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Bhai L, Thomas JK, Conroy DW, Xu Y, Al-Hashimi HM, Jaroniec CP. Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements. Front Mol Biosci 2023; 10:1286172. [PMID: 38111464 PMCID: PMC10726973 DOI: 10.3389/fmolb.2023.1286172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 12/20/2023] Open
Abstract
Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments.
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Affiliation(s)
- Lakshmi Bhai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Justin K. Thomas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Daniel W. Conroy
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
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Fick RJ, Liu AY, Nussbaumer F, Kreutz C, Rangadurai A, Xu Y, Sommer RD, Shi H, Scheiner S, Stelling AL. Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy. J Phys Chem B 2021; 125:7613-7627. [PMID: 34236202 PMCID: PMC8311644 DOI: 10.1021/acs.jpcb.1c01351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
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Measuring the strength
of the hydrogen bonds between DNA base pairs
is of vital importance for understanding how our genetic code is physically
accessed and recognized in cells, particularly during replication
and transcription. Therefore, it is important to develop probes for
these key hydrogen bonds (H-bonds) that dictate events critical to
cellular function, such as the localized melting of DNA. The vibrations
of carbonyl bonds are well-known probes of their H-bonding environment,
and their signals can be observed with infrared (IR) spectroscopy.
Yet, pinpointing a single bond of interest in the complex IR spectrum
of DNA is challenging due to the large number of carbonyl signals
that overlap with each other. Here, we develop a method using isotope
editing and infrared (IR) spectroscopy to isolate IR signals from
the thymine (T) C2=O carbonyl. We use solvatochromatic studies
to show that the TC2=O signal’s position in the IR spectrum
is sensitive to the H-bonding capacity of the solvent. Our results
indicate that C2=O of a single T base within DNA duplexes experiences
weak H-bonding interactions. This finding is consistent with the existence
of a third, noncanonical CH···O H-bond between adenine
and thymine in both Watson–Crick and Hoogsteen base pairs in
DNA.
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Affiliation(s)
- Robert J Fick
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Amy Y Liu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Atul Rangadurai
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Roger D Sommer
- Molecular Education, Technology, and Research Innovation Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States.,Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
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3
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Probing the effect of N-alkylation on the molecular recognition abilities of the major groove N7-binding site of purine ligands. J Inorg Biochem 2019; 200:110801. [DOI: 10.1016/j.jinorgbio.2019.110801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/08/2019] [Accepted: 08/17/2019] [Indexed: 12/12/2022]
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4
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Zhang C, Bell D, Harger M, Ren P. Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases. J Chem Theory Comput 2017; 13:666-678. [PMID: 28030769 PMCID: PMC5312700 DOI: 10.1021/acs.jctc.6b00918] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Aromatic molecules with π electrons
are commonly involved
in chemical and biological recognitions. For example, nucleobases
play central roles in DNA/RNA structure and their interactions with
proteins. The delocalization of the π electrons is responsible
for the high polarizability of aromatic molecules. In this work, the
AMOEBA force field has been developed and applied to 5 regular nucleobases
and 12 aromatic molecules. The permanent electrostatic energy is expressed
as atomic multipole interactions between atom pairs, and many-body
polarization is accounted for by mutually induced atomic dipoles.
We have systematically investigated aromatic ring stacking and aromatic-water
interactions for nucleobases and aromatic molecules, as well as base–base
hydrogen-bonding pair interactions, all at various distances and orientations.
