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Marcus AH, Matsika S, Heussman D, Sorour MI, Maurer J, Albrecht CS, Enkhbaatar L, Herbert P, Kistler KA, von Hippel PH. Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA. ARXIV 2024:arXiv:2403.16251v2. [PMID: 38584614 PMCID: PMC10996769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.
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Affiliation(s)
- Andrew H. Marcus
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Mohammed I. Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Jack Maurer
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Claire S. Albrecht
- Center for Optical, Molecular and Quantum Science, Department of Physics, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Physics, and University of Oregon, Eugene, Oregon 97403
| | - Lulu Enkhbaatar
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Kurt A. Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063
| | - Peter H. von Hippel
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
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2
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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.
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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
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3
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Albrecht CS, Scatena LF, von Hippel PH, Marcus AH. Two-photon excitation two-dimensional fluorescence spectroscopy (2PE-2DFS) of the fluorescent nucleobase 6-MI. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2024; 12863:1286305. [PMID: 39149416 PMCID: PMC11326479 DOI: 10.1117/12.3001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Base stacking is fundamentally important to the stability of double-stranded DNA. However, few experiments can directly probe the local conformations and conformational fluctuations of the DNA bases. Here we report a new spectroscopic approach to study the local conformations of DNA bases using the UV-absorbing fluorescent guanine analogue, 6-methyl isoxanthopterin (6-MI), which can be used as a site-specific probe to label DNA. In these experiments, we apply a two-photon excitation (2PE) approach to two-dimensional fluorescence spectroscopy (2DFS), which is a fluorescence-detected nonlinear Fourier transform spectroscopy. In 2DFS, a repeating sequence of four collinear laser pulses (with center wavelength ~ 675 nm and relative phases swept at radio frequencies) is used to excite the lowest energy electronic-vibrational (vibronic) transitions of 6-MI (with center wavelength ~ 340 nm). The ensuing low flux fluorescence is phase-synchronously detected at the level of individual photons and as a function of inter-pulse delay. The 2PE transition pathways that give rise to electronically excited state populations include optical coherences between electronic ground and excited states and non-resonant (one-photon-excited) virtual states. Our results indicate that 2PE-2DFS experiments can provide information about the electronic-vibrational spectrum of the 6-MI monomer, in addition to the conformation-dependent exciton coupling between adjacent 6-MI monomers within a (6-MI)2 dimer. In principle, this approach can be used to determine the local base-stacking conformations of (6-MI)2 dimer-substituted DNA constructs.
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Affiliation(s)
- 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
| | - Lawrence F Scatena
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- 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
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4
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Cashen BA, Morse M, Rouzina I, Karpel R, Williams M. Dynamic structure of T4 gene 32 protein filaments facilitates rapid noncooperative protein dissociation. Nucleic Acids Res 2023; 51:8587-8605. [PMID: 37449435 PMCID: PMC10484735 DOI: 10.1093/nar/gkad595] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Bacteriophage T4 gene 32 protein (gp32) is a model single-stranded DNA (ssDNA) binding protein, essential for DNA replication. gp32 forms cooperative filaments on ssDNA through interprotein interactions between its core and N-terminus. However, detailed understanding of gp32 filament structure and organization remains incomplete, particularly for longer, biologically-relevant DNA lengths. Moreover, it is unclear how these tightly-bound filaments dissociate from ssDNA during complementary strand synthesis. We use optical tweezers and atomic force microscopy to probe the structure and binding dynamics of gp32 on long (∼8 knt) ssDNA substrates. We find that cooperative binding of gp32 rigidifies ssDNA while also reducing its contour length, consistent with the ssDNA helically winding around the gp32 filament. While measured rates of gp32 binding and dissociation indicate nM binding affinity, at ∼1000-fold higher protein concentrations gp32 continues to bind into and restructure the gp32-ssDNA filament, leading to an increase in its helical pitch and elongation of the substrate. Furthermore, the oversaturated gp32-ssDNA filament becomes progressively unwound and unstable as observed by the appearance of a rapid, noncooperative protein dissociation phase not seen at lower complex saturation, suggesting a possible mechanism for prompt removal of gp32 from the overcrowded ssDNA in front of the polymerase during replication.
