1
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Yudkina AV, Kim DV, Zharkov TD, Zharkov DO, Endutkin AV. Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides. Int J Mol Sci 2024; 25:6006. [PMID: 38892193 PMCID: PMC11172447 DOI: 10.3390/ijms25116006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA building blocks 2'-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.
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Affiliation(s)
- Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
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2
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Leonard P, Zhang A, Budow-Busse S, Daniliuc C, Seela F. α-D-2'-Deoxyadenosine, an irradiation product of canonical DNA and a component of anomeric nucleic acids: crystal structure, packing and Hirshfeld surface analysis. Acta Crystallogr C Struct Chem 2024; 80:21-29. [PMID: 38252461 PMCID: PMC10844955 DOI: 10.1107/s2053229624000457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.
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Affiliation(s)
- Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Simone Budow-Busse
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Constantin Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, Osnabrück 49069, Germany
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3
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Chandy SK, Raghavachari K. MIM-ML: A Novel Quantum Chemical Fragment-Based Random Forest Model for Accurate Prediction of NMR Chemical Shifts of Nucleic Acids. J Chem Theory Comput 2023; 19:6632-6642. [PMID: 37703522 DOI: 10.1021/acs.jctc.3c00563] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
We developed a random forest machine learning (ML) model for the prediction of 1H and 13C NMR chemical shifts of nucleic acids. Our ML model is trained entirely on reproducing computed chemical shifts obtained previously on 10 nucleic acids using a Molecules-in-Molecules (MIM) fragment-based density functional theory (DFT) protocol including microsolvation effects. Our ML model includes structural descriptors as well as electronic descriptors from an inexpensive low-level semiempirical calculation (GFN2-xTB) and trained on a relatively small number of DFT chemical shifts (2080 1H chemical shifts and 1780 13C chemical shifts on the 10 nucleic acids). The ML model is then used to make chemical shift predictions on 8 new nucleic acids ranging in size from 600 to 900 atoms and compared directly to experimental data. Though no experimental data was used in the training, the performance of our model is excellent (mean absolute deviation of 0.34 ppm for 1H chemical shifts and 2.52 ppm for 13C chemical shifts for the test set), despite having some nonstandard structures. A simple analysis suggests that both structural and electronic descriptors are critical for achieving reliable predictions. This is the first attempt to combine ML from fragment-based DFT calculations to predict experimental chemical shifts accurately, making the MIM-ML model a valuable tool for NMR predictions of nucleic acids.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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4
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Chandy SK, Raghavachari K. Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method. J Chem Theory Comput 2023; 19:544-561. [PMID: 36630261 DOI: 10.1021/acs.jctc.2c00967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have developed, implemented, and assessed an efficient protocol for the prediction of NMR chemical shifts of large nucleic acids using our molecules-in-molecules (MIM) fragment-based quantum chemical approach. To assess the performance of our approach, MIM-NMR calculations are calibrated on a test set of three nucleic acids, where the structure is derived from solution-phase NMR studies. For DNA systems with multiple conformers, the one-layer MIM method with trimer fragments (MIM1trimer) is benchmarked to get the lowest energy structure, with an average error of only 0.80 kcal/mol with respect to unfragmented full molecule calculations. The MIMI-NMRdimer calibration with respect to unfragmented full molecule calculations shows a mean absolute deviation (MAD) of 0.06 and 0.11 ppm, respectively, for 1H and 13C nuclei, but the performance with respect to experimental NMR chemical shifts is comparable to the more expensive MIM1-NMR and MIM2-NMR methods with trimer subsystems. To compare with the experimental chemical shifts, a standard protocol is derived using DNA systems with Protein Data Bank (PDB) IDs 1SY8, 1K2K, and 1KR8. The effect of structural minimizations is employed using a hybrid mechanics/semiempirical approach and used for computations in solution with implicit and explicit-implicit solvation models in our MIM1-NMRdimer methodology. To demonstrate the applicability of our protocol, we tested it on seven nucleic acids, including structures with nonstandard residues, heteroatom substitutions (F and B atoms), and side chain mutations with a size ranging from ∼300 to 1100 atoms. The major improvement for predicted MIM1-NMRdimer calculations is obtained from structural minimizations and implicit solvation effects. A significant improvement with the explicit-implicit solvation model is observed only for two smaller nucleic acid systems (1KR8 and 7NBK), where the expensive first solvation shell is replaced by the microsolvation model, in which a single water molecule is added for each solvent-exposed amino and imino protons, along with the implicit solvation. Overall, our target accuracy of ∼0.2-0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for large nucleic acids. The proposed MIM-NMR approach is accurate and cost-effective (linear scaling with system size), and it can aid in the structural assignments of a wide range of complex biomolecules.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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5
