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Peng HC, Castro GL, Karthikeyan V, Jarrett A, Katz MA, Hargrove JA, Hoang D, Hilber S, Meng W, Wang L, Fick RJ, Ahn JM, Kreutz C, Stelling AL. Measuring the Enthalpy of an Individual Hydrogen Bond in a DNA Duplex with Nucleobase Isotope Editing and Variable-Temperature Infrared Spectroscopy. J Phys Chem Lett 2023; 14:4313-4321. [PMID: 37130045 DOI: 10.1021/acs.jpclett.3c00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The level of interest in probing the strength of noncovalent interactions in DNA duplexes is high, as these weak forces dictate the range of suprastructures the double helix adopts under different conditions, in turn directly impacting the biological functions and industrial applications of duplexes that require making and breaking them to access the genetic code. However, few experimental tools can measure these weak forces embedded within large biological suprastructures in the native solution environment. Here, we develop experimental methods for detecting the presence of a single noncovalent interaction [a hydrogen bond (H-bond)] within a large DNA duplex in solution and measure its formation enthalpy (ΔHf). We report that introduction of a H-bond into the TC2═O group from the noncanonical nucleobase 2-aminopurine produces an expected decrease ∼10 ± 0.76 cm-1 (from ∼1720 cm-1 in Watson-Crick to ∼1710 cm-1 in 2-aminopurine), which correlates with an enthalpy of ∼0.93 ± 0.066 kcal/mol for this interaction.
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Affiliation(s)
- Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Gabrielle L Castro
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Varshini Karthikeyan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Alina Jarrett
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Melanie A Katz
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - James A Hargrove
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - David Hoang
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Wenting Meng
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Robert J Fick
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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Montoro-García C, Camacho-García J, López-Pérez AM, Mayoral MJ, Bilbao N, González-Rodríguez D. Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes. Angew Chem Int Ed Engl 2015; 55:223-7. [DOI: 10.1002/anie.201508854] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 11/09/2022]
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3
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Montoro-García C, Camacho-García J, López-Pérez AM, Mayoral MJ, Bilbao N, González-Rodríguez D. Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Janssen P, Ruiz-Carretero A, González-Rodríguez D, Meijer E, Schenning A. pH-Switchable Helicity of DNA-Templated Assemblies. Angew Chem Int Ed Engl 2009; 48:8103-6. [DOI: 10.1002/anie.200903507] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Janssen P, Ruiz-Carretero A, González-Rodríguez D, Meijer E, Schenning A. pH-Switchable Helicity of DNA-Templated Assemblies. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903507] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH. An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA. Biochemistry 2006; 45:6889-903. [PMID: 16734425 PMCID: PMC4121271 DOI: 10.1021/bi0524464] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.
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Affiliation(s)
- Gang Chen
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Jing Qiao
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627
| | - Thomas R. Krugh
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627
- Center for Pediatric Biomedical Research and Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642
- To whom correspondence should be addressed. Phone: (585) 275-3207. Fax: (585) 276-0205.
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7
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Šponer J, Sabat M, Burda JV, Leszczynski J, Hobza P. Interaction of the Adenine−Thymine Watson−Crick and Adenine−Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) Metal Cations: Absence of the Base Pair Stabilization by Metal-Induced Polarization Effects. J Phys Chem B 1999. [DOI: 10.1021/jp983744w] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Michal Sabat
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Jaroslav V. Burda
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
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8
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Ornstein RL, Zheng YJ. Ab initio quantum mechanics analysis of imidazole C-H...O water hydrogen bonding and a molecular mechanics forcefield correction. J Biomol Struct Dyn 1997; 14:657-65. [PMID: 9195335 DOI: 10.1080/07391102.1997.10508169] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
While it is well established that classical hydrogen bonds play an important role in enzyme structure, function and dynamics, the role of weaker, but 'activated' C-H donor hydrogen bonds is poorly understood. The most important such case involves histidine which often plays a direct role in enzyme catalysis and possesses the most acidic C-H donor group of the standard amino acids. In the present study, we obtained optimized geometries and hydrogen bond interaction energies for C-H...O hydrogen bonded complexes between methane, ethylene, benzene, acetylene, and imidazole with water at the MP2-FC/6-31++G(2d,2p) and MP2-FC/aug-cc-pVDZ/MP2-FC/6-31++G(2d,2p) levels of theory. A strong linear relationship is obtained between the stability of the various hydrogen bonded complexes and both separation distances for H...O and C----O. In general, these calculations indicate that C-H...O interactions can be classified as hydrogen bonding interactions, albeit significantly weaker than the classical hydrogen bonds, but significantly stronger than just van der Waals interactions. For instance, while the electronic energy of stabilization at the MP2-FC/aug-cc-pVDZ/MP2-FC/6-31++G(2d,2p) level of theory of a water O-H...O water hydrogen bond is 4.36 kcal/mol more stable than the methane C-H...O water interaction, the water-water hydrogen bond is only 2.06 kcal/mol more stable than the imidazole Ce-H...O water hydrogen bond. Neglecting this latter hydrogen bonding interaction is obviously unacceptable. We next compare the potential energy surfaces for the imidazole Ce-H...O water and imidazole Na-H...O hydrogen bonded complexes computed at the MP2/6-31++G(2d,2p) level of theory with the potential energy surface computed using the AMBER molecular mechanics program and forcefields. While the Weiner et al and Cornell et al AMBER forcefields reasonably account for the imidazole N-H...O water interaction, these forcefields do not adequately account for the imidazole Ce-H...O water hydrogen bond. A forcefield modification is offered that results in excellent agreement between the ab initio and molecular mechanics geometry and energy for this C-H...O hydrogen bonded complex.