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Affiliation(s)
- Ben A Cashen
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Richard L Karpel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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5
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Xu L, Halma MTJ, Wuite GJL. Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches. Int J Mol Sci 2023; 24:ijms24032806. [PMID: 36769124 PMCID: PMC9917605 DOI: 10.3390/ijms24032806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. In this review, we discuss how single-molecule assays, such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations, have advanced our understanding of the binding dynamics of SSBs to ssDNA and their interaction with other proteins partners. We highlight the central coordination role that the SSB protein plays by directly modulating other proteins' activities, rather than as an accessory player. Many possible modes of SSB interaction with protein partners are discussed, which together provide a bigger picture of the interaction network shaped by SSB.
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6
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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.
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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
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7
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Lechuga A, Kazlauskas D, Salas M, Redrejo-Rodríguez M. Unlimited Cooperativity of Betatectivirus SSB, a Novel DNA Binding Protein Related to an Atypical Group of SSBs From Protein-Primed Replicating Bacterial Viruses. Front Microbiol 2021; 12:699140. [PMID: 34267740 PMCID: PMC8276246 DOI: 10.3389/fmicb.2021.699140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/08/2021] [Indexed: 11/20/2022] Open
Abstract
Bam35 and related betatectiviruses are tail-less bacteriophages that prey on members of the Bacillus cereus group. These temperate viruses replicate their linear genome by a protein-primed mechanism. In this work, we have identified and characterized the product of the viral ORF2 as a single-stranded DNA binding protein (hereafter B35SSB). B35SSB binds ssDNA with great preference over dsDNA or RNA in a sequence-independent, highly cooperative manner that results in a non-specific stimulation of DNA replication. We have also identified several aromatic and basic residues, involved in base-stacking and electrostatic interactions, respectively, that are required for effective protein-ssDNA interaction. Although SSBs are essential for DNA replication in all domains of life as well as many viruses, they are very diverse proteins. However, most SSBs share a common structural domain, named OB-fold. Protein-primed viruses could constitute an exception, as no OB-fold DNA binding protein has been reported. Based on databases searches as well as phylogenetic and structural analyses, we showed that B35SSB belongs to a novel and independent group of SSBs. This group contains proteins encoded by protein-primed viral genomes from unrelated viruses, spanning betatectiviruses and Φ29 and close podoviruses, and they share a conserved pattern of secondary structure. Sensitive searches and structural predictions indicate that B35SSB contains a conserved domain resembling a divergent OB-fold, which would constitute the first occurrence of an OB-fold-like domain in a protein-primed genome.
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Affiliation(s)
- Ana Lechuga
- Centro de Biologiìa Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, Vilnius, Lithuania
| | - Margarita Salas
- Centro de Biologiìa Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Modesto Redrejo-Rodríguez
- Centro de Biologiìa Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
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8
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Lin M, Malik FK, Guo JT. A comparative study of protein-ssDNA interactions. NAR Genom Bioinform 2021; 3:lqab006. [PMID: 33655206 PMCID: PMC7902235 DOI: 10.1093/nargab/lqab006] [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: 09/07/2020] [Revised: 11/24/2020] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Fareeha K Malik
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Research Center of Modeling and Simulation, National University of Science and Technology, Islamabad, 44000, Pakistan
| | - Jun-tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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9
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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: 9] [Impact Index Per Article: 3.0] [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.