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Senchurova SI, Syryamina VN, Kuznetsova AA, Novopashina DS, Ishchenko AA, Saparbaev M, Dzuba SA, Fedorova OS, Kuznetsov NA. The mechanism of damage recognition by apurinic/apyrimidinic endonuclease Nfo from Escherichia coli. Biochim Biophys Acta Gen Subj 2022; 1866:130216. [PMID: 35905924 DOI: 10.1016/j.bbagen.2022.130216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 07/18/2022] [Indexed: 12/12/2022]
Abstract
Apurinic/apyrimidinic (AP) endonuclease Nfo from Escherichia coli recognises AP sites in DNA and catalyses phosphodiester bond cleavage on the 5' side of AP sites and some damaged or undamaged nucleotides. Here, the mechanism of target nucleotide recognition by Nfo was analysed by pulsed electron-electron double resonance (PELDOR, also known as DEER) spectroscopy and pre-steady-state kinetic analysis with Förster resonance energy transfer detection of DNA conformational changes during DNA binding. The efficiency of endonucleolytic cleavage of a target nucleotide in model DNA substrates was ranked as (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran [F-site] > 5,6-dihydro-2'-deoxyuridine > α-anomer of 2'-deoxyadenosine >2'-deoxyuridine > undamaged DNA. Real-time conformational changes of DNA during interaction with Nfo revealed an increase of distances between duplex ends during the formation of the initial enzyme-substrate complex. The use of rigid-linker spin-labelled DNA duplexes in DEER measurements indicated that double-helix bending and unwinding by the target nucleotide itself is one of the key factors responsible for indiscriminate recognition of a target nucleotide by Nfo. The results for the first time show that AP endonucleases from different structural families utilise a common strategy of damage recognition, which globally may be integrated with the mechanism of searching for specific sites in DNA by other enzymes.
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Affiliation(s)
- Svetlana I Senchurova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentieva, Novosibirsk 630090, Russia
| | - Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, SB RAS, 3 Institutskaya Str., Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentieva, Novosibirsk 630090, Russia
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentieva, Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Murat Saparbaev
- Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, SB RAS, 3 Institutskaya Str., Novosibirsk 630090, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentieva, Novosibirsk 630090, Russia.
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentieva, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia.
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6
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Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022; 126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Although molecular
dynamics (MD) simulations have been used extensively
to study the structural dynamics of proteins, the role of MD simulation
in studies of nucleic acid based systems has been more limited. One
contributing factor to this disparity is the historically lower level
of accuracy of the physical models used in such simulations to describe
interactions involving nucleic acids. By modifying nonbonded and torsion
parameters of a force field from the Amber family of models, we recently
developed force field parameters for RNA that achieve a level of accuracy
comparable to that of state-of-the-art protein force fields. Here
we report force field parameters for DNA, which we developed by transferring
nonbonded parameters from our recently reported RNA force field and
making subsequent adjustments to torsion parameters. We have also
modified the backbone charges in both the RNA and DNA parameter sets
to make the treatment of electrostatics compatible with our recently
developed variant of the Amber protein and ion force field. We name
the force field resulting from the union of these three parameter
sets (the new DNA parameters, the revised RNA parameters, and the
existing protein and ion parameters) DES-Amber. Extensive
testing of DES-Amber indicates that it can describe the thermal stability
and conformational flexibility of single- and double-stranded DNA
systems with a level of accuracy comparable to or, especially for
disordered systems, exceeding that of state-of-the-art nucleic acid
force fields. Finally, we show that, in certain favorable cases, DES-Amber
can be used for long-timescale simulations of protein–nucleic
acid complexes.
