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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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Ashwood B, Jones MS, Ferguson AL, Tokmakoff A. Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site. Proc Natl Acad Sci U S A 2023; 120:e2219124120. [PMID: 36976762 PMCID: PMC10083564 DOI: 10.1073/pnas.2219124120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
DNA duplex stability arises from cooperative interactions between multiple adjacent nucleotides that favor base pairing and stacking when formed as a continuous stretch rather than individually. Lesions and nucleobase modifications alter this stability in complex manners that remain challenging to understand despite their centrality to biology. Here, we investigate how an abasic site destabilizes small DNA duplexes and reshapes base pairing dynamics and hybridization pathways using temperature-jump infrared spectroscopy and coarse-grained molecular dynamics simulations. We show how an abasic site splits the cooperativity in a short duplex into two segments, which destabilizes small duplexes as a whole and enables metastable half-dissociated configurations. Dynamically, it introduces an additional barrier to hybridization by constraining the hybridization mechanism to a step-wise process of nucleating and zipping a stretch on one side of the abasic site and then the other.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
| | - Michael S. Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL60637
| | - Andrew L. Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL60637
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
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4
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Su D, Hou Y, Dong C, Ren J. Fluctuation correlation spectroscopy and its applications in homogeneous analysis. Anal Bioanal Chem 2019; 411:4523-4540. [DOI: 10.1007/s00216-019-01884-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
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5
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Meng L, He S, Zhao XS. Determination of Equilibrium Constant and Relative Brightness in FRET-FCS by Including the Third-Order Correlations. J Phys Chem B 2017; 121:11262-11272. [PMID: 29155588 DOI: 10.1021/acs.jpcb.7b09229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) encodes the information on the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k+ and k-) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence autocorrelation spectroscopy (FACS). Here, we extend the method to fluorescence cross-correlation spectroscopy (FCCS), which appears when FCS is coupled with fluorescence resonance energy transfer (FRET). Among 12 total second-order and third-order pre-exponential factors in a relaxation process probed by the FRET-FCS technique, 3 are independent. We presented and discussed 3 sets of explicit solutions to use these pre-exponential factors to calculate K and Q. Together with the relaxation time, the acquired K will allow people to obtain k+ and k-, so that the goal of deciphering the FRET-FCS data will be fully reached. The theory is verified by extensive computer simulations and tested experimentally on a system of oligonucleotide hybridization.
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Affiliation(s)
- Lingyi Meng
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,School of Life Sciences, Peking University , Beijing 100871, China
| | - Shanshan He
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Xin Sheng Zhao
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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6
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Sharma A, Enderlein J, Kumbhakar M. Photon Antibunching Reveals Static and Dynamic Quenching Interaction of Tryptophan with Atto-655. J Phys Chem Lett 2017; 8:5821-5826. [PMID: 29125301 DOI: 10.1021/acs.jpclett.7b02430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) of photoinduced electron transfer (PET) between the dye Atto-655 and the amino acid tryptophan has been extensively used for studying fast conformational dynamics of small disordered peptides and proteins. However, a precise understanding of the quenching mechanism and its exact rates that would explain ensemble as well as single-molecule spectroscopy results is still lacking. In this contribution, a general unified model for intermolecular PET between Atto-655 and tryptophan is developed, which involves ground-state complex formation, quenching sphere of action, and dynamic quenching at the single-molecule level. We present measurements of fluorescence antibunching, fluorescence lifetime, and steady-state fluorescence intensity and absorbance and demonstrate that our model is capable to describe all results in a global and coherent manner.
