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Schaich MA, Schnable BL, Kumar N, Roginskaya V, Jakielski R, Urban R, Zhong Z, Kad NM, Van Houten B. Single-molecule analysis of DNA-binding proteins from nuclear extracts (SMADNE). Nucleic Acids Res 2023; 51:e39. [PMID: 36861323 PMCID: PMC10123111 DOI: 10.1093/nar/gkad095] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
Single-molecule characterization of protein-DNA dynamics provides unprecedented mechanistic details about numerous nuclear processes. Here, we describe a new method that rapidly generates single-molecule information with fluorescently tagged proteins isolated from nuclear extracts of human cells. We demonstrated the wide applicability of this novel technique on undamaged DNA and three forms of DNA damage using seven native DNA repair proteins and two structural variants, including: poly(ADP-ribose) polymerase (PARP1), heterodimeric ultraviolet-damaged DNA-binding protein (UV-DDB), and 8-oxoguanine glycosylase 1 (OGG1). We found that PARP1 binding to DNA nicks is altered by tension, and that UV-DDB did not act as an obligate heterodimer of DDB1 and DDB2 on UV-irradiated DNA. UV-DDB bound to UV photoproducts with an average lifetime of 39 seconds (corrected for photobleaching, τc), whereas binding lifetimes to 8-oxoG adducts were < 1 second. Catalytically inactive OGG1 variant K249Q bound oxidative damage 23-fold longer than WT OGG1, at 47 and 2.0 s, respectively. By measuring three fluorescent colors simultaneously, we also characterized the assembly and disassembly kinetics of UV-DDB and OGG1 complexes on DNA. Hence, the SMADNE technique represents a novel, scalable, and universal method to obtain single-molecule mechanistic insights into key protein-DNA interactions in an environment containing physiologically-relevant nuclear proteins.
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Affiliation(s)
- Matthew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Brittani L Schnable
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Namrata Kumar
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Rachel C Jakielski
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Roman Urban
- School of Biosciences, University of Kent, Kent, UK
| | - Zhou Zhong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- LUMICKS, Waltham, MA, USA
| | - Neil M Kad
- School of Biosciences, University of Kent, Kent, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
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2
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Jang S, Kumar N, Schaich MA, Zhong Z, van Loon B, Watkins S, Van Houten B. Cooperative interaction between AAG and UV-DDB in the removal of modified bases. Nucleic Acids Res 2022; 50:12856-12871. [PMID: 36511855 PMCID: PMC9825174 DOI: 10.1093/nar/gkac1145] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 11/05/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
UV-DDB is a DNA damage recognition protein recently discovered to participate in the removal of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxoG) by stimulating multiple steps of base excision repair (BER). In this study, we examined whether UV-DDB has a wider role in BER besides oxidized bases and found it has specificity for two known DNA substrates of alkyladenine glycosylase (AAG)/N-methylpurine DNA glycosylase (MPG): 1, N6-ethenoadenine (ϵA) and hypoxanthine. Gel mobility shift assays show that UV-DDB recognizes these two lesions 4-5 times better than non-damaged DNA. Biochemical studies indicated that UV-DDB stimulated AAG activity on both substrates by 4- to 5-fold. Native gels indicated UV-DDB forms a transient complex with AAG to help facilitate release of AAG from the abasic site product. Single molecule experiments confirmed the interaction and showed that UV-DDB can act to displace AAG from abasic sites. Cells when treated with methyl methanesulfonate resulted in foci containing AAG and UV-DDB that developed over the course of several hours after treatment. While colocalization did not reach 100%, foci containing AAG and UV-DDB reached a maximum at three hours post treatment. Together these data indicate that UV-DDB plays an important role in facilitating the repair of AAG substrates.