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Affiliation(s)
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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7
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Lameiras P, Nuzillard JM. Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:1-50. [PMID: 34078536 DOI: 10.1016/j.pnmrs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between 1H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).
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Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
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8
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Kuznetsova AA, Matveeva AG, Milov AD, Vorobjev YN, Dzuba SA, Fedorova OS, Kuznetsov NA. Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway. Nucleic Acids Res 2019; 46:11454-11465. [PMID: 30329131 PMCID: PMC6265485 DOI: 10.1093/nar/gky912] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5′ side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Here, to examine the mechanism of broad substrate specificity of APE1, we performed pulsed electron–electron double resonance (PELDOR) spectroscopy and pre-steady-state kinetic analysis with Förster resonance energy transfer (FRET) detection of DNA conformational changes during DNA binding and lesion recognition. Equilibrium PELDOR and kinetic FRET data revealed that DNA binding by APE1 leads to noticeable damage-dependent bending of a DNA duplex. Molecular dynamics simulations showed that the damaged nucleotide is everted from the DNA helix and placed into the enzyme’s binding pocket, which is formed by Asn-174, Asn-212, Asn-229, Ala-230, Phe-266 and Trp-280. Nevertheless, no damage-specific contacts were detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, α-adenosine, 5,6-dihydrouridine or F-site. These data suggest that the substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion.
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Affiliation(s)
- Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna G Matveeva
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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9
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Ferris ZE, Li Q, Germann MW. Substituting Inosine for Guanosine in DNA: Structural and Dynamic Consequences. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19850032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Inosine differs from the guanosine nucleoside only by the absence of the N2 amino group. Both nucleosides also have similar electrostatic potentials. Therefore, substituting I for G has been used to probe various properties of nucleic acids and to facilitate the interpretation of binding studies. In particular, the absence of the amino group permits the assessment of its importance in the binding of ligands to the minor groove of duplex DNA. It has been known for some time that an I-C base pair is of lower stability than a regular G-C base pair, which needs to be considered when making DNA constructs containing inosine. However, it is generally assumed that both base pairs are structurally highly similar. To test this assumption in an identical sequence environment, we have determined the fine structure of two hairpin DNA substrates that differ only in the substitution of an I-C base pair for a G-C base pair. The structures have been solved using nuclear magnetic resonance (NMR) restraints in conjunction with Mardigras and molecular dynamics. The structural data are complemented with thermodynamic and dynamic data to get a comprehensive evaluation of the consequences of G-C vs I-C base pair substitutions. Our data show a strong similarity in the structures of the hairpins, but a significant difference in the melting temperatures, T m. This difference is also reflected in the drastically decreased base pair lifetime of 7.4 milliseconds compared to the G-C base pair lifetime of 155 milliseconds. The substitution of I-C for G-C is to probe for specific effect due to the amino group is satisfactory, as long as the lowered thermal stability and the drastically increased local dynamics are considered.
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Affiliation(s)
| | - Qiushi Li
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Department of Biology, Georgia State University, Atlanta, GA, USA
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10
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Ni G, Du Y, Tang F, Liu J, Zhao H, Chen Q. Review of α-nucleosides: from discovery, synthesis to properties and potential applications. RSC Adv 2019; 9:14302-14320. [PMID: 35519323 PMCID: PMC9064229 DOI: 10.1039/c9ra01399g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023] Open
Abstract
Nucleic acids play an important role in the genetic process of organisms; nucleosides, the building block of nucleic acids, typically exist in nature in a β configuration. As an anomer of β-nucleoside, α-nucleoside is extremely rare in nature. Because of their unique and interesting properties such as high stability, specific parallel double-stranded structure and some other biochemical properties, α-nucleosides have attracted wide attention. Various methods including but not limited to the mercuri procedure, fusion reaction and Vorbrüggen glycosylation have been used to synthesize α-nucleosides and their derivatives. However, to the best of our knowledge, there is no review that has summarized these works. Therefore, we systematically review the discovery, synthesis, properties, and potential applications of α-nucleosides in this article and look to provide a reference for subsequent studies in the coming years.