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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
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10
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Ji H, Johnson NP, von Hippel PH, Marcus AH. Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes. Biophys J 2019; 117:1101-1115. [PMID: 31474304 PMCID: PMC6818173 DOI: 10.1016/j.bpj.2019.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/31/2019] [Accepted: 08/05/2019] [Indexed: 01/18/2023] Open
Abstract
Understanding local conformations of DNA at the level of individual nucleic acid bases and base pairs is important for elucidating molecular processes that depend on DNA sequence. Here, we apply linear absorption and circular dichroism measurements to the study of local DNA conformations, using the guanine base analog 6-methyl isoxanthopterin (6-MI) as a structural probe. We show that the spectroscopic properties of this probe can provide detailed information about the average local base and basepair conformations as a function of the surrounding DNA sequence. Based on these results we apply a simple theoretical model to calculate the circular dichroism spectra of 6-MI-substituted DNA constructs and show that our model can be used to extract information about how the local conformations of the 6-MI probe are influenced by the local base or basepair environment. We also use this probe to examine the pathway for the insertion (intercalation) of a tethered acridine ligand (9-amino-6-chloro methoxyacridine) into duplex DNA. We show that this model intercalator interacts with duplex DNA by a "displacement insertion intercalation" mechanism, whereby the acridine moiety is inserted into the DNA structure and displaces the base located opposite its attachment site. These findings suggest that site-specifically positioned base analog probes can be used to characterize the molecular and structural details of binding ligand effects on local base stacking and unstacking reactions in single- and double-stranded DNA and thus may help to define the molecular mechanisms of DNA-protein interactions that involve the site-specific intercalation of aromatic amino acid side chains into genomic DNA.
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Affiliation(s)
- Huiying Ji
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon
| | - Neil P Johnson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon; Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon.
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11
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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.
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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:
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12
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Iijima K, Kobayashi J, Ishizaka Y. Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response. Retrovirology 2018; 15:8. [PMID: 29338752 PMCID: PMC5771197 DOI: 10.1186/s12977-018-0391-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/04/2018] [Indexed: 11/10/2022] Open
Abstract
Background Viral protein R (Vpr) is an accessory protein of HIV-1, which is potentially involved in the infection of macrophages and the induction of the ataxia-telangiectasia and Rad3-related protein (ATR)-mediated DNA damage response (DDR). It was recently proposed that the SLX4 complex of structure-specific endonuclease is involved in Vpr-induced DDR, which implies that aberrant DNA structures are responsible for this phenomenon. However, the mechanism by which Vpr alters the DNA structures remains unclear. Results We found that Vpr unwinds double-stranded DNA (dsDNA) and invokes the loading of RPA70, which is a single-stranded DNA-binding subunit of RPA that activates the ATR-dependent DDR. We demonstrated that Vpr influenced RPA70 to accumulate in the corresponding region utilizing the LacO/LacR system, in which Vpr can be tethered to the LacO locus. Interestingly, RPA70 recruitment required chromatin remodelling via Vpr-mediated ubiquitination of histone H2B. On the contrary, Q65R mutant of Vpr, which lacks ubiquitination activity, was deficient in both chromatin remodelling and RPA70 loading on to the chromatin. Moreover, Vpr-induced unwinding of dsDNA coincidently resulted in the accumulation of negatively supercoiled DNA and covalent complexes of topoisomerase 1 and DNA, which caused DNA double-strand breaks (DSBs) and DSB-directed integration of proviral DNA. Lastly, we noted the dependence of Vpr-promoted HIV-1 infection in resting macrophages on topoisomerase 1. Conclusions The findings of this study indicate that Vpr-induced structural alteration of DNA is a primary event that triggers both DDR and DSB, which ultimately contributes to HIV-1 infection. Electronic supplementary material The online version of this article (10.1186/s12977-018-0391-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenta Iijima
- Department of Intractable Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Junya Kobayashi
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yukihito Ishizaka
- Department of Intractable Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan.
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13
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Cernooka E, Rumnieks J, Tars K, Kazaks A. Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34. Sci Rep 2017; 7:15529. [PMID: 29138440 PMCID: PMC5686142 DOI: 10.1038/s41598-017-15774-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/01/2017] [Indexed: 11/29/2022] Open
Abstract
Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2.5 protein from bacteriophage T7, and likewise is a single-stranded DNA (ssDNA)-binding protein (SSB) that consists of a variation of the oligosaccharide/oligonucleotide-binding (OB)-fold and an unstructured C-terminal segment. We further report the crystal structure of a C-terminally truncated ORF6 in complex with an ssDNA oligonucleotide that reveals a DNA-binding mode involving two aromatic stacks and multiple electrostatic interactions, with implications for a common ssDNA recognition mechanism for all T7-type SSBs.