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Affiliation(s)
- Arjun Sharma
- Radiation & Photochemistry Division, Bhabha Atomic Research Center , Mumbai 400085, India
- Homi Bhabha National Institute , Training School Complex, , Anushaktinagar, Mumbai 400094, India
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University , 37077 Göttingen, Germany
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center , Mumbai 400085, India
- Homi Bhabha National Institute , Training School Complex, , Anushaktinagar, Mumbai 400094, India
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7
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Wu Z, Bi H, Pan S, Meng L, Zhao XS. Determination of Equilibrium Constant and Relative Brightness in Fluorescence Correlation Spectroscopy by Considering Third-Order Correlations. J Phys Chem B 2016; 120:11674-11682. [DOI: 10.1021/acs.jpcb.6b07953] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhenqin Wu
- Department of Chemical Biology, Beijing National Laboratory for Molecular
Sciences, State Key Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry and Molecular Engineering, ‡Biodynamic Optical
Imaging Center (BIOPIC), and §School of Life Sciences, Peking University, Beijing 100871, China
| | - Huimin Bi
- Department of Chemical Biology, Beijing National Laboratory for Molecular
Sciences, State Key Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry and Molecular Engineering, ‡Biodynamic Optical
Imaging Center (BIOPIC), and §School of Life Sciences, Peking University, Beijing 100871, China
| | - Sichen Pan
- Department of Chemical Biology, Beijing National Laboratory for Molecular
Sciences, State Key Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry and Molecular Engineering, ‡Biodynamic Optical
Imaging Center (BIOPIC), and §School of Life Sciences, Peking University, Beijing 100871, China
| | - Lingyi Meng
- Department of Chemical Biology, Beijing National Laboratory for Molecular
Sciences, State Key Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry and Molecular Engineering, ‡Biodynamic Optical
Imaging Center (BIOPIC), and §School of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Sheng Zhao
- Department of Chemical Biology, Beijing National Laboratory for Molecular
Sciences, State Key Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry and Molecular Engineering, ‡Biodynamic Optical
Imaging Center (BIOPIC), and §School of Life Sciences, Peking University, Beijing 100871, China
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8
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Bi H, Yin Y, Pan B, Li G, Zhao XS. Scanning Single-Molecule Fluorescence Correlation Spectroscopy Enables Kinetics Study of DNA Hairpin Folding with a Time Window from Microseconds to Seconds. J Phys Chem Lett 2016; 7:1865-1871. [PMID: 27140004 DOI: 10.1021/acs.jpclett.6b00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule fluorescence measurements have been widely used to explore kinetics and dynamics of biological systems. Among them, single-molecule imaging (SMI) is good at tracking processes slower than tens of milliseconds, whereas fluorescence correlation spectroscopy (FCS) is good at probing processes faster than submilliseconds. However, there is still shortage of simple yet effective single-molecule fluorescence method to cover the time-scale between submilliseconds and tens of milliseconds. To effectively bridge this millisecond gap, we developed a single-molecule fluorescence correlation spectroscopy (smFCS) method that works on surface-immobilized single molecules through surface scanning. We validated it by monitoring the classical DNA hairpin folding process. With a wide time window from microseconds to seconds, the experimental data are well fitted to the two-state folding model. All relevant molecular parameters, including the relative fluorescence brightness, equilibrium constant, and reaction rate constants, were uniquely determined.
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Affiliation(s)
- Huimin Bi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Yandong Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Bailong Pan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Geng Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
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9
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Zhang Y, Yuan S, Lu R, Yu A. Ultrafast fluorescence quenching dynamics of Atto655 in the presence of N-acetyltyrosine and N-acetyltryptophan in aqueous solution: proton-coupled electron transfer versus electron transfer. J Phys Chem B 2013; 117:7308-16. [PMID: 23721323 DOI: 10.1021/jp404466f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We studied the ultrafast fluorescence quenching dynamics of Atto655 in the presence of N-acetyltyrosine (AcTyr) and N-acetyltryptophan (AcTrp) in aqueous solution with femtosecond transient absorption spectroscopy. We found that the charge-transfer rate between Atto655 and AcTyr is about 240 times smaller than that between Atto655 and AcTrp. The pH value and D2O dependences of the excited-state decay kinetics of Atto655 in the presence of AcTyr and AcTrp reveal that the quenching of Atto655 fluorescence by AcTyr in aqueous solution is via a proton-coupled electron-transfer (PCET) process and that the quenching of Atto655 fluorescence by AcTrp in aqueous solution is via an electron-transfer process. With the version of the semiclassical Marcus ET theory, we derived that the electronic coupling constant for the PCET reaction between Atto655 and AcTyr in aqueous solution is 8.3 cm(-1), indicating that the PCET reaction between Atto655 and AcTyr in aqueous solution is nonadiabatic.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Republic of China
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10
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Yin Y, Yuan R, Zhao XS. Amplitude of Relaxations in Fluorescence Correlation Spectroscopy for Fluorophores That Diffuse Together. J Phys Chem Lett 2013; 4:304-309. [PMID: 26283439 DOI: 10.1021/jz301871f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The amplitude of chemical relaxations in fluorescence correlation spectroscopy (FCS) is an important parameter that directly relates to not only the equilibrium constant of the relaxations but also the number of individual fluorophores that diffuse together. In this Letter we answer the question how exactly the amplitude of the relaxations in FCS changes with respect to the number of identical fluorophores on one cargo. We anchored tetramethylrhodamine molecules onto each arm of a DNA Holliday junction molecule so that the codiffusing dyes were capable of performing independent fluorescent fluctuations. We found that the amplitudes of the relaxations were inversely proportional to the number of the dyes on each cargo molecule, well agreeing with the theoretical prediction derived in this Letter. The result provides a guideline for the FCS data analysis and points out a simple way to determine the number of molecules that a cargo carries.