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Affiliation(s)
- Guangcheng Ni
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Yuqi Du
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Fan Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Jiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
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11
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Du H, Wang P, Li L, Amato NJ, Wang Y. Cytotoxic and Mutagenic Properties of C1' and C3'-Epimeric Lesions of 2'-Deoxyribonucleosides in Human Cells. ACS Chem Biol 2019; 14:478-485. [PMID: 30768892 DOI: 10.1021/acschembio.8b01126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genomic integrity is constantly challenged by exposure to environmental and endogenous genotoxic agents. Reactive oxygen species (ROS) represent one of the most common types of DNA damaging agents. While ROS mainly induce single-nucleobase lesions, epimeric 2-deoxyribose lesions can also be induced upon hydrogen atom abstraction from the C1', C3', or C4' carbon and the subsequent incorrect chemical repair of the resulting carbon-centered radicals. Herein, we investigated the replicative bypass of the C1'- and C3'-epimeric lesions of the four 2'-deoxynucleosides in HEK293T human embryonic kidney epithelial cells. Our results revealed distinct bypass efficiencies and mutagenic properties of these two types of epimeric lesions. Replicative bypasses of all C1'-epimeric lesions except α-dA are mutagenic in HEK293T cells, and their mutagenic properties are further modulated by translesion synthesis (TLS) DNA polymerases. By contrast, none of the four C3'-epimeric lesions are mutagenic, and the replicative bypass of these lesions is not compromised upon depletion of polymerase η, ι, κ, or ζ. Together, our results provide important new knowledge about the cytotoxic and mutagenic properties of C1' and C3' epimeric lesions, and reveal the roles of TLS DNA polymerases in bypassing these lesions in human cells.
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Affiliation(s)
- Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Nicholas J. Amato
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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12
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Spring-Connell AM, Evich M, Germann MW. NMR Structure Determination for Oligonucleotides. ACTA ACUST UNITED AC 2019; 72:7.28.1-7.28.39. [PMID: 29927124 DOI: 10.1002/cpnc.48] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
NMR spectroscopy is a versatile tool for determining the structure and dynamics of nucleic acids under solution conditions. In this unit, we provide an overview and detail of the experiments and methods used in our laboratory to determine the structure of oligonucleotides at natural abundance, thus limiting our approach to 1 H, 13 C, and 31 P NMR techniques. Isotopic labeling is heavily used in RNA NMR studies, however, labeling of DNA is still less common and, if modified nucleotides are investigated, is exceptionally expensive or not feasible. Each method described here is extensively documented and annotated with tips and observations to facilitate their application. Sections are devoted to sample preparation, NMR experiments and setup, resonance assignment, structure generation protocols, evaluation, tips that may be useful, and software sources. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Marina Evich
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, Georgia.,Neuroscience Institute, Georgia State University, Atlanta, Georgia
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13
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Bamberger SN, Malik CK, Voehler MW, Brown SK, Pan H, Johnson-Salyard TL, Rizzo CJ, Stone MP. Configurational and Conformational Equilibria of N 6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA. Chem Res Toxicol 2018; 31:924-935. [PMID: 30169026 DOI: 10.1021/acs.chemrestox.8b00135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The most common lesion in DNA occurring due to clinical treatment with Temozolomide or cellular exposures to other methylating agents is 7-methylguanine (N7-Me-dG). It can undergo a secondary reaction to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG). MeFapy-dG undergoes epimerization in DNA to produce