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Affiliation(s)
- Elina Cernooka
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia.
- Faculty of Biology, Department of Molecular Biology, Riga, LV-1004, Latvia.
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia.
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14
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Zhang Y, Tanner NA. Isothermal Amplification of Long, Discrete DNA Fragments Facilitated by Single-Stranded Binding Protein. Sci Rep 2017; 7:8497. [PMID: 28819114 PMCID: PMC5561150 DOI: 10.1038/s41598-017-09063-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 11/25/2022] Open
Abstract
Isothermal amplification methods for detection of DNA and RNA targets have expanded significantly in recent years, promising a new wave of simple and rapid molecular diagnostics. Current isothermal methods result in the generation of short fragments (<150 base pairs) or highly branched long DNA products. Here we report the amplification of discrete target fragments of several kilobases at 37 °C from both double- and single-stranded circular template DNA using specific primer pairs. In contrast to existing methods, this amplification requires only the single-stranded DNA-binding protein gp32 from bacteriophage T4 and a strand-displacing DNA polymerase. In addition to the discrete amplicon products, this method also produces higher molecular weight products consisting of multiple repeated copies of the amplicon and template DNA. We demonstrate that two features of gp32 enable this amplification: a facilitation of primer strand invasion into double-stranded DNA, and a suppression of non-homologous primer annealing and nonspecific amplification. The ability presented here to produce long, discrete DNA products in an isothermal reaction extends the scope of isothermal amplification to enable more useful applications of these promising methods.
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Affiliation(s)
- Yinhua Zhang
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Nathan A Tanner
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.
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15
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Using microsecond single-molecule FRET to determine the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks. Proc Natl Acad Sci U S A 2017; 114:E3612-E3621. [PMID: 28416680 DOI: 10.1073/pnas.1619819114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA replication is a core biological process that occurs in prokaryotic cells at high speeds (∼1 nucleotide residue added per millisecond) and with high fidelity (fewer than one misincorporation event per 107 nucleotide additions). 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 DNA synthesis. We here report microsecond single-molecule FRET (smFRET) measurements on Cy3/Cy5-labeled primer-template (p/t) DNA constructs in the presence of gp32. These measurements probe the distance between Cy3/Cy5 fluorophores that label the ends of a short (15-nt) segment of ssDNA attached to a model p/t DNA construct and permit us to track the stochastic interconversion between various protein bound and unbound states. The length of the 15-nt ssDNA lattice is sufficient to accommodate up to two cooperatively bound gp32 proteins in either of two positions. We apply a unique multipoint time correlation function analysis to the microsecond-resolved smFRET data obtained to determine and compare the kinetics of various possible reaction pathways for the assembly of cooperatively bound gp32 protein onto ssDNA sequences located at the replication fork. The results of our analysis reveal the presence and translocation mechanisms of short-lived intermediate bound states that are likely to play a critical role in the assembly mechanisms of ssDNA binding proteins at replication forks and other ss duplex junctions.
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16
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Phelps C, Israels B, Marsh MC, von Hippel PH, Marcus AH. Using Multiorder Time-Correlation Functions (TCFs) To Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments. J Phys Chem B 2016; 120:13003-13016. [PMID: 27992233 DOI: 10.1021/acs.jpcb.6b08449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in single-molecule fluorescence imaging have made it possible to perform measurements on microsecond time scales. Such experiments have the potential to reveal detailed information about the conformational changes in biological macromolecules, including the reaction pathways and dynamics of the rearrangements involved in processes, such as sequence-specific DNA "breathing" and the assembly of protein-nucleic acid complexes. Because microsecond-resolved single-molecule trajectories often involve "sparse" data, that is, they contain relatively few data points per unit time, they cannot be easily analyzed using the standard protocols that were developed for single-molecule experiments carried out with tens-of-millisecond time resolution and high "data density." Here, we describe a generalized approach, based on time-correlation functions, to obtain kinetic information from microsecond-resolved single-molecule fluorescence measurements. This approach can be used to identify short-lived intermediates that lie on reaction pathways connecting relatively long-lived reactant and product states. As a concrete illustration of the potential of this methodology for analyzing specific macromolecular systems, we accompany the theoretical presentation with the description of a specific biologically relevant example drawn from studies of reaction mechanisms of the assembly of the single-stranded DNA binding protein of the T4 bacteriophage replication complex onto a model DNA replication fork.
