, double-, and single-strand complexes studied. The triple-strand complex did not show disproportionation to double strand on heating under these added salt conditions. The unusual VCD pattern for low temperature poly(rA).poly(rU), as compared to high G--C content RNAs and DNAs, is qualitatively, but not quantitatively, explained using exciton coupling of localized dipolar transitions in each type of base within the strand.
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Affiliation(s)
- L Yang
- Department of Chemistry, University of Illinois, Chicago 60680
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50
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Wyssbrod HR, Diem M. IR (vibrational) CD of peptide beta-turns: a theoretical and experimental study of cyclo-(-Gly-Pro-Gly-D-Ala-Pro-). Biopolymers 1992; 32:1237-42. [PMID: 1420990 DOI: 10.1002/bip.360320912] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
IR vibrational CD (VCD) has been observed for the cyclic pentapeptide cyclo-(-Gly-Pro-Gly-D-Ala-Pro-) in solution in CDBr3. The observed VCD spectra do not resemble the VCD features of any of the previously reported peptide secondary structures, such as alpha-helical, "random coil," or sheet structures, and might be due to the beta-turn contained in this molecule. To shed light onto the origin of the observed spectra, VCD intensity calculations, based on the solution and solid-state structures of cyclo-(-Gly-Pro-Gly-D-Ala-Pro-), have been carried out. In addition, calculated VCD data for pure beta-turns are discussed.
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Affiliation(s)
- H R Wyssbrod
- Environmental Sciences Laboratory, Brooklyn College of CUNY 11210
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