either α or β deoxyribose anomers. Additionally, conformational rotation around the formyl bond, C5- N5 bond, and glycosidic bond may occur. To characterize and quantitate the mixture of these isomers in DNA, a 13C-MeFapy-dG lesion, in which the CH3 group of the MeFapy-dG was isotopically labeled, was incorporated into the trimer 5'-TXT-3' and the dodecamer 5'-CATXATGACGCT-3' (X = 13C-MeFapy-dG). NMR spectroscopy of both the trimer and dodecamer revealed that the MeFapy-dG lesion exists in single strand DNA as ten configurationally and conformationally discrete species, eight of which may be unequivocally assigned. In the duplex dodecamer, the MeFapy-dG lesion exists as six configurationally and conformationally discrete species. Analyses of NMR data in the single strand trimer confirm that for each deoxyribose anomer, atropisomerism occurs around the C5- N5 bond to produce R a and S a atropisomers. Each atropisomer exhibits geometrical isomerism about the formyl bond yielding E and Z conformations. 1H NMR experiments allow the relative abundances of the species to be determined. For the single strand trimer, the α and β anomers exist in a 3:7 ratio, favoring the β anomer. For the β anomer, with respect to the C5- N5 bond, the R a and S a atropisomers are equally populated. However, the Z geometrical isomer of the formyl moiety is preferred. For the α anomer, the E- S a isomer is present at 12%, whereas all other isomers are present at 5-7%. DNA processing enzymes may differentially recognize different isomers of the MeFapy-dG lesion. Moreover, DNA sequence-specific differences in the populations of configurational and conformational species may modulate biological responses to the MeFapy-dG lesion.
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Affiliation(s)
- Stephanie N Bamberger
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Chanchal K Malik
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Markus W Voehler
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Summer K Brown
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Hope Pan
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Tracy L Johnson-Salyard
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Carmelo J Rizzo
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Michael P Stone
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
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14
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Timofeyeva NA, Fedorova OS. A kinetic mechanism of repair of DNA containing α-anomeric deoxyadenosine by human apurinic/apyrimidinic endonuclease 1. MOLECULAR BIOSYSTEMS 2017; 12:3435-3446. [PMID: 27722620 DOI: 10.1039/c6mb00511j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Anomers of 2'-deoxyadenosine (αdA) are major products of deoxyadenosine damage when DNA is γ-irradiated under anoxic conditions. Such lesions are a threat to genomic stability and are known to be processed by human apurinic/apyrimidinic endonuclease 1 (APE1). The aim of this study was to determine whether the α-anomeric structure enhances enzyme recognition. For this purpose, we analyzed the kinetic mechanism of αdA conversion by APE1 using a stopped-flow fluorescence technique. Our data reveals that the initial formation of the complex of APE1 with an αdA-containing substrate is followed by at least three conformational transitions in this complex that correspond to the induced fit leading to the formation of a catalytically competent complex. A local perturbation around the αdA lesion in the DNA duplex allows APE1 to avoid the initial conformational changes observed earlier in the case of the enzyme binding to an undamaged ligand, abasic-site-, tetrahydrofuran-, or 5,6-dihydrouridine-containing substrates. The αdA structure promotes recognition by the enzyme but dramatically impedes formation of the catalytically competent complex and hydrolysis of the 5'-phosphodiester bond. A step following the chemical reaction, possibly a release of the αdA-containing product, is rate-limiting for the overall enzymatic process, though an α-anomeric nucleotide at the 5' terminus of the DNA nick accelerates dissociation of the enzyme-product complex. Our results show that the efficiency of αdA lesion conversion by APE1 is very low. Nonetheless, αdA repair by APE1 is probably a biologically relevant process.