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Affiliation(s)
- R L Ornstein
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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9
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Sponer J, Leszczynski J, Hobza P. Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. J Biomol Struct Dyn 1996; 14:117-35. [PMID: 8877568 DOI: 10.1080/07391102.1996.10508935] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. J.S.-
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10
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Sponer J, Leszczynski J, Vetterl V, Hobza P. Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions. J Biomol Struct Dyn 1996; 13:695-706. [PMID: 8906890 DOI: 10.1080/07391102.1996.10508882] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are more stable than the neutral base pairs. Two energy contributions not present in the neutral base pairs stabilize the protonated base pairs: the molecular ion - dipole interaction, and the induction interaction. The molecular ion - dipole stabilization dominates in base pairs with highly polar neutral monomers, such as the C...CH+ base pair. The induction interaction is not included in the commonly used empirical potentials, which do not reproduce the changes in intermolecular stabilization due to protonation. We demonstrate that the base stacking of several consecutive C...CH + pairs, as proposed for polycytidylic acid and i-DNA, is strongly repulsive. We also show that the intermolecular interactions strongly prefer protonation of adenine in protonated adenine-cytosine pairs.
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Affiliation(s)
- J Sponer
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague.
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11
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Lavelle L, Fresco JR. UV spectroscopic identification and thermodynamic analysis of protonated third strand deoxycytidine residues at neutrality in the triplex d(C(+)-T)6:[d(A-G)6.d(C-T)6]; evidence for a proton switch. Nucleic Acids Res 1995; 23:2692-705. [PMID: 7651830 PMCID: PMC307094 DOI: 10.1093/nar/23.14.2692] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Near-UV difference spectral analysis of the triplex formed from d(C-T)6 and d(A-G)6.d(C-T)6 in neutral and acidic solution shows that the third strand dC residues are protonated at pH 7.0, far above their intrinsic pKa. Additional support for ion-dipole interactions between the third strand dC residues and the G.C target base pairs comes from reduced positive dependence of triplet stability on ionic strength below 0.9 M Na+, inverse dependence above 0.9 M Na+ and strong positive dependence on hydrogen ion concentration. Molecular modeling (AMBER) of C:G.C and C+:G.C base triplets with the third strand base bound in the Hoogsteen geometry shows that only the C+:G.C triplet is energetically feasible. van't Hoff analysis of the melting of the triplex and target duplex shows that between pH 5.0 and 8.5 in 0.15 M NaCl/0.005 M MgCl2 the enthalpy of melting (delta H degree obs) varies from 5.7 to 6.6 kcal.mol-1 for the duplex in a duplex mixture and from 7.3 to 9.7 kcal.mol-1 for third strand dissociation in the triplex mixture. We have extended the condensation-screening theory of Manning to pH-dependent third strand binding. In this development we explicitly include the H+ contribution to the electrostatic free energy and obtain [formula: see text]. The number of protons released in the dissociation of the third strand from the target duplex at pH 7.0, delta n2, is thereby calculated to be 5.5, in good agreement with approximately six third strand dc residues per mole of triplex. This work shows that when third strand binding requires protonated residues that would otherwise be neutral, triplex formation and dissociation are mediated by proton uptake and release, i.e., a proton switch. As a by-product of this study, we have found that at low pH the Watson-Crick duplex d(A-G)6.d(C-T)6 undergoes a transition to a parallel Hoogsteen duplex d(A-G)6.d(C(+)-T)6.