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Affiliation(s)
- Sunbok Jang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15261, USA
- UPMC Hillman Cancer Center, PA 15213, USA
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, South Korea
| | - Namrata Kumar
- UPMC Hillman Cancer Center, PA 15213, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, PA 15261, USA
| | - Mathew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15261, USA
- UPMC Hillman Cancer Center, PA 15213, USA
| | - Zhou Zhong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15261, USA
- UPMC Hillman Cancer Center, PA 15213, USA
| | - Barbara van Loon
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Simon C Watkins
- Center for Biologic Imaging, University of Pittsburgh, PA 15261, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15261, USA
- UPMC Hillman Cancer Center, PA 15213, USA
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3
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Leighton GO, Irvin EM, Kaur P, Liu M, You C, Bhattaram D, Piehler J, Riehn R, Wang H, Pan H, Williams DC. Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3. J Biol Chem 2022; 298:102428. [PMID: 36037972 PMCID: PMC9520026 DOI: 10.1016/j.jbc.2022.102428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 10/29/2022] Open
Abstract
The methyl-CpG-binding domain 2 and 3 proteins (MBD2 and MBD3) provide structural and DNA-binding function for the Nucleosome Remodeling and Deacetylase (NuRD) complex. The two proteins form distinct NuRD complexes and show different binding affinity and selectivity for methylated DNA. Previous studies have shown that MBD2 binds with high affinity and selectivity for a single methylated CpG dinucleotide while MBD3 does not. However, the NuRD complex functions in regions of the genome that contain many CpG dinucleotides (CpG islands). Therefore, in this work, we investigate the binding and diffusion of MBD2 and MBD3 on more biologically relevant DNA templates that contain a large CpG island or limited CpG sites. Using a combination of single-molecule and biophysical analyses, we show that both MBD2 and MBD3 diffuse freely and rapidly across unmethylated CpG-rich DNA. In contrast, we found methylation of large CpG islands traps MBD2 leading to stable and apparently static binding on the CpG island while MBD3 continues to diffuse freely. In addition, we demonstrate both proteins bend DNA, which is augmented by methylation. Together, these studies support a model in which MBD2-NuRD strongly localizes to and compacts methylated CpG islands while MBD3-NuRD can freely mobilize nucleosomes independent of methylation status.
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Affiliation(s)
- Gage O Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Ming Liu
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Dhruv Bhattaram
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University of Medicine, Atlanta, Georgia, USA
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, North Carolina, USA; Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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4
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Bangalore DM, Tessmer I. Direct hOGG1-Myc interactions inhibit hOGG1 catalytic activity and recruit Myc to its promoters under oxidative stress. Nucleic Acids Res 2022; 50:10385-10398. [PMID: 36156093 PMCID: PMC9561264 DOI: 10.1093/nar/gkac796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The base excision repair (BER) glycosylase hOGG1 (human oxoguanine glycosylase 1) is responsible for repairing oxidative lesions in the genome, in particular oxidised guanine bases (oxoG). In addition, a role of hOGG1 in transcription regulation by recruitment of various transcription factors has been reported. Here, we demonstrate direct interactions between hOGG1 and the medically important oncogene transcription factor Myc that is involved in transcription initiation of a large number of genes including inflammatory genes. Using single molecule atomic force microscopy (AFM), we reveal recruitment of Myc to its E-box promoter recognition sequence by hOGG1 specifically under oxidative stress conditions, and conformational changes in hOGG1-Myc complexes at oxoG lesions that suggest loading of Myc at oxoG lesions by hOGG1. Importantly, our data show suppression of hOGG1 catalytic activity in oxoG repair by Myc. Furthermore, mutational analyses implicate the C28 residue in hOGG1 in oxidation induced protein dimerisation and suggest a role of hOGG1 dimerisation under oxidising conditions in hOGG1-Myc interactions. From our data we develop a mechanistic model for Myc recruitment by hOGG1 under oxidising, inflammatory conditions, which may be responsible for the observed enhanced gene expression of Myc target genes.
