1
|
Dhar M, Berg MA. Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Photon and photon-counting noise. J Chem Phys 2024; 161:034116. [PMID: 39028845 DOI: 10.1063/5.0212157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/28/2024] [Indexed: 07/21/2024] Open
Abstract
A preceding paper [M. Dhar, J. A. Dickinson, and M. A. Berg, J. Chem. Phys. 159, 054110 (2023)] shows how to remove additive noise from an experimental time series, allowing both the equilibrium distribution of the system and its Green's function to be recovered. The approach is based on nonlinear-correlation functions and is fully nonparametric: no initial model of the system or of the noise is needed. However, single-molecule spectroscopy often produces time series with either photon or photon-counting noise. Unlike additive noise, photon noise is signal-size correlated and quantized. Photon counting adds the potential for bias. This paper extends noise-corrected-correlation methods to these cases and tests them on synthetic datasets. Neither signal-size correlation nor quantization is a significant complication. Analysis of the sampling error yields guidelines for the data quality needed to recover the properties of a system with a given complexity. We show that bias in photon-counting data can be corrected, even at the high count rates needed to optimize the time resolution. Using all these results, we discuss the factors that limit the time resolution of single-molecule spectroscopy and the conditions that would be needed to push measurements into the submicrosecond region.
Collapse
Affiliation(s)
- Mainak Dhar
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Mark A Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| |
Collapse
|
2
|
Gupta R, Verma SD. Two-Dimensional Fluctuation Correlation Spectroscopy (2D-FlucCS): A Method to Determine the Origin of Relaxation Rate Dispersion. ACS MEASUREMENT SCIENCE AU 2024; 4:153-162. [PMID: 38645580 PMCID: PMC11027202 DOI: 10.1021/acsmeasuresciau.3c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 04/23/2024]
Abstract
Relaxation rate dispersion, i.e., nonexponential or multicomponent kinetics, is observed in complex systems when measuring relaxation kinetics. Often, the origin of rate dispersion is associated with the heterogeneity in the system. However, both homogeneous (where all molecules experience the same rate but inherently nonexponential) and heterogeneous (where all molecules experience different rates) systems can exhibit rate dispersion. A multidimensional correlation analysis method has been demonstrated to detect and quantify rate dispersion observed in molecular rotation, diffusion, solvation, and reaction kinetics. One-dimensional (1D) autocorrelation function detects rate dispersion and measures its extent. Two-dimensional (2D) autocorrelation function measures the origin of rate dispersion and distinguishes homogeneous from heterogeneous. In a heterogeneous system, implicitly there exist subensembles of molecules experiencing different rates. A three-dimensional (3D) autocorrelation function measures subensemble exchange if present and reveals if the system possesses static or dynamic heterogeneity. This perspective discusses the principles, applications, and potential and also presents a future outlook of two-dimensional fluctuation correlation spectroscopy (2D-FlucCS). The method is applicable to any experiment or simulation where a time series of fluctuation in an observable (emission, scattering, current, etc.) around a mean value can be obtained in steady state (equilibrium or nonequilibrium), provided the system is ergodic.
Collapse
Affiliation(s)
- Ruchir Gupta
- Spectroscopy and Dynamics
Visualization Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Sachin Dev Verma
- Spectroscopy and Dynamics
Visualization Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal 462066, Madhya Pradesh, India
| |
Collapse
|
3
|
Zhang Q, Hu J, Li DL, Qiu JG, Jiang BH, Zhang CY. Construction of single-molecule counting-based biosensors for DNA-modifying enzymes: A review. Anal Chim Acta 2024; 1298:342395. [PMID: 38462345 DOI: 10.1016/j.aca.2024.342395] [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: 12/10/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
DNA-modifying enzymes act as critical regulators in a wide range of genetic functions (e.g., DNA damage & repair, DNA replication), and their aberrant expression may interfere with regular genetic functions and induce various malignant diseases including cancers. DNA-modifying enzymes have emerged as the potential biomarkers in early diagnosis of diseases and new therapeutic targets in genomic research. Consequently, the development of highly specific and sensitive biosensors for the detection of DNA-modifying enzymes is of great importance for basic biomedical research, disease diagnosis, and drug discovery. Single-molecule fluorescence detection has been widely implemented in the field of molecular diagnosis due to its simplicity, high sensitivity, visualization capability, and low sample consumption. In this paper, we summarize the recent advances in single-molecule counting-based biosensors for DNA-modifying enzyme (i.e, alkaline phosphatase, DNA methyltransferase, DNA glycosylase, flap endonuclease 1, and telomerase) assays in the past four years (2019 - 2023). We highlight the principles and applications of these biosensors, and give new insight into the future challenges and perspectives in the development of single-molecule counting-based biosensors.