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Affiliation(s)
- L Lavelle
- Department of Molecular Biology, Princeton University, NJ 08544-1014, USA
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Jiang SP, Raghunathan G, Ting KL, Xuan JC, Jernigan RL. Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases. J Biomol Struct Dyn 1994; 12:367-82. [PMID: 7702775 DOI: 10.1080/07391102.1994.10508746] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ab initio molecular orbital calculations with the STO-3G and 4-31G basis sets are performed to study the geometries and interactions of natural and "novel" Watson-Crick base pairs, as well as some non-Watson-Crick base pairs. First the optimized geometries of bases are determined using the STO-3G basis set, and then for the base pairs with the STO-3G and 4-31G basis sets. Interaction energies of these base pairs are evaluated, and their relative stabilities are discussed. Hydrogen bond features, partial charges and dipole moments of the base pairs are described. The calculated stabilities are in reasonable agreement with the limited available experimental data from thermal melting studies. Hydrogen bond geometries at the 4-31G level are in good agreement with the crystal structure data. The order of relative stabilities is found to be: iG:iC > G:C > G:T* > rG:rC > A*:C > Am:U > tau:kappa > chi:kappa > G*:T > A:C* > A:U = A:T where, A*, T*, G* and C* are tautomers, iG and iC are iso-G and iso-C, Am is 2-amino adenine, chi is xanthosine, kappa is 2,4-diaminopyrimidine, tau is 7-methyl oxoformycin B, rG is modified guanine with substitutions at positions 5 and 7, and rC is modified cytosine with a substitution at position 6. Pairing strengths with modified bases may affect the efficiency of protein production.
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Affiliation(s)
- S P Jiang
- Laboratory of Mathematical Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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Sun JS, Giovannangeli C, François JC, Kurfurst R, Montenay-Garestier T, Asseline U, Saison-Behmoaras T, Thuong NT, Hélène C. Triple-helix formation by alpha oligodeoxynucleotides and alpha oligodeoxynucleotide-intercalator conjugates. Proc Natl Acad Sci U S A 1991; 88:6023-7. [PMID: 2068079 PMCID: PMC52014 DOI: 10.1073/pnas.88.14.6023] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Base-pair sequences in double-stranded DNA can be recognized by homopyrimidine oligonucleotides that bind to the major groove at homopurine.homopyrimidine sequences thereby forming a local triple helix. To make oligodeoxynucleotides resistant to nucleases, we replaced the natural (beta) anomers of the nucleotide units by the synthetic (alpha) anomers. The 11-mer alpha oligodeoxynucleotide 5'-d(TCTCCTCCTTT)-3' binds to the major groove of DNA in an antiparallel orientation with respect to the homopurine strand, whereas a beta oligonucleotide adopts a parallel orientation. When an intercalating agent was attached to the 3' end of the alpha oligodeoxynucleotide, a strong stabilization of the triple helix was observed. A 16-base-pair homopurine.homopyrimidine sequence of human immunodeficiency virus proviral DNA was chosen as a target for a 16-mer homopyrimidine alpha oligodeoxynucleotide. A restriction enzyme that cleaves DNA at the junction of the homopurine.homopyrimidine sequence was inhibited by triple-helix formation. The 16-mer alpha oligodeoxynucleotide substituted by an intercalating agent was approximately 20 times more efficient than the unsubstituted oligomer. Nuclease-resistant alpha oligodeoxynucleotides offer additional possibilities to control gene expression at the DNA level.
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Affiliation(s)
- J S Sun
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, Institut National de la Santé et de la Recherche Médicale, Paris, France
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14
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Sarma MH, Umemoto K, Gupta G, Luo J, Sarma RH. In search of a Hoogsteen base paired DNA duplex in aqueous solution. J Biomol Struct Dyn 1990; 8:461-82. [PMID: 2100514 DOI: 10.1080/07391102.1990.10507823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When the oligodeoxynucleotides d(A)6 and d(T)6 are mixed together in a 1:1 ratio (in 100 mM NaCl), the NH signals in the NMR spectrum gave a typical signature of Watson-Crick paired (WC) and Hoogsteen paired (H) AT base pairs. The observation indicates two schemes: Scheme I, WC and H duplexes in slow equilibrium, i.e., WC in equilibrium with H, Scheme II, the WC helix formed is unstable and that it disproportionates into a triple helix (TR) and free d(A)6. We show that (i) addition of extra d(A)6 does not change the helix composition, (ii) addition of a minor-groove specific drug Dst2 (a distamycin analogue) results in an exclusive WC helix-drug duplex, while it does not destabilize triple helix in a 1:2 mixture. In addition we have compared the melting profile, 31P NMR spectra, 1H NMR spectra and the salt dependence of the 1:1 mixture and that of a pure triple helix. All the data from the above experiments overwhelmingly favor Scheme I. However Scheme II cannot be categorically excluded. Based on 1D/2D NMR studies, we have characterized the structural properties of the Hoogsteen double helix in terms of nucleotide conformations. In addition, we computationally demonstrate that the relative stability of the WC over the H duplexes increases with increasing chain length.