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Affiliation(s)
- N A Timofeyeva
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
| | - O S Fedorova
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
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15
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Wang P, Amato NJ, Wang Y. Cytotoxic and Mutagenic Properties of C3'-Epimeric Lesions of 2'-Deoxyribonucleosides in Escherichia coli Cells. Biochemistry 2017. [PMID: 28650656 DOI: 10.1021/acs.biochem.7b00146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactive oxygen species (ROS), resulting from endogenous metabolism and/or environmental exposure, can induce damage to the 2-deoxyribose moiety in DNA. Specifically, a hydrogen atom from each of the five carbon atoms in 2-deoxyribose can be abstracted by hydroxyl radical, and improper chemical repair of the ensuing radicals formed at the C1', C3', and C4' positions can lead to the stereochemical inversion at these sites to yield epimeric 2-deoxyribose lesions. Although ROS-induced single-nucleobase lesions have been well studied, the biological consequences of the C3'-epimeric lesions of 2'-deoxynucleosides, i.e., 2'-deoxyxylonucleosides (dxN), have not been comprehensively investigated. Herein, we assessed the impact of dxN lesions on the efficiency and fidelity of DNA replication in Escherichia coli cells by conducting a competitive replication and adduct bypass assay with single-stranded M13 phage containing a site-specifically incorporated dxN. Our results revealed that, of the four dxN lesions, only dxG constituted a strong impediment to DNA replication, and intriguingly, dxT and dxC conferred replication bypass efficiencies higher than those of the unmodified counterparts. In addition, the three SOS-induced DNA polymerases (Pol II, Pol IV, and Pol V) did not play any appreciable role in bypassing these lesions. Among the four dxNs, only dxA directed a moderate frequency of dCMP misincorporation. These results provided important insights into the impact of the C3'-epimeric lesions on DNA replication in E. coli cells.
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Affiliation(s)
- Pengcheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Nicholas J Amato
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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16
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Evich M, Spring-Connell AM, Germann MW. Impact of modified ribose sugars on nucleic acid conformation and function. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2017-0056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AbstractThe modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.
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Affiliation(s)
- Marina Evich
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
| | | | - Markus W. Germann
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, GA 30303, USA
- Georgia State University, Neuroscience Institute, P.O. 5030, Atlanta, GA 30303, USA
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17
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Evich M, Spring-Connell AM, Storici F, Germann MW. Structural Impact of Single Ribonucleotide Residues in DNA. Chembiochem 2016; 17:1968-1977. [PMID: 27504600 DOI: 10.1002/cbic.201600385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/09/2022]
Abstract
Single ribonucleotide intrusions represent the most common nonstandard nucleotide type found incorporated in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA. To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts-AxC, CxG, and GxC, where x=rG or dG-we report the structures of three single-ribonucleotide-containing DNA duplexes and the corresponding DNA controls. The lesion subtly and locally perturbs the structure asymmetrically on the 3' side of the lesion in both the riboguanosine-containing and the complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3'-downstream deoxyribose units are predominately in N-type conformation; backbone torsion angles ϵ and/or ζ of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'-neighboring base, and/or sugar. Interestingly, even in similar purine-rG-pyrimidine environments (A-rG-C and G-rG-C), a riboguanosine unit affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.
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Affiliation(s)
- Marina Evich
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | | | - Francesca Storici
- Department of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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18
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Spring-Connell AM, Evich MG, Debelak H, Seela F, Germann MW. Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog. Nucleic Acids Res 2016; 44:8576-8587. [PMID: 27566150 PMCID: PMC5062995 DOI: 10.1093/nar/gkw736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/10/2016] [Indexed: 12/30/2022] Open
Abstract
A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2'deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications.