Collapse
Affiliation(s)
- Qian Zhang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China; College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Jian-Ge Qiu
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bing-Hua Jiang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| |
Collapse
|
4
|
Schiopu I, Dragomir I, Asandei A. Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability. RSC Adv 2024; 14:5449-5460. [PMID: 38352678 PMCID: PMC10862658 DOI: 10.1039/d3ra07746b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.
Collapse
Affiliation(s)
- Irina Schiopu
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Isabela Dragomir
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Alina Asandei
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| |
Collapse
|
5
|
Maurer J, Albrecht CS, Herbert P, Heussman D, Chang A, von Hippel PH, Marcus AH. Studies of DNA 'Breathing' by Polarization-Sweep Single-Molecule Fluorescence Microscopy of Exciton-Coupled (iCy3) 2 Dimer-Labeled DNA Fork Constructs. J Phys Chem B 2023; 127:10730-10748. [PMID: 38060691 PMCID: PMC10754251 DOI: 10.1021/acs.jpcb.3c06463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Local fluctuations of the sugar-phosphate backbones and bases of DNA (often called DNA 'breathing') play a variety of critical roles in controlling the functional interactions of the DNA genome with the protein complexes that regulate it. Here, we present a single-molecule fluorescence method that we have used to measure and characterize such conformational fluctuations at and near biologically important positions in model DNA replication fork constructs labeled with exciton-coupled cyanine [(iCy3)2] dimer probes. Previous work has shown that the constructs that we tested here exhibit a broad range of spectral properties at the ensemble level, and these differences can be structurally and dynamically interpreted using our present methodology at the single-molecule level. The (iCy3)2 dimer has one symmetric (+) and one antisymmetric (-) exciton, with the respective transition dipole moments oriented perpendicular to one another. We excite single-molecule samples using a continuous-wave linearly polarized laser, with the polarization direction continuously rotated at the frequency of 1 MHz. The ensuing fluorescence signal is modulated as the laser polarization alternately excites the symmetric and antisymmetric excitons of the (iCy3)2 dimer probe. Phase-sensitive detection of the modulated signal provides information about the distribution of local conformations and the conformational interconversion dynamics of the (iCy3)2 probe. We find that at most construct positions that we examined, the (iCy3)2 dimer-labeled DNA fork constructs can adopt four topologically distinct conformational macrostates. These results suggest that in addition to observing DNA breathing at and near ss-dsDNA junctions, our new methodology should be useful to determine which of these pre-existing macrostates are recognized by, bind to, and are stabilized by various genome-regulatory proteins.
