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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs. Biophys J 2023; 122:3323-3339. [PMID: 37469144 PMCID: PMC10465710 DOI: 10.1016/j.bpj.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023] Open
Abstract
Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 μs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536266. [PMID: 37090657 PMCID: PMC10120721 DOI: 10.1101/2023.04.10.536266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Hybridization of short nucleic acid segments (<4 nucleotides) to single-strand templates occurs as a critical intermediate in processes such as non-enzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood due to experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential non-canonical base pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2 to 40 µs depending on the template and temperature. Dinucleotide hybridization and dehybridization involves a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
- The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, United States
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
- The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
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Ovcherenko SS, Shernyukov AV, Nasonov DM, Endutkin AV, Zharkov DO, Bagryanskaya EG. Dynamics of 8-Oxoguanine in DNA: Decisive Effects of Base Pairing and Nucleotide Context. J Am Chem Soc 2023; 145:5613-5617. [PMID: 36867834 DOI: 10.1021/jacs.2c11230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
8-Oxo-7,8-dihydroguanine (oxoG), an abundant DNA lesion, can mispair with adenine and induce mutations. To prevent this, cells possess DNA repair glycosylases that excise either oxoG from oxoG:C pairs (bacterial Fpg, human OGG1) or A from oxoG:A mispairs (bacterial MutY, human MUTYH). Early lesion recognition steps remain murky and may include enforced base pair opening or capture of a spontaneously opened pair. We adapted the CLEANEX-PM NMR protocol to detect DNA imino proton exchange and analyzed the dynamics of oxoG:C, oxoG:A, and their undamaged counterparts in nucleotide contexts with different stacking energy. Even in a poorly stacking context, the oxoG:C pair did not open easier than G:C, arguing against extrahelical base capture by Fpg/OGG1. On the contrary, oxoG opposite A significantly populated the extrahelical state, which may assist recognition by MutY/MUTYH.
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Affiliation(s)
- Sergey S Ovcherenko
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Andrey V Shernyukov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Dmitry M Nasonov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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Golyshev VM, Abramova TV, Pyshnyi DV, Lomzov AA. A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines. Biophys Chem 2018; 234:24-33. [PMID: 29407768 DOI: 10.1016/j.bpc.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/28/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia.
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
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Abstract
Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276–1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5′-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA
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Short Oligonucleotide Tandem Ligation Assay for Genotyping of Single-Nucleotide Polymorphisms in Y Chromosome. Mol Biotechnol 2009; 45:1-8. [DOI: 10.1007/s12033-009-9208-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Lomzov AA, Pyshnaya IA, Ivanova EM, Pyshnyi DV. Thermodynamic parameters for calculating the stability of complexes of bridged oligonucleotides. DOKL BIOCHEM BIOPHYS 2006; 409:211-5. [PMID: 16986433 DOI: 10.1134/s1607672906040053] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, pr. Akademika Lavrent'eva 8, Novosibirsk 630090, Russia
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Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 2006; 34:564-74. [PMID: 16449200 PMCID: PMC1360284 DOI: 10.1093/nar/gkj454] [Citation(s) in RCA: 624] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na+. From stacking parameters of individual contacts, we calculate base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA stability parameters. For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence.
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Protozanova E, Yakovchuk P, Frank-Kamenetskii MD. Stacked-unstacked equilibrium at the nick site of DNA. J Mol Biol 2004; 342:775-85. [PMID: 15342236 DOI: 10.1016/j.jmb.2004.07.075] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Revised: 06/24/2004] [Accepted: 07/18/2004] [Indexed: 11/23/2022]
Abstract
Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairing between complementary bases. However, their contribution into the duplex stability is yet to be determined. Now we fill this fundamental gap in our knowledge of the DNA double helix. We have prepared a series of 32, 300 bp-long DNA fragments with solitary nicks in the same position differing only in base-pairs flanking the nick. Electrophoretic mobility of these fragments in the gel has been studied. Assuming the equilibrium between stacked and unstacked conformations at the nick site, all 32 stacking free energy parameters have been obtained. Only ten of them are essential and they govern the stacking interactions between adjacent base-pairs in intact DNA double helix. A full set of DNA stacking parameters has been determined for the first time. From these data and from a well-known dependence of DNA melting temperature on G.C content, the contribution of base-pairing into duplex stability has been estimated. The obtained energy parameters of the DNA double helix are of paramount importance for understanding sequence-dependent DNA flexibility and for numerous biotechnology applications.
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Affiliation(s)
- Ekaterina Protozanova
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
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