van der Waals parameters were determined by comparison to the quantum
mechanical interaction energy of these dimers and fine-tuned using
condensed phase simulation. By comparing to quantum mechanical calculations,
we show that the resulting classical potential is able to accurately
describe molecular polarizability, molecular vibrational frequency,
and dimer interaction energy of these aromatic systems. Condensed
phase properties, including hydration free energy, liquid density,
and heat of vaporization, are also in good overall agreement with
experimental values. The structures of benzene liquid phase and benzene-water
solution were also investigated by simulation and compared with experimental
and PDB structure derived statistical results.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - David Bell
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
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5
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Emani PS, Bardaro MF, Huang W, Aragon S, Varani G, Drobny GP. Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles. J Phys Chem B 2014; 118:1726-42. [PMID: 24479561 PMCID: PMC3983377 DOI: 10.1021/jp409386t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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Complex RNA structures are constructed
from helical segments connected
by flexible loops that move spontaneously and in response to binding
of small molecule ligands and proteins. Understanding the conformational
variability of RNA requires the characterization of the coupled time
evolution of interconnected flexible domains. To elucidate the collective
molecular motions and explore the conformational landscape of the
HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized
structures generated by the program “Fragment Assembly of RNA
with Full-Atom Refinement (FARFAR)”. We apply structural filters
in the form of experimental residual dipolar couplings (RDCs) to select
a subset of discrete energy-minimized conformers and carry out principal
component analyses (PCA) to corroborate the choice of the filtered
subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule
using two simulation protocols that we previously published. We match
the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results
introduce a protocol to construct viable dynamic trajectories for
RNA molecules that accord well with experimental NMR data and support
the notion that the motions of the helical portions of this small
RNA can be described by a relatively small number of discrete conformations
exchanging over time scales longer than 1 μs.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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6
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Greve C, Preketes NK, Fidder H, Costard R, Koeppe B, Heisler IA, Mukamel S, Temps F, Nibbering ETJ, Elsaesser T. N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics. J Phys Chem A 2013; 117:594-606. [PMID: 23234439 DOI: 10.1021/jp310177e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.
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Affiliation(s)
- Christian Greve
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
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9
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James SL, Adams CJ, Bolm C, Braga D, Collier P, Friščić T, Grepioni F, Harris KDM, Hyett G, Jones W, Krebs A, Mack J, Maini L, Orpen AG, Parkin IP, Shearouse WC, Steed JW, Waddell DC. Mechanochemistry: opportunities for new and cleaner synthesis. Chem Soc Rev 2012; 41:413-47. [DOI: 10.1039/c1cs15171a] [Citation(s) in RCA: 1921] [Impact Index Per Article: 160.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Ibáñez S, Albertí FM, Sanz Miguel PJ, Lippert B. Exploring the Metal Coordination Properties of the Pyrimidine Part of Purine Nucleobases: Isomerization Reactions in Heteronuclear PtII/PdII of 9-Methyladenine. Inorg Chem 2011; 50:10439-47. [DOI: 10.1021/ic201548k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susana Ibáñez
- Fakultät Chemie, Technische Unversität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Francisca M. Albertí
- Fakultät Chemie, Technische Unversität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Pablo J. Sanz Miguel
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - Bernhard Lippert
- Fakultät Chemie, Technische Unversität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
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11
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Emani PS, Olsen GL, Echodu DC, Varani G, Drobny GP. Slow exchange model of nonrigid rotational motion in RNA for combined solid-state and solution NMR studies. J Phys Chem B 2010; 114:15991-6002. [PMID: 21067190 PMCID: PMC3246393 DOI: 10.1021/jp107193z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Functional RNA molecules are conformationally dynamic and sample a multitude of dynamic modes over a wide range of frequencies. Thus, a comprehensive description of RNA dynamics requires the inclusion of a broad range of motions across multiple dynamic rates which must be derived from multiple spectroscopies. Here we describe a slow conformational exchange theoretical approach to combining the description of local motions in RNA that occur in the nanosecond to microsecond window and are detected by solid-state NMR with nonrigid rotational motion of the HIV-1 transactivation response element (TAR) RNA in solution as observed by solution NMR. This theoretical model unifies the experimental results generated by solution and solid-state NMR and provides a comprehensive view of the dynamics of HIV-1 TAR RNA, a well-known paradigm of an RNA where function requires extensive conformational rearrangements. This methodology provides a quantitative atomic level view of the amplitudes and rates of the local and collective displacements of the TAR RNA molecule and provides directly motional parameters for the conformational capture hypothesis of this classical RNA-ligand interaction.