Collapse
Affiliation(s)
- Jack Maurer
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Claire S. Albrecht
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Physics, University of Oregon, Eugene, Oregon 97403
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Anabel Chang
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Peter H. von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Andrew H. Marcus
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| |
Collapse
|
6
|
Topel M, Ejaz A, Squires A, Ferguson AL. Learned Reconstruction of Protein Folding Trajectories from Noisy Single-Molecule Time Series. J Chem Theory Comput 2023; 19:4654-4667. [PMID: 36701162 DOI: 10.1021/acs.jctc.2c00920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is an experimental methodology to track the real-time dynamics of molecules using fluorescent probes to follow one or more intramolecular distances. These distances provide a low-dimensional representation of the full atomistic dynamics. Under mild technical conditions, Takens' Delay Embedding Theorem guarantees that the full three-dimensional atomistic dynamics of a system are diffeomorphic (i.e., related by a smooth and invertible transformation) to a time-delayed embedding of one or more scalar observables. Appealing to these theoretical guarantees, we employ manifold learning, artificial neural networks, and statistical mechanics to learn from molecular simulation training data the a priori unknown transformation between the atomic coordinates and delay-embedded intramolecular distances accessible to smFRET. This learned transformation may then be used to reconstruct atomistic coordinates from smFRET time series data. We term this approach Single-molecule TAkens Reconstruction (STAR). We have previously applied STAR to reconstruct molecular configurations of a C24H50 polymer chain and the mini-protein Chignolin with accuracies better than 0.2 nm from simulated smFRET data under noise free and high time resolution conditions. In the present work, we investigate the role of signal-to-noise ratio, data volume, and time resolution in simulated smFRET data to assess the performance of STAR under conditions more representative of experimental realities. We show that STAR can reconstruct the Chignolin and Villin mini-proteins to accuracies of 0.12 and 0.42 nm, respectively, and place bounds on these conditions for accurate reconstructions. These results demonstrate that it is possible to reconstruct dynamical trajectories of protein folding from time series in noisy, time binned, experimentally measurable observables and lay the foundations for the application of STAR to real experimental data.
Collapse
Affiliation(s)
- Maximilian Topel
- Department of Physics, University of Chicago, Chicago, Illinois 60637, United States
| | - Ayesha Ejaz
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Allison Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
7
|
Marcus AH, Heussman D, Maurer J, Albrecht CS, Herbert P, von Hippel PH. Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy. Annu Rev Phys Chem 2023; 74:245-265. [PMID: 36696590 PMCID: PMC10590263 DOI: 10.1146/annurev-physchem-090419-041204] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded-double-stranded DNA (ssDNA-dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA-dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2 dimer probes. With the application of these methods, the (iCy3)2 dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein-DNA complex assembly and function.
Collapse
Affiliation(s)
- Andrew H Marcus
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
- Department of Physics, University of Oregon, Eugene, Oregon, USA
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| | - Jack Maurer
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| | - Claire S Albrecht
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Physics, University of Oregon, Eugene, Oregon, USA
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| | - Peter H von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| |
Collapse
|
8
|
Saurabh A, Fazel M, Safar M, Sgouralis I, Pressé S. Single-photon smFRET. I: Theory and conceptual basis. BIOPHYSICAL REPORTS 2022; 3:100089. [PMID: 36582655 PMCID: PMC9793182 DOI: 10.1016/j.bpr.2022.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively.
Collapse
Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennesse
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona,School of Molecular Sciences, Arizona State University, Tempe, Arizona,Corresponding author
| |
Collapse
|
9
|
Lee J, Kim SH, Se T, Kim D. Characterization of Noise in a Single-Molecule Fluorescence Signal. J Phys Chem B 2022; 126:1160-1167. [PMID: 35129336 DOI: 10.1021/acs.jpcb.1c08621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule fluorescence experiments allow monitoring of the structural change and dynamics of a single biomolecule in real time using dye molecules attached to the molecule. Often, the molecules are immobilized on the surface to observe a longer molecular dynamics, yet the finite photon budget available from an individual dye molecule before photobleaching sets the limit to the relatively poor signal-to-noise level. To increase the accuracy of these single-molecule experiments, it is necessary to study the cause of noise in the fluorescence signal from the single molecules. To find the origin of this noise, the lifetime of the fluorescent dye molecules labeled on surface-immobilized DNA was measured by using time-correlation single photon counting. The standard deviation of the fluorescence lifetimes obtained from repeated measurements of a single dye molecule with the total photon number N decreased as 1/N, thus following a shot noise of the Poisson statistics. On the other hand, an additional constant noise source, which is independent of the photon number, was observed from the lifetime uncertainties from many molecules and became more dominant after a certain photon number N. This trend was also followed in the uncertainties of the single-molecule FRET signals obtained from single and many molecules. This additional noise is considered to come from the inhomogeneous environment of each DNA immobilized on the surface.
