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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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2
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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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3
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Grytsyk N, Cianfarani D, Crégut O, Richert L, Boudier C, Humbert N, Didier P, Mély Y, Léonard J. Kinetics of protein-assisted nucleic acid interconversion monitored by transient time resolved fluorescence in microfluidic droplets. Nucleic Acids Res 2021; 49:e111. [PMID: 34450653 PMCID: PMC8565319 DOI: 10.1093/nar/gkab687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/29/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022] Open
Abstract
Interconversions between nucleic acid structures play an important role in transcriptional and translational regulation and also in repair and recombination. These interconversions are frequently promoted by nucleic acid chaperone proteins. To monitor their kinetics, Förster resonance energy transfer (FRET) is widely exploited using ensemble fluorescence intensity measurements in pre-steady-state stopped-flow experiments. Such experiments only provide a weighted average of the emission of all species in solution and consume large quantities of materials. Herein, we lift these limitations by combining time-resolved fluorescence (TRF) with droplet microfluidics (DmF). We validate the innovative TRF-DmF approach by investigating the well characterized annealing of the HIV-1 (+)/(–) Primer Binding Sequences (PBS) promoted by a HIV-1 nucleocapsid peptide. Upon rapid mixing of the FRET-labelled (–)PBS with its complementary (+)PBS sequence inside microdroplets, the TRF-DmF set-up enables resolving the time evolution of sub-populations of reacting species and reveals an early intermediate with a ∼50 ps donor fluorescence lifetime never identified so far. TRF-DmF also favorably compares with single molecule experiments, as it offers an accurate control of concentrations with no upper limit, no need to graft one partner on a surface and no photobleaching issues.
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Affiliation(s)
- Natalia Grytsyk
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France.,Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Damien Cianfarani
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France
| | - Olivier Crégut
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France
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Harris PD, Hamdan SM, Habuchi S. Relative Contributions of Base Stacking and Electrostatic Repulsion on DNA Nicks and Gaps. J Phys Chem B 2020; 124:10663-10672. [PMID: 33179916 DOI: 10.1021/acs.jpcb.0c06941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In duplex DNA, the continuous sugar phosphate backbones prevent the double helix from significant bending, but breaks in the duplex such as nicks, gaps, and flaps present points at which significant bending is possible. The conformational dynamics of these aberrant structures remains poorly understood. Two factors can maintain the duplexlike conformation of these aberrant structures, these being the hydrophobic and aromatic stacking interactions of the nucleobases, and the electrostatic repulsion of the negatively charged backbones. Using confocal single-molecule Förster resonance energy transfer on nicked and gapped DNA structures, we compare the relative contributions of these two factors by modulating the electrostatic repulsion through mono- and divalent cation concentrations. Base stacking interactions dominate the dynamics of nicked DNA, making it behave essentially like duplex DNA. Gapped structures have weaker base stacking and thus backbone electrostatic repulsion becomes important, and shielding from cations results in an average increase in bending around the gap. This bending of gapped structures could be interpreted by increased flexibility of unstacked structures, transient unstacking events, or a combination of the two. Burst variance analysis (BVA) and analysis by photon-by-photon hidden Markov modeling (H2MM), methods capable of detecting submillisecond dynamics of single molecules in solution, only revealed a single state, indicating that dynamics are occurring at time scales shorter than microseconds.
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Affiliation(s)
- Paul D Harris
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia
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Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK, Kapanidis AN. Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic Acids Res 2020; 47:10788-10800. [PMID: 31544938 PMCID: PMC6846080 DOI: 10.1093/nar/gkz797] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/02/2019] [Accepted: 09/18/2019] [Indexed: 01/23/2023] Open
Abstract
DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA–Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA–Pol binary complex. The structure resembled existing crystal structures with regards to the downstream primer-template DNA substrate, and revealed a previously unobserved sharp bend (∼120°) in the DNA substrate; this pronounced bend was present in living cells. MD simulations and single-molecule assays also revealed that 4–5 nt of downstream gap-proximal DNA are unwound in the binary complex. Further, experiments and coarse-grained modelling showed the substrate alone frequently adopts bent conformations with 1–2 nt fraying around the gap, suggesting a mechanism wherein Pol recognises a pre-bent, partially-melted conformation of gapped DNA. We propose a general mechanism for substrate recognition by structure-specific enzymes driven by protein sensing of the conformational dynamics of their DNA substrates.