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Affiliation(s)
- Prashant S. Emani
- Department of Physics, University of Washington, Box 351560, Seattle, USA 98195
| | - Gregory L. Olsen
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
| | - Dorothy C. Echodu
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
- Department of Biochemistry, University of Washington, Box 357350, Seattle, USA 98195
| | - Gary P. Drobny
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
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12
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Boczar M, Boda Ł, Wójcik MJ. Theoretical model of infrared spectra of hydrogen bonds in molecular crystals and its application to interpretation of infrared spectra of 1-methylthymine. J Chem Phys 2006; 125:084709. [PMID: 16965041 DOI: 10.1063/1.2335843] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A theoretical model for vibrational interactions in the hydrogen bonds in molecular crystals with four molecules forming two centrosymmetric dimers in the unit cell is presented. The model takes into account anharmonic-type couplings between the high-frequency N-H(D) and the low-frequency N...O stretching vibrations in each hydrogen bond, resonance interactions (Davydov coupling) between equivalent hydrogen bonds in each dimer, resonance interdimer interactions within a unit cell, and Fermi resonance between the N-H(D) stretching fundamental and the first overtone of the N-H(D) in-plane bending vibrations. The vibrational Hamiltonian, selection rules, and expressions for the integral properties of an absorption spectrum are derived. The model is used for theoretical simulation of the NH stretching bands of 1-methylthymine and its ND derivative at 300 K. The effect of deuteration is successfully reproduced by our model. Infrared, far-infrared, Raman, and low-frequency Raman spectra of 1-methylthymine and its deuterated derivative have been measured. Experimental geometry and frequencies are compared with the results of density functional theory calculations performed at the B3LYP6-311++G**, B3LYP/cc-pVTZ, B3PW916-311++G**, and B3PW91/cc-pVTZ levels.
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Affiliation(s)
- Marek Boczar
- Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
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13
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Padmanabhan J, Parthasarathi R, Subramanian V, Chattaraj PK. Molecular Structure, Reactivity, and Toxicity of the Complete Series of Chlorinated Benzenes. J Phys Chem A 2005; 109:11043-9. [PMID: 16331949 DOI: 10.1021/jp0538621] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and chemical reactivity profiles of all 12 chlorobenzenes have been investigated using the density functional theory and ab initio molecular orbital calculations. Global and local reactivity descriptors such as electrophilicity index and local philicity, respectively, of the selected systems have been calculated in order to gain insights into the reactive nature and the reactive sites of these compounds. Also, the effects of chlorine substitution on the aromaticity of the compounds have been analyzed by calculating the nucleus-independent chemical shift. Interaction through charge transfer between chlorobenzenes and nucleic acid bases/selected base pairs are determined using Parr's formula. The results revealed that the chlorobenzenes act as electron acceptors in their interaction with biomolecules. Structure-toxicity analysis of this entire set of chlorobenzenes demonstrates the importance of the electrophilicity index in the prediction of reactivity/toxicity.
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Affiliation(s)
- J Padmanabhan
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
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14
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Current measurements as a tool to characterise the H-bonding between 1-ferrocenylmethylthymine and 9-octyladenine: a voltammetric and chronoamperometric analysis. J Electroanal Chem (Lausanne) 2004. [DOI: 10.1016/j.jelechem.2004.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Sherer EC, York DM, Cramer CJ. Fast approximate methods for calculating nucleic acid base pair interaction energies. J Comput Chem 2003; 24:57-67. [PMID: 12483675 DOI: 10.1002/jcc.10150] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Interaction enthalpies for six base pairs have been computed at a variety of efficient levels of electronic structure theory and compared to experiment. In addition to previously defined levels of theory, modified Hamiltonians with adjusted parameters in hybrid Hartree-Fock/density functionals and semiempirical neglect-of-diatomic-differential-overlap models were examined. Of the pure and hybrid density functional levels, mPWPW91/MIDI! performed most satisfactorily, as judged by comparison not only to the available experimental data, but also to data from more robust electronic structure methods for 22 additional base pairs. The low computational cost of the mPWPW91/MIDI! model was further exploited in an investigation of various base trimers, tetramers, and one base pentamer. A carefully reparameterized semiempirical model, PM3(BP), was able to achieve similar levels of accuracy at a still greater savings in terms of computational effort.