Collapse
Affiliation(s)
- Jaejin Lee
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107 Korea
| | - Sung Hyun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 JB, Netherlands
| | - Tola Se
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107 Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107 Korea
| |
Collapse
|
10
|
Heussman D, Kittell J, von Hippel PH, Marcus AH. Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy. J Chem Phys 2022; 156:045101. [PMID: 35105081 PMCID: PMC9448411 DOI: 10.1063/5.0076261] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.
Collapse
Affiliation(s)
| | - Justin Kittell
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
| | - Peter H. von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | |
Collapse
|
11
|
Blevins MS, Walker JN, Schaub JM, Finkelstein IJ, Brodbelt JS. Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry. Chem Sci 2021; 12:13764-13776. [PMID: 34760161 PMCID: PMC8549804 DOI: 10.1039/d1sc02861h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Protein-DNA interactions play crucial roles in DNA replication across all living organisms. Here, we apply a suite of mass spectrometry (MS) tools to characterize a protein-ssDNA complex, T4 gp32·ssDNA, with results that both support previous studies and simultaneously uncover novel insight into this non-covalent biological complex. Native mass spectrometry of the protein reveals the co-occurrence of Zn-bound monomers and homodimers, while addition of differing lengths of ssDNA generates a variety of protein:ssDNA complex stoichiometries (1 : 1, 2 : 1, 3 : 1), indicating sequential association of gp32 monomers with ssDNA. Ultraviolet photodissociation (UVPD) mass spectrometry allows characterization of the binding site of the ssDNA within the protein monomer via analysis of holo ions, i.e. ssDNA-containing protein fragments, enabling interrogation of disordered regions of the protein which are inaccessible via traditional crystallographic techniques. Finally, two complementary cross-linking (XL) approaches, bottom-up analysis of the crosslinked complexes as well as MS1 analysis of the intact complexes, are used to showcase the absence of ssDNA binding with the intact cross-linked homodimer and to generate two homodimer gp32 model structures which highlight that the homodimer interface overlaps with the monomer ssDNA-binding site. These models suggest that the homodimer may function in a regulatory capacity by controlling the extent of ssDNA binding of the protein monomer. In sum, this work underscores the utility of a multi-faceted mass spectrometry approach for detailed investigation of non-covalent protein-DNA complexes.
Collapse
Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | | |
Collapse
|
12
|
Israels B, Albrecht CS, Dang A, Barney M, von Hippel PH, Marcus AH. Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer. J Phys Chem B 2021; 125:9426-9440. [PMID: 34379430 DOI: 10.1021/acs.jpcb.1c04119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Thermally driven conformational fluctuations (or "breathing") of DNA play important roles in the function and regulation of the "macromolecular machinery of genome expression." Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here, we use microsecond-resolved single-molecule Förster resonance energy transfer (smFRET) experiments to investigate the backbone fluctuations of short [oligo(dT)n] templates within DNA constructs that also serve as models for ss-dsDNA junctions. Such junctions, together with the attached ssDNA sequences, are involved in interactions with the ssDNA binding (ssb) proteins that control and integrate the functions of DNA replication complexes. We analyze these data using a chemical network model based on multiorder time-correlation functions and probability distribution functions that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT)n tails of ss-dsDNA constructs interconvert, on submillisecond time scales, between three macrostates with distinctly different end-to-end distances. These are (i) a "compact" macrostate that represents the dominant species at equilibrium; (ii) a "partially extended" macrostate that exists as minority species; and (iii) a "highly extended" macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA-associating proteins.
Collapse
Affiliation(s)
- Brett Israels
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, United States
| | - Claire S Albrecht
- Department of Physics, Center for Optical, Molecular and Quantum Science, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Anson Dang
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Megan Barney
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, United States.,Department of Physics, Center for Optical, Molecular and Quantum Science, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| |
Collapse
|
13
|
Abstract
Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low- and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.