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Affiliation(s)
- Disha M Bangalore
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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5
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Jang S, Schaich MA, Khuu C, Schnable BL, Majumdar C, Watkins SC, David SS, Van Houten B. Single molecule analysis indicates stimulation of MUTYH by UV-DDB through enzyme turnover. Nucleic Acids Res 2021; 49:8177-8188. [PMID: 34232996 PMCID: PMC8373069 DOI: 10.1093/nar/gkab591] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 11/30/2022] Open
Abstract
The oxidative base damage, 8-oxo-7,8-dihydroguanine (8-oxoG) is a highly mutagenic lesion because replicative DNA polymerases insert adenine (A) opposite 8-oxoG. In mammalian cells, the removal of A incorporated across from 8-oxoG is mediated by the glycosylase MUTYH during base excision repair (BER). After A excision, MUTYH binds avidly to the abasic site and is thus product inhibited. We have previously reported that UV-DDB plays a non-canonical role in BER during the removal of 8-oxoG by 8-oxoG glycosylase, OGG1 and presented preliminary data that UV-DDB can also increase MUTYH activity. In this present study we examine the mechanism of how UV-DDB stimulates MUTYH. Bulk kinetic assays show that UV-DDB can stimulate the turnover rate of MUTYH excision of A across from 8-oxoG by 4-5-fold. Electrophoretic mobility shift assays and atomic force microscopy suggest transient complex formation between MUTYH and UV-DDB, which displaces MUTYH from abasic sites. Using single molecule fluorescence analysis of MUTYH bound to abasic sites, we show that UV-DDB interacts directly with MUTYH and increases the mobility and dissociation rate of MUTYH. UV-DDB decreases MUTYH half-life on abasic sites in DNA from 8800 to 590 seconds. Together these data suggest that UV-DDB facilitates productive turnover of MUTYH at abasic sites during 8-oxoG:A repair.
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Affiliation(s)
- Sunbok Jang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew A Schaich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Cindy Khuu
- Department of Chemistry and Biochemistry, Molecular, Cell and Development Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Brittani L Schnable
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburg, PA 15260, USA
| | - Chandrima Majumdar
- Department of Chemistry and Biochemistry, Molecular, Cell and Development Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Simon C Watkins
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sheila S David
- Department of Chemistry and Biochemistry, Molecular, Cell and Development Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburg, PA 15260, USA
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6
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Dynamic human MutSα-MutLα complexes compact mismatched DNA. Proc Natl Acad Sci U S A 2020; 117:16302-16312. [PMID: 32586954 DOI: 10.1073/pnas.1918519117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DNA mismatch repair (MMR) corrects errors that occur during DNA replication. In humans, mutations in the proteins MutSα and MutLα that initiate MMR cause Lynch syndrome, the most common hereditary cancer. MutSα surveilles the DNA, and upon recognition of a replication error it undergoes adenosine triphosphate-dependent conformational changes and recruits MutLα. Subsequently, proliferating cell nuclear antigen (PCNA) activates MutLα to nick the error-containing strand to allow excision and resynthesis. The structure-function properties of these obligate MutSα-MutLα complexes remain mostly unexplored in higher eukaryotes, and models are predominately based on studies of prokaryotic proteins. Here, we utilize atomic force microscopy (AFM) coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα-MutLα-DNA complexes. We find that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. On the timescale of a few minutes, these complexes rearrange, folding and compacting the DNA. These observations contrast with dominant models of MMR initiation that envision diffusive MutS-MutL complexes that move away from the mismatch. Our results suggest MutSα localizes MutLα near the mismatch and promotes DNA configurations that could enhance MMR efficiency by facilitating MutLα nicking the DNA at multiple sites around the mismatch. In addition, such complexes may also protect the mismatch region from nucleosome reassembly until repair occurs, and they could potentially remodel adjacent nucleosomes.