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Affiliation(s)
- Timothy D Craggs
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Marko Sustarsic
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.,School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
| | - Hendrik Kaju
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Cuthbert
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen 6708 WE, The Netherlands.,Microspectroscopy Research Facility Wageningen, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Laura Domicevica
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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6
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Chakraborty S, Steinbach PJ, Paul D, Mu H, Broyde S, Min JH, Ansari A. Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex. Nucleic Acids Res 2019; 46:1240-1255. [PMID: 29267981 PMCID: PMC5815138 DOI: 10.1093/nar/gkx1216] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 12/12/2017] [Indexed: 12/15/2022] Open
Abstract
Rad4/XPC recognizes diverse DNA lesions including ultraviolet-photolesions and carcinogen-DNA adducts, initiating nucleotide excision repair. Studies have suggested that Rad4/XPC senses lesion-induced helix-destabilization to flip out nucleotides from damaged DNA sites. However, characterizing how DNA deformability and/or distortions impact recognition has been challenging. Here, using fluorescence lifetime measurements empowered by a maximum entropy algorithm, we mapped the conformational heterogeneities of artificially destabilized mismatched DNA substrates of varying Rad4-binding specificities. The conformational distributions, as probed by FRET between a cytosine-analog pair exquisitely sensitive to DNA twisting/bending, reveal a direct connection between intrinsic DNA deformability and Rad4 recognition. High-specificity CCC/CCC mismatch, free in solution, sampled a strikingly broad range of conformations from B-DNA-like to highly distorted conformations that resembled those observed with Rad4 bound; the extent of these distortions increased with bound Rad4 and with temperature. Conversely, the non-specific TAT/TAT mismatch had a homogeneous, B-DNA-like conformation. Molecular dynamics simulations also revealed a wide distribution of conformations for CCC/CCC, complementing experimental findings. We propose that intrinsic deformability promotes Rad4 damage recognition, perhaps by stalling a diffusing protein and/or facilitating ‘conformational capture’ of pre-distorted damaged sites. Surprisingly, even mismatched DNA specifically bound to Rad4 remains highly dynamic, a feature that may reflect the versatility of Rad4/XPC to recognize many structurally dissimilar lesions.
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Affiliation(s)
- Sagnik Chakraborty
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debamita Paul
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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7
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Craggs TD, Hutton RD, Brenlla A, White MF, Penedo JC. Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Res 2014; 42:1857-72. [PMID: 24234453 PMCID: PMC3919604 DOI: 10.1093/nar/gkt1116] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 11/21/2022] Open
Abstract
Flap endonuclease 1 (Fen1) is a highly conserved structure-specific nuclease that catalyses a specific incision to remove 5' flaps in double-stranded DNA substrates. Fen1 plays an essential role in key cellular processes, such as DNA replication and repair, and mutations that compromise Fen1 expression levels or activity have severe health implications in humans. The nuclease activity of Fen1 and other FEN family members can be stimulated by processivity clamps such as proliferating cell nuclear antigen (PCNA); however, the exact mechanism of PCNA activation is currently unknown. Here, we have used a combination of ensemble and single-molecule Förster resonance energy transfer together with protein-induced fluorescence enhancement to uncouple and investigate the substrate recognition and catalytic steps of Fen1 and Fen1/PCNA complexes. We propose a model in which upon Fen1 binding, a highly dynamic substrate is bent and locked into an open flap conformation where specific Fen1/DNA interactions can be established. PCNA enhances Fen1 recognition of the DNA substrate by further promoting the open flap conformation in a step that may involve facilitated threading of the 5' ssDNA flap. Merging our data with existing crystallographic and molecular dynamics simulations we provide a solution-based model for the Fen1/PCNA/DNA ternary complex.
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Affiliation(s)
- Timothy D. Craggs
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Richard D. Hutton
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Alfonso Brenlla
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Malcolm F. White
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - J. Carlos Penedo
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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He Q, Shumate CK, White MA, Molineux IJ, Yin YW. Exonuclease of human DNA polymerase gamma disengages its strand displacement function. Mitochondrion 2013; 13:592-601. [PMID: 23993955 PMCID: PMC5017585 DOI: 10.1016/j.mito.2013.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/15/2013] [Accepted: 08/15/2013] [Indexed: 12/21/2022]
Abstract
Pol γ, the only DNA polymerase found in human mitochondria, functions in both mtDNA repair and replication. During mtDNA base-excision repair, gaps are created after damaged base excision. Here we show that Pol γ efficiently gap-fills except when the gap is only a single nucleotide. Although wild-type Pol γ has very limited ability for strand displacement DNA synthesis, exo(-) (3'-5' exonuclease-deficient) Pol γ has significantly high activity and rapidly unwinds downstream DNA, synthesizing DNA at a rate comparable to that of the wild-type enzyme on a primer-template. The catalytic subunit Pol γA alone, even when exo(-), is unable to synthesize by strand displacement, making this the only known reaction of Pol γ holoenzyme that has an absolute requirement for the accessory subunit Pol γB.
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Affiliation(s)
- Quan He
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Christie K. Shumate
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
| | - Mark A White
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Ian J. Molineux
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Y. Whitney Yin
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555
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