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Affiliation(s)
| | - Marina G Evich
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Harald Debelak
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany
| | - Frank Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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19
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Amato NJ, Zhai Q, Navarro DC, Niedernhofer LJ, Wang Y. In vivo detection and replication studies of α-anomeric lesions of 2'-deoxyribonucleosides. Nucleic Acids Res 2015. [PMID: 26202973 PMCID: PMC4787794 DOI: 10.1093/nar/gkv725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA damage, arising from endogenous metabolism or exposure to environmental agents, may perturb the transmission of genetic information by blocking DNA replication and/or inducing mutations, which contribute to the development of cancer and likely other human diseases. Hydroxyl radical attack on the C1′, C3′ and C4′ of 2-deoxyribose can give rise to epimeric 2-deoxyribose lesions, for which the in vivo occurrence and biological consequences remain largely unexplored. Through independent chemical syntheses of all three epimeric lesions of 2′-deoxyguanosine (dG) and liquid chromatography-tandem mass spectrometry analysis, we demonstrated unambiguously the presence of substantial levels of the α-anomer of dG (α-dG) in calf thymus DNA and in DNA isolated from mouse pancreatic tissues. We further assessed quantitatively the impact of all four α-dN lesions on DNA replication in Escherichia coli by employing a shuttle-vector method. We found that, without SOS induction, all α-dN lesions except α-dA strongly blocked DNA replication and, while replication across α-dA was error-free, replicative bypass of α-dC and α-dG yielded mainly C→A and G→A mutations. In addition, SOS induction could lead to markedly elevated bypass efficiencies for the four α-dN lesions, abolished the G→A mutation for α-dG, pronouncedly reduced the C→A mutation for α-dC and triggered T→A mutation for α-dT. The preferential misincorporation of dTMP opposite the α-dNs could be attributed to the unique base-pairing properties of the nucleobases elicited by the inversion of the configuration of the N-glycosidic linkage. Our results also revealed that Pol V played a major role in bypassing α-dC, α-dG and α-dT in vivo. The abundance of α-dG in mammalian tissue and the impact of the α-dNs on DNA replication demonstrate for the first time the biological significance of this family of DNA lesions.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Qianqian Zhai
- Department of Chemistry, University of California, Riverside, CA 92521, USA Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Diana C Navarro
- Department of Metabolism and Aging, The Scripps Research Institute Florida, FL 33458, USA
| | - Laura J Niedernhofer
- Department of Metabolism and Aging, The Scripps Research Institute Florida, FL 33458, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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20
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Singh V, Kumari B, Maity B, Seth D, Das P. Direct observation of preferential processing of clustered abasic DNA damages with APE1 in TATA box and CpG island by reaction kinetics and fluorescence dynamics. Mutat Res 2014; 766-767:56-65. [PMID: 25847273 DOI: 10.1016/j.mrfmmm.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 06/04/2023]
Abstract
Sequences like the core element of TATA box and CpG island are frequently encountered in the genome and related to transcription. The fate of repair of clustered abasic sites in such sequences of genomic importance is largely unknown. This prompted us to investigate the sequence dependence of cleavage efficiency of APE1 enzyme at abasic sites within the core sequences of TATA box and CpG island using fluorescence dynamics and reaction kinetics. Simultaneous molecular dynamics study through steady state and time resolved fluorescence spectroscopy using unique ethidium bromide dye release assay confirmed an elevated amount of abasic site cleavage of the TATA box sequence as compared to the core CpG island. Reaction kinetics showed that catalytic efficiency of APE1 for abasic site cleavage of core CpG island sequence was ∼4 times lower as compared to that of the TATA box. Higher value of Km was obtained from the core CpG island sequence than the TATA box sequence. This suggests a greater binding effect of APE1 enzyme on TATA sequence that signifies a prominent role of the sequence context of the DNA substrate. Evidently, a faster response from APE1 was obtained for clustered abasic damage repair of TATA box core sequences than CpG island consensus sequences. The neighboring bases of the abasic sites in the complementary DNA strand were found to have significant contribution in addition to the flanking bases in modulating APE1 activity. The repair refractivity of the bistranded clustered abasic sites arise from the slow processing of the second abasic site, consequently resulting in decreased overall production of potentially lethal double strand breaks.
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Affiliation(s)
- Vandana Singh
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Bhavini Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Banibrata Maity
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Debabrata Seth
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India.