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Affiliation(s)
- Edward C Sherer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, USA
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16
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Rojas-González PX, Castiñeiras A, González-Pérez JM, Choquesillo-Lazarte D, Niclós-Gutiérrez J. Interligand interactions controlling the mu-N7,N9-metal bonding of adenine (AdeH) to the N-benzyliminodiacetato(2-) copper(II) chelate and promoting the N9 versus N3 tautomeric proton transfer: molecular and crystal structure of [Cu2(NBzIDA)(2)(H2O)(2)(mu-N7,N9-Ade(N3)H)].(3)H2O. Inorg Chem 2002; 41:6190-2. [PMID: 12444757 DOI: 10.1021/ic025881k] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction in water of the N-benzyliminodiacetate-copper(II) chelate ([Cu(NBzIDA)]) and the adenine:thymine base pair complex (AdeH:ThyH) with a Cu/NBzIDA/AdeH/ThyH molar ratio of 2:2:1:1 yields [Cu(2)(NBzIDA)(2)(H(2)O)(2)(mu-N7,N9-Ade(N3)H)].3H(2)O and free ThyH. The compound has been studied by thermal, spectral, and X-ray diffraction methods. In the asymmetric dinuclear complex units both Cu(II) atoms exhibit a square pyramidal coordination, where the four closest donors are supplied by NBzIDA in a mer-tridentate conformation and the N7 or N9 donors of AdeH, which is protonated at N3. The mu-N7,N9 bridge represents a new coordination mode for nonsubstituted AdeH, except for some adeninate(1-)-[methylmercury(II)] derivatives studied earlier. The dinuclear complex is stabilized by the Cu-N7 and Cu-N9 bonds and N6-H(exocyclic)...O(carboxyl) and N3-H(heterocyclic)...O(carboxyl) interligand interactions, respectively. The structure of the new compound differs from that of the mononuclear compound [Cu(NBzIDA)(Ade(N9)H)(H(2)O)].H(2)O, in which the unusual Cu-N3(AdeH) bond is stabilized by a N9-H...O(carboxyl) interligand interaction and where alternating benzyl-AdeH intermolecular pi,pi-stacking interactions produce infinite stacked chains. The possibility for ThyH to be involved in the molecular recognition between [Cu(NBzIDA)] and the AdeH:ThyH base pair is proposed.
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Affiliation(s)
- Perla X Rojas-González
- Inorganic Chemistry Department, Faculty of Pharmacy, University of Granada, Granada, Spain
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17
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Castellano RK, Gramlich V, Diederich F. Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution. Chemistry 2002; 8:118-29. [PMID: 11822445 DOI: 10.1002/1521-3765(20020104)8:1<118::aid-chem118>3.0.co;2-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rebek imides (3), formed from Kemp's triacid, were developed in the mid-1980's as model receptors for adenine derivatives. We report here the first account of their hydrogen-bonding preferences upon binding 9-ethyladenine (1a) in the solid state. Structural analysis begins with simple imides 3a-e that form discrete dimers, while bis-imide 4 forms ribbon-like structures in the crystalline phase. The hydrogen-bonding interface within each of the representative assemblies features short intermolecular N(3)imide...O(8*)imide* distances (ca. 2.95 A), indicative of two-point hydrogen bonding. Imides 3f-h could be co-crystallized with 1a; single-crystal X-ray analysis of the resulting complexes reveals hydrogen-bonding geometries nearly identical to those observed in nucleobase complexes of adenine and pyrimidine derivatives. Imides 3f and 3g form 2:1 ternary assemblies with 1a; the complex of the former, (3f)2 x 1a, displays both Watson-Crick- and Hoogsteen-type hydrogen bonding, whereas the complex of the latter, (3g)2 x 1a, shows the Hoogsteen motif and imide hydrogen bonding to N(3) of the purine base (N(3)adenine...N(3'')imide = 3.07(1) A). Imide 3h forms a 1:1 complex with 1a (3h x 1a x CHCl3) and displays Hoogsteen binding exclusively. All of the 3 x 1a assemblies show C(adenine)...O(imide) distances (3.38-3.75 A) that are consistent with C-H...O hydrogen bonding. Base-pairing preferences for the Rebek imides are further explored in solution by 1H NMR one-dimensional NOE experiments and by computational means; in all cases the Hoogsteen motif is modestly favored relative to its Watson-Crick counterpart.