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7
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Pan H, Jin M, Ghadiyaram A, Kaur P, Miller HE, Ta HM, Liu M, Fan Y, Mahn C, Gorthi A, You C, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA. Nucleic Acids Res 2020; 48:5639-5655. [PMID: 32352519 PMCID: PMC7261166 DOI: 10.1093/nar/gkaa284] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/28/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
Cohesin SA1 (STAG1) and SA2 (STAG2) are key components of the cohesin complex. Previous studies have highlighted the unique contributions by SA1 and SA2 to 3D chromatin organization, DNA replication fork progression, and DNA double-strand break (DSB) repair. Recently, we discovered that cohesin SA1 and SA2 are DNA binding proteins. Given the recently discovered link between SA2 and RNA-mediated biological pathways, we investigated whether or not SA1 and SA2 directly bind to RNA using a combination of bulk biochemical assays and single-molecule techniques, including atomic force microscopy (AFM) and the DNA tightrope assay. We discovered that both SA1 and SA2 bind to various RNA containing substrates, including ssRNA, dsRNA, RNA:DNA hybrids, and R-loops. Importantly, both SA1 and SA2 localize to regions on dsDNA that contain RNA. We directly compared the SA1/SA2 binding and R-loops sites extracted from Chromatin Immunoprecipitation sequencing (ChIP-seq) and DNA-RNA Immunoprecipitation sequencing (DRIP-Seq) data sets, respectively. This analysis revealed that SA1 and SA2 binding sites overlap significantly with R-loops. The majority of R-loop-localized SA1 and SA2 are also sites where other subunits of the cohesin complex bind. These results provide a new direction for future investigation of the diverse biological functions of SA1 and SA2.
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Affiliation(s)
- Hai Pan
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Miao Jin
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashwin Ghadiyaram
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Henry E Miller
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, TX 78229, USA
| | - Hai Minh Ta
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ming Liu
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanlin Fan
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Chelsea Mahn
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Aparna Gorthi
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, TX 78229, USA
| | - Changjiang You
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, TX 78229, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxiology Program, North Carolina State University, Raleigh, NC 27695, USA
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8
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Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions. Proc Natl Acad Sci U S A 2020; 117:9318-9328. [PMID: 32273391 DOI: 10.1073/pnas.1916860117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alkylation of guanine bases in DNA is detrimental to cells due to its high mutagenic and cytotoxic potential and is repaired by the alkyltransferase AGT. Additionally, alkyltransferase-like proteins (ATLs), which are structurally similar to AGTs, have been identified in many organisms. While ATLs are per se catalytically inactive, strong evidence has suggested that ATLs target alkyl lesions to the nucleotide excision repair system (NER). Using a combination of single-molecule and ensemble approaches, we show here recruitment of UvrA, the initiating enzyme of prokaryotic NER, to an alkyl lesion by ATL. We further characterize lesion recognition by ATL and directly visualize DNA lesion search by highly motile ATL and ATL-UvrA complexes on DNA at the molecular level. Based on the high similarity of ATLs and the DNA-interacting domain of AGTs, our results provide important insight in the lesion search mechanism, not only by ATL but also by AGT, thus opening opportunities for controlling the action of AGT for therapeutic benefit during chemotherapy.
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9
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Koehler M, Farka D, Yumusak C, Serdar Sariciftci N, Hinterdorfer P. Localizing Binding Sites on Bioconjugated Hydrogen-Bonded Organic Semiconductors at the Nanoscale. Chemphyschem 2020; 21:659-666. [PMID: 31867830 PMCID: PMC7187352 DOI: 10.1002/cphc.201901064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/19/2019] [Indexed: 01/09/2023]
Abstract
Hydrogen‐bonded organic semiconductors are extraordinarily stable organic solids forming stable, large crystallites with the ability to preserve favorable electrical properties upon bioconjugation. Lately, tremendous efforts have been made to use these bioconjugated semiconductors as platforms for stable multifunctional bioelectronics devices, yet the detailed characterization of bio‐active binding sites (orientation, density, etc.) at the nanoscale has not been achieved yet. The presented work investigates the bioconjugation of epindolidione and quinacridone, two representative semiconductors, with respect to their exposed amine‐functionalities. Relying on the biotin‐avidin lock‐and‐key system and applying the atomic force microscopy (AFM) derivative topography and recognition (TREC) imaging, we used activated biotin to flag crystal‐faces with exposed amine functional groups. Contrary to previous studies, biotin bonds were found to be stable towards removal by autolysis. The resolution strength and clear recognition capability makes TREC‐AFM a valuable tool in the investigation of bio‐conjugated, hydrogen‐bonded semiconductors.