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21
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The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once. DNA Repair (Amst) 2014; 19:95-107. [PMID: 24754999 DOI: 10.1016/j.dnarep.2014.03.022] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To avoid genome instability, DNA repair nucleases must precisely target the correct damaged substrate before they are licensed to incise. Damage identification is a challenge for all DNA damage response proteins, but especially for nucleases that cut the DNA and necessarily create a cleaved DNA repair intermediate, likely more toxic than the initial damage. How do these enzymes achieve exquisite specificity without specific sequence recognition or, in some cases, without a non-canonical DNA nucleotide? Combined structural, biochemical, and biological analyses of repair nucleases are revealing their molecular tools for damage verification and safeguarding against inadvertent incision. Surprisingly, these enzymes also often act on RNA, which deserves more attention. Here, we review protein-DNA structures for nucleases involved in replication, base excision repair, mismatch repair, double strand break repair (DSBR), and telomere maintenance: apurinic/apyrimidinic endonuclease 1 (APE1), Endonuclease IV (Nfo), tyrosyl DNA phosphodiesterase (TDP2), UV Damage endonuclease (UVDE), very short patch repair endonuclease (Vsr), Endonuclease V (Nfi), Flap endonuclease 1 (FEN1), exonuclease 1 (Exo1), RNase T and Meiotic recombination 11 (Mre11). DNA and RNA structure-sensing nucleases are essential to life with roles in DNA replication, repair, and transcription. Increasingly these enzymes are employed as advanced tools for synthetic biology and as targets for cancer prognosis and interventions. Currently their structural biology is most fully illuminated for DNA repair, which is also essential to life. How DNA repair enzymes maintain genome fidelity is one of the DNA double helix secrets missed by James Watson and Francis Crick, that is only now being illuminated though structural biology and mutational analyses. Structures reveal motifs for repair nucleases and mechanisms whereby these enzymes follow the old carpenter adage: measure twice, cut once. Furthermore, to measure twice these nucleases act as molecular level transformers that typically reshape the DNA and sometimes themselves to achieve extraordinary specificity and efficiency.
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22
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Amato NJ, Wang Y. Epimeric 2-deoxyribose lesions: Products from the improper chemical repair of 2-deoxyribose radicals. Chem Res Toxicol 2014; 27:470-9. [PMID: 24517165 PMCID: PMC4002128 DOI: 10.1021/tx400430g] [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: 01/18/2023]
Abstract
![]()
Genomic
integrity is constantly challenged by DNA damaging agents
such as reactive oxygen species (ROS). Consequently, DNA damage can
compromise the fidelity and efficiency of essential DNA metabolic
processes, including replication and transcription, which may contribute
significantly to the etiology of many human diseases. Here, we review
one family of DNA lesions, the epimeric 2-deoxyribose lesions, which
arise from the improper chemical repair of the 2-deoxyribose radicals.
Unlike most other DNA lesions, the epimeric 2-deoxyribose lesions
are indistinguishable from their corresponding unmodified nucleosides
in both molecular mass and chemical reactivity. We placed our emphasis
of discussion on the formation of these lesions, their impact on the
structure and stability of duplex DNA, their biological consequences,
their potential therapeutic relevance, and future research directions
about these modified nucleosides.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, University of California , 900 University Avenue, Riverside, California 92521, United States
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23
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Spring AM, Germann MW. Supercooled aqueous nuclear magnetic resonance using agarose gels. Anal Biochem 2012; 427:79-81. [PMID: 22609075 DOI: 10.1016/j.ab.2012.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 11/27/2022]
Abstract
Low-temperature nuclear magnetic resonance (NMR), especially under supercooled conditions, can give critical insight into biomolecular systems via slowed dynamics and exchange rates. These conditions can also increase correlation times of small molecules, potentially allowing for NMR structural study of small molecules at moderate field strengths. Agarose gels allow for supercooled conditions and are simple to prepare, invisible to NMR, and noninteractive with most biomolecules and organics. Here we demonstrate their use with nucleic acids, small organic molecules, and peptides.
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Affiliation(s)
- Alexander M Spring
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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