Collapse
Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| |
Collapse
|
14
|
Camel BR, Jose D, Meze K, Dang A, von Hippel P. Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution. Nucleic Acids Res 2021; 49:916-927. [PMID: 33367802 PMCID: PMC7826291 DOI: 10.1093/nar/gkaa1230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 11/29/2022] Open
Abstract
In this study, we use single-stranded DNA (oligo-dT) lattices that have been position-specifically labeled with monomer or dimer 2-aminopurine (2-AP) probes to map the local interactions of the DNA bases with the nucleic acid binding cleft of gp32, the single-stranded binding (ssb) protein of bacteriophage T4. Three complementary spectroscopic approaches are used to characterize these local interactions of the probes with nearby nucleotide bases and amino acid residues at varying levels of effective protein binding cooperativity, as manipulated by changing lattice length. These include: (i) examining local quenching and enhancing effects on the fluorescence spectra of monomer 2-AP probes at each position within the cleft; (ii) using acrylamide as a dynamic-quenching additive to measure solvent access to monomer 2-AP probes at each ssDNA position; and (iii) employing circular dichroism spectra to characterize changes in exciton coupling within 2-AP dimer probes at specific ssDNA positions within the protein cleft. The results are interpreted in part by what we know about the topology of the binding cleft from crystallographic studies of the DNA binding domain of gp32 and provide additional insights into how gp32 can manipulate the ssDNA chain at various steps of DNA replication and other processes of genome expression.
Collapse
Affiliation(s)
- Benjamin R Camel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Davis Jose
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Department of Chemistry and Physics, Monmouth University, West Long Branch, NJ 07764, USA
| | - Katarina Meze
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Anson Dang
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
15
|
Li B, Liu Y, Liu Y, Tian T, Yang B, Huang X, Liu J, Liu B. Construction of Dual-Color Probes with Target-Triggered Signal Amplification for In Situ Single-Molecule Imaging of MicroRNA. ACS NANO 2020; 14:8116-8125. [PMID: 32568523 DOI: 10.1021/acsnano.0c01061] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The in vitro detection of low abundance biomolecules via nonenzymatic signal amplification is an attractive strategy. However, it remains a challenge to monitor targets of interest in situ in living cells by low-background interference and visualized enzyme-free signal amplification strategies. Taking advantage of the single-molecule imaging and dynamic DNA nanotechnologies, we have achieved the target-triggered self-assembly of nanostructure-based dual-color fluorescent probes (NDFPs) by an enzyme-free toehold-mediated strand displacement cascade. NDFPs will facilitate the simple and visualized monitoring of microRNA (miRNA) at the femtomolar level. The recycled miRNA can be considered as the catalyst for the assembly of multiple H1/H2 duplexes. This generated the fluorescence signal of the enhanced target expression, indicating both in vitro and in vivo signal-amplified imaging. Moreover, the NDFPs improved the measurement accuracy by dual-color colocalization imaging to greatly avoid false-positive signals and enabled the successful in situ imaging of miRNA in living cells in real time. This work provides a strategy to visually monitor and study the integration of signal amplification detection and single-molecule imaging. NDFPs may be an important step toward the enzyme-free amplified monitoring and imaging of various biomolecules in living cells at the single-molecule level.