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18
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Sigel RK, Thompson SM, Freisinger E, Glahé F, Lippert B. Metal-modified nucleobase sextet: joining four linear metal fragments (trans-a2PtII) and six model nucleobases to an exceedingly stable entity. Chemistry 2001; 7:1968-80. [PMID: 11405476 DOI: 10.1002/1521-3765(20010504)7:9<1968::aid-chem1968>3.0.co;2-b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Crosslinking of three different model nucleobases (9-ethyladenine, 9-EtA; 9-ethylguanine, 9-EtGH; 1-methyluracil, 1-MeU) by two linear trans-aPtII (a = NH3 or CH3NH2) entities leads to a flat metal-modified base triplet, trans,trans-[(NH3)2Pt(1-MeU-N3)(mu-9-EtA-N7,N1)Pt(CH3NH2)2(9-EtGH-N7)]3+ (4b). Upon hemideprotonation of the 9-ethylguanine base at the N1 position. 4b spontaneously dimerizes to the metalated nucleobase sextet 5, [(4b)(triple bond)(4b-H)]5+. In this dimeric structure a neutral and an anionic guanine ligand, which are complementary to each other, are joined through three H bonds and additionally by two H bonds between guanine and uracil nucleobases. Four additional interbase H bonds maintain the approximate coplanarity of all six bases. The two base triplets form an exceedingly stable entity (KD = 500 +/- 150 M(-1) in DMSO), which is unprecedented in nucleobase chemistry. The precursor of 4b and several related complexes are described and their structures and solution properties are reported.
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Affiliation(s)
- R K Sigel
- Fachbereich Chemie, Universität Dortmund, Germany
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20
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Scheurer C, Brüschweiler R. Quantum-Chemical Characterization of Nuclear Spin−Spin Couplings Across Hydrogen Bonds. J Am Chem Soc 1999. [DOI: 10.1021/ja9917417] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Scheurer
- Gustaf H. Carlson School of Chemistry Clark University, Worcester, Massachusetts 01610
| | - R. Brüschweiler
- Gustaf H. Carlson School of Chemistry Clark University, Worcester, Massachusetts 01610
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21
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Rao P, Ghosh S, Maitra U. Binding of 9-N-Butyladenine by Carboxylic Acids: Evidence that Hoogsteen Binding Can Dominate in Solution. J Phys Chem B 1999. [DOI: 10.1021/jp984235x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Photon Rao
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Suhrit Ghosh
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Uday Maitra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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22
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Ojima N, Gekko K, Yamaoka K. Pulsed Electric Linear Dichroism of Poly(dA)·Poly(dT)·Poly(dT) and Poly(rA)·Poly(rU)·Poly(rU) in Solutions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1997. [DOI: 10.1246/bcsj.70.1559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Zamora F, Kunsman M, Sabat M, Lippert B. Metal-Stabilized Rare Tautomers of Nucleobases. 6. Imino Tautomer of Adenine in a Mixed-Nucleobase Complex of Mercury(II). Inorg Chem 1997; 36:1583-1587. [PMID: 11669746 DOI: 10.1021/ic961167p] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(1,3-Dimethyluracil-5-yl)mercury(II), (1,3-DimeU-C5)Hg(II), reacts with the model nucleobase 9-methyladenine (9-MeA) to give the mixed-nucleobase complex [Hg(1,3-DimeU-C5)(9-MeA-N6)]NO(3).H(2)O. Hg(II) binds to the adenine via the N6 position with N1 being protonated. The neutral adenine nucleobase is therefore present in its imino form, which represents the rare tautomer form of this nucleobase. The X-ray crystal structure analysis reveals an anti orientation of the (1,3-DimeU-C5)Hg(II) entity with respect to N1 of 9-MeA and substantial differences in nucleobase geometry as compared to the amino tautomer form of 9-MeA. These differences refer to both the pyrimidine and the imidazole rings of the purine base. The possible relevance of this compound with regard to nucleobase cross-linking in DNA and nucleobase mispairing is discussed. Attempts to demonstrate mispairing between the metalated rare tautomer and "the wrong" bases 1-methylcytosine (1-MeC) and 9-ethylguanine (9-EtGH) in DMSO-d(6) proved unsuccessful due to a ligand exchange process at the heavy metal.