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Affiliation(s)
- Melanie Koehler
- Institute of Biophysics, Johannes Kepler University Linz, 4020, Linz, Austria.,Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Dominik Farka
- Linz Institute for Organic Solar Cells (LIOS), Physical Chemistry, Johannes Kepler University Linz, 4040, Linz, Austria.,Institute of Solid State Physics, Johannes Kepler University Linz, 4040, Linz, Austria
| | - Cigdem Yumusak
- Linz Institute for Organic Solar Cells (LIOS), Physical Chemistry, Johannes Kepler University Linz, 4040, Linz, Austria
| | - Niyazi Serdar Sariciftci
- Linz Institute for Organic Solar Cells (LIOS), Physical Chemistry, Johannes Kepler University Linz, 4040, Linz, Austria
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University Linz, 4020, Linz, Austria
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10
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Springall L, Hughes CD, Simons M, Azinas S, Van Houten B, Kad NM. Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival. Nucleic Acids Res 2019; 46:1256-1265. [PMID: 29240933 PMCID: PMC5814901 DOI: 10.1093/nar/gkx1244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 02/05/2023] Open
Abstract
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex.
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Affiliation(s)
- Luke Springall
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Craig D Hughes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Stavros Azinas
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
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11
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Xue H, Zhan Z, Zhang K, Fu YV. Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified λ DNA at the Single Molecule Level. J Vis Exp 2018:57967. [PMID: 30080193 PMCID: PMC6126486 DOI: 10.3791/57967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The fluorescence microscopy has made great contributions in dissecting the mechanisms of complex biological processes at the single molecule level. In single molecule assays for studying DNA-protein interactions, there are two important factors for consideration: the DNA substrate with enough length for easy observation and labeling a protein with a suitable fluorescent probe. 48.5 kb λ DNA is a good candidate for the DNA substrate. Quantum dots (Qdots), as a class of fluorescent probes, allow long-time observation (minutes to hours) and high-quality image acquisition. In this paper, we present a protocol to study DNA-protein interactions at the single-molecule level, which includes preparing a site-specifically modified λ DNA and labeling a target protein with streptavidin-coated Qdots. For a proof of concept, we choose ORC (origin recognition complex) in budding yeast as a protein of interest and visualize its interaction with an ARS (autonomously replicating sequence) using TIRFM. Compared with other fluorescent probes, Qdots have obvious advantages in single molecule studies due to its high stability against photobleaching, but it should be noted that this property limits its application in quantitative assays.
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Affiliation(s)
- Huijun Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences; Savaid Medical School, University of Chinese Academy of Sciences
| | - Zhengyan Zhan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences
| | - Kaining Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences; Savaid Medical School, University of Chinese Academy of Sciences
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences; Savaid Medical School, University of Chinese Academy of Sciences;
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12
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Countryman P, Fan Y, Gorthi A, Pan H, Strickland E, Kaur P, Wang X, Lin J, Lei X, White C, You C, Wirth N, Tessmer I, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates. J Biol Chem 2018; 293:1054-1069. [PMID: 29175904 PMCID: PMC5777247 DOI: 10.1074/jbc.m117.806406] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single-molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA. We observed that SA2 can switch between the 1D diffusing (search) mode on dsDNA and stable binding (recognition) mode at ssDNA gaps. Although SA2 does not specifically bind to centromeric or telomeric sequences, it does recognize DNA structures often associated with DNA replication and double-strand break repair, such as a double-stranded end, single-stranded overhang, flap, fork, and ssDNA gap. SA2 loss leads to a defect in homologous recombination-mediated DNA double-strand break repair. These results suggest that SA2 functions at intermediate DNA structures during DNA transactions in genome maintenance pathways. These findings have important implications for understanding the function of cohesin in these pathways.