Collapse
Affiliation(s)
- Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Yujie Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Yixin Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Tongtong Tian
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Beibei Yang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Jianwei Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| |
Collapse
|
16
|
Heussman D, Kittell J, Kringle L, Tamimi A, von Hippel PH, Marcus AH. Measuring local conformations and conformational disorder of (Cy3) 2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy. Faraday Discuss 2019; 216:211-235. [PMID: 31038134 DOI: 10.1039/c8fd00245b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The sugar-phosphate backbone of DNA near single-stranded (ss)-double-stranded (ds) junctions likely fluctuates within a broad distribution of conformations to permit the proper binding of genome regulatory proteins that function at these sites. In this work we use absorbance, circular dichroism (CD), and two-dimensional fluorescence spectroscopy (2DFS) to study the local conformations and conformational disorder within chromophore-labeled DNA constructs. These constructs employ dimers of the fluorescent chromophore Cy3 that are site-specifically incorporated into the sugar-phosphate backbones of DNA strands at ss-ds DNA fork junctions. We show that these data can be analyzed to determine the local conformations of the (Cy3)2 dimer, and the degree of conformational disorder. Our analysis employs an essential-state Holstein-Frenkel Hamiltonian model, which takes into account the internal electronic-vibrational motions within each Cy3 chromophore, and the resonant electronic interaction that couples the two chromophores together. Our results suggest that this approach may be applied generally to understand local backbone conformation and conformational disorder at ss-ds DNA fork junctions.
Collapse
Affiliation(s)
- Dylan Heussman
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Justin Kittell
- Department of Physics, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA
| | - Loni Kringle
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Amr Tamimi
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA. and Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
17
|
Zhang H, Zhang K, Yao Y, Liu Y, Ji J, Huang X, Liu J, Liu B. Single-Molecule Fluorescence Imaging for Ultrasensitive DNA Methyltransferase Activity Measurement and Inhibitor Screening. Anal Chem 2019; 91:9500-9507. [PMID: 31291094 DOI: 10.1021/acs.analchem.9b00379] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hongding Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Kun Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Yuanyuan Yao
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Yujie Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Ji Ji
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jianwei Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| |
Collapse
|
18
|
Abstract
Multiplex detection of biomolecules is important in bionanotechnology and clinical diagnostics. Multiplexing using engineered solutions such as microarrays, synthetic nanopores, and DNA barcodes is promising, but they require sophisticated design/engineering and typically yield semiquantitative information. Single-molecule fluorescence resonance energy transfer (smFRET) is an attractive tool in this regard as it enables both sensitive and quantitative detection. However, multiplexing with smFRET remains a great challenge as it requires either multiple excitation sources, an antenna system created by multiple FRET pairs, or multiple acceptors of the donor fluorophore, which complicates not only the labeling schemes but also data analysis, due to overlapping of FRET efficiencies ( EFRET). Here, we address these currently outstanding issues by designing interconvertible hairpin-based sensors (iHabSs) with nonoverlapping EFRET utilizing a single donor/acceptor pair and demonstrate a high-confidence multiplex detection of unlabeled nucleic acid sequences. We validated the reliability of our approach by systematically omitting one target at a time. Further, we demonstrate that these iHabSs are fully recyclable, sensitive with a limit of detection of ∼200 pM, and able to discriminate against single base mismatches. The multiplexed approach developed here has the potential to benefit the fields of biosensing and diagnostics by allowing simultaneous and quantitative detection of unlabeled nucleic acid biomarkers.
Collapse
Affiliation(s)
- Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| |
Collapse
|
19
|
Kringle L, Sawaya NPD, Widom J, Adams C, Raymer MG, Aspuru-Guzik A, Marcus AH. Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA. J Chem Phys 2018; 148:085101. [PMID: 29495791 DOI: 10.1063/1.5020084] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.
Collapse
Affiliation(s)
- Loni Kringle
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Julia Widom
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Carson Adams
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Michael G Raymer
- Department of Physics, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| |
Collapse
|
20
|
Pant K, Anderson B, Perdana H, Malinowski MA, Win AT, Pabst C, Williams MC, Karpel RL. The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies. PLoS One 2018; 13:e0194357. [PMID: 29634784 PMCID: PMC5892887 DOI: 10.1371/journal.pone.0194357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/01/2018] [Indexed: 11/19/2022] Open
Abstract
The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.
Collapse
Affiliation(s)
- Kiran Pant
- Department of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
| | - Brian Anderson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Hendrik Perdana
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Matthew A. Malinowski
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Aye T. Win
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Christopher Pabst
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
| | - Mark C. Williams
- Department of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Dana Research Center, Boston, Massachusetts, United States of America
| | - Richard L. Karpel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Hilltop Circle, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|