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Affiliation(s)
- Carey Phelps
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Brett Israels
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Morgan C Marsh
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Andrew H Marcus
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
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17
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Lee W, Gillies JP, Jose D, Israels BA, von Hippel PH, Marcus AH. Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions. Nucleic Acids Res 2016; 44:10691-10710. [PMID: 27694621 PMCID: PMC5159549 DOI: 10.1093/nar/gkw863] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/20/2016] [Accepted: 09/19/2016] [Indexed: 11/14/2022] Open
Abstract
Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex. DNA primer/template (p/t) constructs are used as models to determine the effects of ssDNA lattice length, gp32 concentration, salt concentration, binding cooperativity and binding polarity at p/t junctions. Hidden Markov models (HMMs) and transition density plots (TDPs) are used to characterize the dynamics of the multi-step assembly pathway of gp32 at p/t junctions of differing polarity, and show that isolated gp32 molecules bind to their ssDNA targets weakly and dissociate quickly, while cooperatively bound dimeric or trimeric clusters of gp32 bind much more tightly, can 'slide' on ssDNA sequences, and exhibit binding dynamics that depend on p/t junction polarities. The potential relationships of these binding dynamics to interactions with other components of the T4 DNA replication complex are discussed.
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Affiliation(s)
- Wonbae Lee
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - John P Gillies
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Davis Jose
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Brett A Israels
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.,Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Peter H von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA .,Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Andrew H Marcus
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA .,Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.,Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
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18
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Morten MJ, Peregrina JR, Figueira-Gonzalez M, Ackermann K, Bode BE, White MF, Penedo JC. Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach. Nucleic Acids Res 2015; 43:10907-24. [PMID: 26578575 PMCID: PMC4678828 DOI: 10.1093/nar/gkv1225] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/29/2015] [Indexed: 01/28/2023] Open
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all organisms and are characterized by the presence of an OB (oligonucleotide/oligosaccharide/oligopeptide) binding motif to recognize single-stranded DNA (ssDNA). Despite their critical role in genome maintenance, our knowledge about SSB function is limited to proteins containing multiple OB-domains and little is known about single OB-folds interacting with ssDNA. Sulfolobus solfataricus SSB (SsoSSB) contains a single OB-fold and being the simplest representative of the SSB-family may serve as a model to understand fundamental aspects of SSB:DNA interactions. Here, we introduce a novel approach based on the competition between Förster resonance energy transfer (FRET), protein-induced fluorescence enhancement (PIFE) and quenching to dissect SsoSSB binding dynamics at single-monomer resolution. We demonstrate that SsoSSB follows a monomer-by-monomer binding mechanism that involves a positive-cooperativity component between adjacent monomers. We found that SsoSSB dynamic behaviour is closer to that of Replication Protein A than to Escherichia coli SSB; a feature that might be inherited from the structural analogies of their DNA-binding domains. We hypothesize that SsoSSB has developed a balance between high-density binding and a highly dynamic interaction with ssDNA to ensure efficient protection of the genome but still allow access to ssDNA during vital cellular processes.
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Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Jose R Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Maria Figueira-Gonzalez
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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19
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Jose D, Weitzel SE, Baase WA, Michael MM, von Hippel PH. Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity. Nucleic Acids Res 2015; 43:9291-305. [PMID: 26275774 PMCID: PMC4627071 DOI: 10.1093/nar/gkv818] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/31/2015] [Indexed: 11/16/2022] Open
Abstract
We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5′-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex.
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Affiliation(s)
- Davis Jose
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403-1229, USA
| | - Steven E Weitzel
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403-1229, USA
| | - Walter A Baase
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403-1229, USA
| | - Miya M Michael
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403-1229, USA
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403-1229, USA
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