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Affiliation(s)
| | - Yanlin Fan
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Aparna Gorthi
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | | | | | | | | | - Jiangguo Lin
- From the Physics Department
- the Institute of Biomechanics, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaoying Lei
- the Department of BioSciences, Rice University, Houston, Texas 77251
- the School of Public Health, Shandong University, Jinan 250012, China
| | | | - Changjiang You
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | - Nicolas Wirth
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Jacob Piehler
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | | | - Alexander J R Bishop
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | - Yizhi Jane Tao
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Hong Wang
- From the Physics Department,
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
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13
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Liu L, Kong M, Gassman NR, Freudenthal BD, Prasad R, Zhen S, Watkins SC, Wilson SH, Van Houten B. PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1. Nucleic Acids Res 2018; 45:12834-12847. [PMID: 29121337 PMCID: PMC5728402 DOI: 10.1093/nar/gkx1047] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/20/2017] [Indexed: 12/12/2022] Open
Abstract
PARP1-dependent poly-ADP-ribosylation (PARylation) participates in the repair of many forms of DNA damage. Here, we used atomic force microscopy (AFM) and single molecule fluorescence microscopy to examine the interactions of PARP1 with common DNA repair intermediates. AFM volume analysis indicates that PARP1 binds to DNA at nicks, abasic (AP) sites, and ends as a monomer. Single molecule DNA tightrope assays were used to follow the real-time dynamic behavior of PARP1 in the absence and presence of AP endonuclease (APE1) on AP DNA damage arrays. These experiments revealed that PARP1 conducted damage search mostly through 3D diffusion. Co-localization of APE1 with PARP1 on DNA was found capable of inducing 1D diffusion of otherwise nonmotile PARP1, while excess APE1 also facilitated the dissociation of DNA-bound PARP1. Moreover, auto-PARylation of PARP1 allowed the protein to switch its damage search strategy by causing a 3-fold increase in linear diffusion. Finally, we demonstrated that PARP inhibitor olaparib did not significantly alter the rate of PARP1 dissociation from DNA, but instead resulted in more motility of DNA-bound PARP1 molecules.
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Affiliation(s)
- Lili Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Muwen Kong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Natalie R Gassman
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Bret D Freudenthal
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Rajendra Prasad
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Stephanie Zhen
- Department of Chemistry, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Simon C Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Samuel H Wilson
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
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14
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Beckwitt EC, Kong M, Van Houten B. Studying protein-DNA interactions using atomic force microscopy. Semin Cell Dev Biol 2017; 73:220-230. [PMID: 28673677 DOI: 10.1016/j.semcdb.2017.06.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.
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Affiliation(s)
- Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Muwen Kong
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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15
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LeBlanc S, Wilkins H, Li Z, Kaur P, Wang H, Erie DA. Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein-DNA Complexes That Carry Out DNA Repair. Methods Enzymol 2017; 592:187-212. [PMID: 28668121 PMCID: PMC5761736 DOI: 10.1016/bs.mie.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of single biomolecules and complexes deposited on a surface with nanometer resolution. AFM is a powerful tool for characterizing protein-protein and protein-DNA interactions. It can be used to capture snapshots of protein-DNA solution dynamics, which in turn, enables the characterization of the conformational properties of transient protein-protein and protein-DNA interactions. With AFM, it is possible to determine the stoichiometries and binding affinities of protein-protein and protein-DNA associations, the specificity of proteins binding to specific sites on DNA, and the conformations of the complexes. We describe methods to prepare and deposit samples, including surface treatments for optimal depositions, and how to quantitatively analyze images. We also discuss a new electrostatic force imaging technique called DREEM, which allows the visualization of the path of DNA within proteins in protein-DNA complexes. Collectively, these methods facilitate the development of comprehensive models of DNA repair and provide a broader understanding of all protein-protein and protein-nucleic acid interactions. The structural details gleaned from analysis of AFM images coupled with biochemistry provide vital information toward establishing the structure-function relationships that govern DNA repair processes.