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Affiliation(s)
- Félix Zamora
- Fachbereich Chemie, Universität Dortmund, D-44221 Dortmund, Germany, and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901
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24
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Leonard † NJ, Neelima. Methodology for the Synthesis of Dinucleoside Monophosphates Containing A 2′-Deoxy-3-Isoadenosine Unit: 3-iso-dApT and Tp(3-iso-dA). ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002437] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Wann M, Harbison GS. Axial asymmetry in the nuclear magnetic resonance spectra of deuterated methyl groups: An alternative explanation. J Chem Phys 1994. [DOI: 10.1063/1.468174] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Nicholson LK, Kay LE, Baldisseri DM, Arango J, Young PE, Bax A, Torchia DA. Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. Biochemistry 1992; 31:5253-63. [PMID: 1606149 DOI: 10.1021/bi00138a003] [Citation(s) in RCA: 205] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This paper describes the application of recently developed nuclear magnetic resonance (NMR) pulse sequences to obtain information about the internal dynamics of isotopically enriched hydrophobic side chains in proteins. The two-dimensional spectra provided by the pulse sequences enable one to make accurate measurements of nuclear Overhauser effects (NOE) and longitudinal (T1) and transverse (T2) relaxation times of enriched methyl carbons in proteins. Herein, these techniques are used to investigate the internal dynamics of the 11 leucine side chains of staphylococcal nuclease (SNase), a small enzyme having Mr = 16.8K, in the absence and presence of ligands thymidine 3',5'-bisphosphate (pdTp) and Ca2+. We report the synthesis of [5,5'-13C2]leucine, the preparation of SNase containing the labeled leucine, the sequential assignment of the leucine methyl carbons and protons in the liganded and unliganded proteins, and the measurement of the 13C T1, T2, and NOE values for the SNase leucine methyl carbons. Analysis of the relaxation parameters using the formalism of Lipari and Szabo shows that the internal motions of the leucine methyl carbons are characterized by effective correlation times tau f (5-80 ps) and tau s (less than 2 ns). The fast motion is identified with the rapid rotation of the methyl group about the C gamma-C delta bond axis, while the slow motion is associated with reorientation of the C gamma-C delta bond axis itself. The mean squared order parameters associated with the latter motion, Ss2, lie in the range 0.34-0.92. The values of Ss2 correlate reasonably well with the temperature factors of the leucine methyl carbons obtained from the crystal structures, but some are smaller than anticipated on the basis of the fact that nearly all leucine methyl carbons are buried and have temperature factors no larger than that of the leucine backbone atoms. Five leucine residues in liganded SNase and eight in unliganded SNase have values of Ss2 less than 0.71. These order parameters correspond to large amplitude motions (angular excursions of 27-67 degrees) of the C gamma-C delta bond axis. These results indicate that, in solution, the internal motions of the leucine side chains of SNase are significantly larger than suggested by the X-ray structures or by qualitative analysis of NOESY spectra. Comparison of Ss2 values obtained from liganded and unliganded SNase reveals a strong correlation between delta Ss2 and distance between the leucine methyl carbon and the ligands.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- L K Nicholson
- Bone Research Branch, National Institute of Dental Research, National Institutes of Health, Bethesda, Maryland 20892
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27