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Affiliation(s)
- M H Sarma
- Department of Chemistry, State University of New York, Albany 12222
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15
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Kricker MC, Drake JW. Heat mutagenesis in bacteriophage T4: another walk down the transversion pathway. J Bacteriol 1990; 172:3037-9. [PMID: 2345133 PMCID: PMC209105 DOI: 10.1128/jb.172.6.3037-3039.1990] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Extracellular nonreplicating bacteriophage T4 particles accumulate mutations as functions of temperature, time, pH, and ionic environment via two mechanisms: 5-hydroxymethylcytidine deamination produces G.C----A.T transitions while a guanosine modification produces transversions. Neither frameshift mutations nor mutations at A.T base pairs are appreciably induced. We now show that heat induces G.C----T.A transversions which we suggest may arise via a G*.A mispair, in which G* is a modified guanosine that has experienced a glycosylic bond migration. The rate of this reaction at 37 degrees C is sufficient to present a genetic hazard, particularly to large genomes; thus, the lesion is probably efficiently repaired in cellular genomes.
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Affiliation(s)
- M C Kricker
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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16
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Bertolasi V, Ferretti V, Gilli G, Borea PA. Stereochemistry of benzodiazepine receptor ligands. Possible role of C–H ⋯ X interactions in drug–receptor binding and crystal structures of CL218–872, Zopiclone and DMCM. ACTA ACUST UNITED AC 1990. [DOI: 10.1039/p29900000283] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Novel base pairing in nucleic acids: CH donor group mediated base pairing involving 3-methyluracil. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0166-1280(88)80131-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Abraham RJ, Smith PE. Charge calculations in molecular mechanics 6: the calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing. Nucleic Acids Res 1988; 16:2639-57. [PMID: 3362677 PMCID: PMC336395 DOI: 10.1093/nar/16.6.2639] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A previously described scheme for the direct calculation of the partial atomic charges in molecules (CHARGE2) is applied to the nucleic acid bases. It is shown that inclusion of the omega-technique for the calculation of HMO derived pi charges is of particular importance for these highly polar systems. The molecular dipole moments obtained for the resulting charges are in very good agreement with the observed values for a variety of substituted purine and pyrimidine bases. The partial atomic charges for cytosine, thymine, guanine and adenine (as the 1-methyl and 9-methyl forms) are given and compared with values calculated by a variety of molecular orbital and empirical schemes. All the schemes reproduce the same general trends, with the possible exception of those calculated by the Del Re method, though the charges given by Kollman are in general somewhat larger than the others. The electrostatic contribution to the Watson-Crick base pair interaction energies are calculated using these partial atomic charges. The electrostatic contributions obtained from the M.O. derived atomic charges are less than half the observed values, as are those obtained by the Gasteiger method. The electrostatic contributions calculated from the CHARGE2 atomic charges and those of Kollman are in reasonable agreement with the observed values. The influence of a distant-dependent dielectric constant is examined, but no clear pattern emerges.
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Affiliation(s)
- R J Abraham
- Robert Robinson Laboratories, University of Liverpool, UK
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Williams LD, Chawla B, Shaw BR. The hydrogen bonding of cytosine with guanine: calorimetric and 1H-nmr analysis of the molecular interactions of nucleic acid bases. Biopolymers 1987; 26:591-603. [PMID: 3567328 DOI: 10.1002/bip.360260411] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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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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Rao SN, Kollman PA. Hydrogen-bonding preferences in 2,6-diaminopurine: uracil (thymine) and 8-methyl adenine:uracil (thymine) complexes. Biopolymers 1986; 25:267-80. [PMID: 3955191 DOI: 10.1002/bip.360250208] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Pearlman DA, Kim SH. Determinations of atomic partial charges for nucleic acid constituents from x-ray diffraction data. I. 2'-Deoxycytidine-5'-monophosphate. Biopolymers 1985; 24:327-57. [PMID: 3978222 DOI: 10.1002/bip.360240204] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ornstein RL, Fresco JR. Correlation of Tm, sequence, and delta H of complementary RNA helices and comparison with DNA helices. Biopolymers 1983; 22:2001-16. [PMID: 6193821 DOI: 10.1002/bip.360220812] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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