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Affiliation(s)
- Yandong Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Rongfeng Yuan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China
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11
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Yang X, Duan J, Li S, Wang P, Ma S, Ye K, Zhao XS. Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation. Nucleic Acids Res 2012; 40:10925-36. [PMID: 23012266 PMCID: PMC3510513 DOI: 10.1093/nar/gks882] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 12/20/2022] Open
Abstract
The box H/ACA RNA-guided pseudouridine synthase is a complicated ribonucleoprotein enzyme that recruits substrate via both the guide RNA and the catalytic subunit Cbf5. Structural studies have revealed multiple conformations of the enzyme, but a quantitative description of the reaction pathway is still lacking. Using fluorescence correlation spectroscopy, we here measured the equilibrium dissociation constants and kinetic association and dissociation rates of substrate and product complexes mimicking various reaction intermediate states. These data support a sequential model for substrate loading and product release regulated by the thumb loop of Cbf5. The uridine substrate is first bound primarily through interaction with the guide RNA and then loaded into the active site while progressively interacted with the thumb. After modification, the subtle chemical structure change from uridine to pseudouridine at the target site triggers the release of the thumb, resulting in an intermediate complex with the product bound mainly by the guide RNA. By dissecting the role of Gar1 in individual steps of substrate turnover, we show that Gar1 plays a major role in catalysis and also accelerates product release about 2-fold. Our biophysical results integrate with previous structural knowledge into a coherent reaction pathway of H/ACA RNA-guided pseudouridylation.
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Affiliation(s)
- Xinxing Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Jingqi Duan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Shuang Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Peng Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Shoucai Ma
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
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12
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Su X, Xiao X, Zhang C, Zhao M. Nucleic acid fluorescent probes for biological sensing. APPLIED SPECTROSCOPY 2012; 66:1249-1262. [PMID: 23146180 DOI: 10.1366/12-06803] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.
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Affiliation(s)
- Xin Su
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, China
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13
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Chen T, Fu L, Zu L. Steady-state and time-resolved fluorescence of tetramethylrhodamine attached to DNA: correlation with DNA sequences. LUMINESCENCE 2012; 28:860-4. [DOI: 10.1002/bio.2446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/30/2012] [Accepted: 09/06/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Tingting Chen
- Department of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| | - Leixiaomeng Fu
- Department of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| | - Lily Zu
- Department of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
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14
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Tamilavan V, Cho N, Kim C, Ko J, Hyun MH. Synthesis of triphenylamine-based thiophene-(N-aryl)pyrrole-thiophene dyes for dye-sensitized solar cell applications. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.04.104] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Sun Q, Lu R, Yu A. Structural Heterogeneity in the Collision Complex between Organic Dyes and Tryptophan in Aqueous Solution. J Phys Chem B 2011; 116:660-6. [DOI: 10.1021/jp2100304] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Qinfang Sun
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
| | - Rong Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
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16
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Abstract
DNA hybridization, wherein strands of DNA form duplex or larger hybrids through noncovalent, sequence-specific interactions, is one of the most fundamental processes in biology. Developing a better understanding of the kinetic and dynamic properties of DNA hybridization will thus help in the elucidation of molecular mechanisms involved in numerous biochemical processes. Moreover, because DNA hybridization has been widely adapted in biotechnology, its study is invaluable to the development of a range of commercially important processes. In this Account, we examine recent studies of the kinetics and dynamics of DNA hybridization, including (i) intramolecular collision of random coil, single-stranded DNA (ssDNA), (ii) nucleic acid hairpin folding, and (iii) considerations of DNA hybridization from both a global view and a detailed base-by-base view. We also examine the spontaneous single-base-pair flipping in duplex DNA because of its importance to both DNA hybridization and repair. Intramolecular collision of random coil ssDNA, with chemical relaxation times ranging from hundreds of nanoseconds to a few microseconds, is investigated both theoretically and experimentally. The first passage time theory