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Infrared matrix isolation and ab initio quantum mechanical studies of purine and adenine. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/0584-8539(91)80182-i] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Nerdal W, Hare DR, Reid BR. Solution structure of the EcoRI DNA sequence: refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations. Biochemistry 1989; 28:10008-21. [PMID: 2620059 DOI: 10.1021/bi00452a020] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The solution structure of the self-complementary DNA duplex [d(CGCGAATTCGCG)]2, which contains the EcoRI restriction site sequence GAATTC at the center, has been studied by two-dimensional nuclear magnetic resonance spectroscopy. Time-dependent nuclear Overhauser effect spectra were used to obtain the initial cross-relaxation rates between 155 pairs of protons. These initial cross-relaxation rates were converted into interproton distances and entered into a distance (bounds) matrix. A distance geometry algorithm (DSPACE) was used to create embedded starting structures and to refine these structures until they showed good agreement with the distance matrix; symmetry constraints were included in the refinement procedure, making the two strands in the refined distance geometry structures virtually identical and significantly improving the agreement with the distance matrix. The NOESY spectrum for one of these distance geometry structures was then calculated from the explicit coordinates by numerically integrating all the z-magnetization transfer pathways among neighboring protons within a specified radius. Distances in this distance geometry structure that did not agree with the experimental NOESY time course were then adjusted accordingly. This process was iterated until a good agreement between calculated and experimental NOESY spectra was reached. The final structure, which generates good agreement with the experimental NOESY spectrum, displays kinks at the C3-G4 base step and at the A6-T7 base step that appear to be similar to those reported for the EcoRI restriction site DNA bound to its endonuclease. The solution structure is not the same as the crystal structure of this DNA duplex.
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Affiliation(s)
- W Nerdal
- Department of Chemistry, University of Washington, Seattle 98195
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29
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Nerdal W, Hare DR, Reid BR. Three-dimensional structure of the wild-type lac Pribnow promoter DNA in solution. Two-dimensional nuclear magnetic resonance studies and distance geometry calculations. J Mol Biol 1988; 201:717-39. [PMID: 3172200 DOI: 10.1016/0022-2836(88)90469-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The solution structure of a 12 base-pair DNA duplex containing the wt-lac promoter Pribnow sequence TATGTT has been studied by two-dimensional nuclear magnetic resonance spectroscopy. Proton assignments for the 24 sugar and base residues were obtained from two-dimensional correlated nuclear magnetic resonance and two-dimensional nuclear Overhauser effect spectra in both 2H2O and H2O, and by two-dimensional relayed coherence transfer nuclear magnetic resonance spectroscopy experiments. Time-dependent, two-dimensional nuclear Overhauser effect spectra were used to determine the initial cross-relaxation rates between 212 pairs of assigned protons, leading to 212 interproton distances in the double helix (8 to 9 per nucleotide). These distance constraints, and known bond lengths and angles, were entered into a distance matrix. After smoothing the bounds of the distance matrix, 12 trial matrices within the bounds constraints were independently generated and embedded in three-dimensional space using a distance geometry algorithm, to generate 12 trial structures. These trial structures were then refined until they no longer violated the distance matrix. The resulting structures are very similar at the local base-pair and nearest-neighbor base-pair level, but exhibit increasing variation at more distant and global levels. At the nearest-neighbor level, the A to T step and the G to T step within the Pribnow hexamer, as well as the G to T step preceding the hexamer, all exhibit very low screw pitch, i.e. 5(+/- 6) degrees. Conversely, the T to G step in the center of the promoter has a large screw pitch (47(+/- 2) degrees) and the T to G step at the 3' end of the promoter has a very large screw pitch (60(+/- 3) degrees). The limitations of nuclear magnetic resonance spectroscopy distance determination of structure are discussed in terms of resolution and spectral overlap of two-dimensional nuclear Overhauser effect crosspeaks. In the present duplex, the inability to measure several 1'-2' and 1'-2" distances resulted in underdetermination of the precise local sugar conformation for seven of the 24 residues, although the spatial position of all sugars was well defined.