of Szabo, Schulten, and Schulten, which determines the average reaction time of the intrachain collision, was tested. Although it was found to provide an acceptable approximation, a more sophisticated theoretical treatment is desirable. Nucleic acid hairpin folding has been extensively investigated as an important model system of DNA hybridization. The relaxation time of hairpin folding and unfolding strongly depends on the stem length, and it may range from hundreds of microseconds to hundreds of milliseconds. The traditional two-state model has been revised to a multistate model as a result of new experimental observations and theoretical study, and partially folded intermediate states have been introduced to the folding energy landscape. On the other hand, new techniques are needed to provide more accurate and detailed information on the dynamics of DNA hairpin folding in the time domain of sub-milliseconds to tens of milliseconds. From a global view, the hybridization of unstructured ssDNA goes through an entropy-controlled nucleation step, whereas the hybridization of ssDNA with a hairpin structure must overcome an extra, enthalpy-controlled energy barrier to eliminate the hairpin. From a detailed base-by-base view, however, there exist many intermediate states. The average single-base-pair hybridization and dehybridization rates in a duplex DNA formation have been determined to be on the order of a millisecond. Meanwhile, accurate information on the early stages of hybridization, such as the dynamics of nucleation, is still lacking. The investigation of spontaneous flipping of a single base in a mismatched base pair in a duplex DNA, although very important, has only recently been initiated because of the earlier lack of suitable probing tools. In sum, the study of DNA hybridization offers a rich range of research opportunities; recent progress is highlighting areas that are ripe for more detailed investigation.
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Affiliation(s)
- Yandong Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
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17
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Lam JD, Culbertson MJ, Skinner NP, Barton ZJ, Burden DL. Information Content in Fluorescence Correlation Spectroscopy: Binary Mixtures and Detection Volume Distortion. Anal Chem 2011; 83:5268-74. [DOI: 10.1021/ac200641y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Lam
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | - Nathan P. Skinner
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Zachary J. Barton
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Daniel L. Burden
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
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18
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Li X, Zhu R, Yu A, Zhao XS. Ultrafast Photoinduced Electron Transfer between Tetramethylrhodamine and Guanosine in Aqueous Solution. J Phys Chem B 2011; 115:6265-71. [DOI: 10.1021/jp200455b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xun Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, People's Republic of China
| | - Ruixue Zhu
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Republic of China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Republic of China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, People's Republic of China
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19
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Zhu R, Li X, Zhao XS, Yu A. Photophysical Properties of Atto655 Dye in the Presence of Guanosine and Tryptophan in Aqueous Solution. J Phys Chem B 2011; 115:5001-7. [DOI: 10.1021/jp200876d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruixue Zhu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xun Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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20
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Cheng RR, Uzawa T, Plaxco KW, Makarov DE. Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides. Biophys J 2011; 99:3959-68. [PMID: 21156138 DOI: 10.1016/j.bpj.2010.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 11/03/2010] [Accepted: 11/15/2010] [Indexed: 11/19/2022] Open
Abstract
Understanding the rate at which various parts of a molecular chain come together to facilitate the folding of a biopolymer (e.g., a protein or RNA) into its functional form remains an elusive goal. Here we use experiments, simulations, and theory to study the kinetics of internal loop closure in disordered biopolymers such as single-stranded oligonucleotides and unfolded proteins. We present theoretical arguments and computer simulation data to show that the relationship between the timescale of internal loop formation and the positions of the monomers enclosing the loop can be recast in a form of a universal master dependence. We also perform experimental measurements of the loop closure times of single-stranded oligonucleotides and show that both these and previously reported internal loop closure kinetics of unfolded proteins are well described by this theoretically predicted dependence. Finally, we propose that experimental deviations from the master dependence can then be used as a sensitive probe of dynamical and structural order in unfolded proteins and other biopolymers.
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Affiliation(s)
- Ryan R Cheng
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, USA
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