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Affiliation(s)
- W Nerdal
- Department of Chemistry and Biochemistry, University of Washington, Seattle 98195
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30
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Shindo H, Hiyama Y, Roy S, Cohen JS, Torchia DA. Deuterium Nuclear Magnetic Resonance of Oriented DNA Fibers. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1987. [DOI: 10.1246/bcsj.60.1631] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Rossi C, Marchettini N, Pogliani L, Laschi F, Niccolai N. Structural and dynamical studies of the relaxation effects induced by proton perturbation during 13C spin-lattice relaxation rate measurements. Chem Phys Lett 1987. [DOI: 10.1016/0009-2614(87)80507-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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A survey of the geometry of hydrogen bonds in the crystal structures of barbiturates, purines and pyrimidines. J Mol Struct 1986. [DOI: 10.1016/0022-2860(86)87064-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Poltev VI, Shulyupina NV. Simulation of interactions between nucleic acid bases by refined atom-atom potential functions. J Biomol Struct Dyn 1986; 3:739-65. [PMID: 3271047 DOI: 10.1080/07391102.1986.10508459] [Citation(s) in RCA: 107] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H . . . O and (or) N-H . . . N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component in polynucleotide complexes and in tRNA is close to the position in one of these minima. Besides, for each pair there are energy minima corresponding to the formation of a single N-H . . . O or N-H . . . N and one C-H . . . O or C-H . . . N hydrogen bond. The form of potential surface in the vicinity of minima has been characterized. The results of calculations agree with the experimental data and with more rigorous calculations based on quantum-mechanical approach.
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Affiliation(s)
- V I Poltev
- Institute of Biological Physics, USSR Academy of Sciences, Moscow Region
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34
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Naito A, Barker PB, McDowell CA. Two‐dimensional nuclear magnetic resonance studies on a single crystal ofl‐alanine. Separation of the local dipolar fields; and 2Dexchange spectroscopy of the14N relaxation processes. J Chem Phys 1984. [DOI: 10.1063/1.447887] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Ornstein RL, Fresco JR. Correlation of Tm and sequence of DNA duplexes with delta H computed by an improved empirical potential method. Biopolymers 1983; 22:1979-2000. [PMID: 6616016 DOI: 10.1002/bip.360220811] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Strobel JL, Scovell WM. Laser raman spectroscopy of a complementary base pair in the Hoogsteen configuration. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 608:201-14. [PMID: 7397183 DOI: 10.1016/0005-2787(80)90167-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cocrystallization of m9Ade and m1Thy from water yielded crystals of te Hoogsteen base pair, m9Ade x m1Thy, as demonstrated by X-ray diffraction data. The Raman spectrum of the Hoogsteen base pair in the crystalline state was obtained and compared to the crystals of the individual monomers. Frequency changes between the heterobase dimer and both m9Ade and m1Thy are indicative of the base pairing interaction. Utilizing previously reported vibrational analyses for m9Ade, the frequency changes are clearly associated with modes involving the internal coordinates most sensitive to a Hoogsteen hydrogen bonding interaction. The spectrum of an equimolar mixture of e9Ade and ch1Ura in CHCl3 was also compared to the spectrum of the separate monomers in solution. The numerous frequency shifts and band intensity changes observed in the mixture from that of the individual monomers suggest a cyclic dimer is formed although the nature of the base pairing interaction is not clear.
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38
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Yanson IK, Teplitsky AB, Sukhodub LF. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers 1979; 18:1149-70. [PMID: 435611 DOI: 10.1002/bip.1979.360180510] [Citation(s) in RCA: 307] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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39
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Effect of water on the tautomeric equilibrium of uracil monoanions. A PCILO study. ACTA ACUST UNITED AC 1976. [DOI: 10.1007/bf00548293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Taulomerism and Electronic Structure of Biological Pyrimidines. ADVANCES IN HETEROCYCLIC CHEMISTRY VOLUME 18 1975. [DOI: 10.1016/s0065-2725(08)60131-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Kvick Å, Koetzle TF, Thomas R. Hydrogen bond studies. 89. A neutron diffraction study of hydrogen bonding in 1‐methylthymine. J Chem Phys 1974. [DOI: 10.1063/1.1682404] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Kvick Å, Koetzle TF, Thomas R, Takusagawa F. Hydrogen bond studies. 85. A very short, asymmetrical, intramolecular hydrogen bond: A neutron diffraction study of pyridine‐2,3‐dicarboxylic acid (C7H5NO4). J Chem Phys 1974. [DOI: 10.1063/1.1680831] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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