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Affiliation(s)
- Sharonda LeBlanc
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hunter Wilkins
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zimeng Li
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Parminder Kaur
- North Carolina State University, Raleigh, NC, United States
| | - Hong Wang
- North Carolina State University, Raleigh, NC, United States
| | - Dorothy A Erie
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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16
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One-step in situ solid-substrate-based whole blood immunoassay based on FRET between upconversion and gold nanoparticles. Biosens Bioelectron 2017; 92:335-341. [DOI: 10.1016/j.bios.2016.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/18/2016] [Accepted: 11/02/2016] [Indexed: 11/30/2022]
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17
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Kong M, Beckwitt EC, Springall L, Kad NM, Van Houten B. Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time. Methods Enzymol 2017; 592:213-257. [PMID: 28668122 DOI: 10.1016/bs.mie.2017.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair.
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Affiliation(s)
- Muwen Kong
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Emily C Beckwitt
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Luke Springall
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Bennett Van Houten
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States.
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18
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Luo J, Kong M, Liu L, Samanta S, Van Houten B, Deiters A. Optical Control of DNA Helicase Function through Genetic Code Expansion. Chembiochem 2017; 18:466-469. [PMID: 28120472 DOI: 10.1002/cbic.201600624] [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] [Received: 11/17/2016] [Indexed: 12/14/2022]
Abstract
Nucleotide excision repair (NER) is a general DNA repair mechanism that is capable of removing a wide variety of DNA lesions induced by physical or chemical insults. UvrD, a member of the helicase SF1 superfamily, plays an essential role in bacterial NER by unwinding the duplex DNA in the 3' to 5' direction to displace the lesion-containing strand. In order to achieve conditional control over NER, we generated a light-activated DNA helicase. This was achieved through a site-specific incorporation of a genetically encoded hydroxycoumarin lysine at a crucial position in the ATP-binding pocket of UvrD. The resulting caged enzyme was completely inactive in several functional assays. Moreover, enzymatic activity of the optically triggered UvrD was comparable to that of the wild-type protein, thus demonstrating excellent OFF to ON switching of the helicase. The developed approach provides optical control of NER, thereby laying a foundation for the regulation of ATP-dependent helicase functions in higher organisms. In addition, this methodology is applicable to the light-activation of a wide range of ATPases.
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Affiliation(s)
- Ji Luo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Muwen Kong
- Department of Pharmacology and Chemical Biology, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, 15213, USA
| | - Lili Liu
- The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, 15213, USA
| | - Subhas Samanta
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, 15213, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, 15213, USA
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19
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Zhang R, Deng T, Wang J, Wu G, Li S, Gu Y, Deng D. Organic-to-aqueous phase transfer of Zn–Cu–In–Se/ZnS quantum dots with multifunctional multidentate polymer ligands for biomedical optical imaging. NEW J CHEM 2017. [DOI: 10.1039/c7nj00573c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ZnCuInSe/ZnS QDs with widely tunable PL emissions were synthesized and water-solubilized with cRGD modified multifunctional multidentate polymer (cRGD-PME) for bioimaging.
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Affiliation(s)
- Rong Zhang
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing
- China
| | - Tao Deng
- Department of Pharmaceutical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing
- China
| | - Jie Wang
- Department of Pharmaceutical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing
- China
| | - Gang Wu
- Department of Biology
- School of Life Science and Technology
- China Pharmaceutical University
- Nanjing
- China
| | - Sirui Li
- Department of Pharmaceutical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing
- China
| | - Yueqing Gu
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing
- China
| | - Dawei Deng
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing
- China
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20
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Wirth N, Gross J, Roth HM, Buechner CN, Kisker C, Tessmer I. Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition. J Biol Chem 2016; 291:18932-46. [PMID: 27405761 DOI: 10.1074/jbc.m116.739425] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/06/2022] Open
Abstract
Nucleotide excision repair is an important and highly conserved DNA repair mechanism with an exceptionally large range of chemically and structurally unrelated targets. Lesion verification is believed to be achieved by the helicases UvrB and XPD in the prokaryotic and eukaryotic processes, respectively. Using single molecule atomic force microscopy analyses, we demonstrate that UvrB and XPD are able to load onto DNA and pursue lesion verification in the absence of the initial lesion detection proteins. Interestingly, our studies show different lesion recognition strategies for the two functionally homologous helicases, as apparent from their distinct DNA strand preferences, which can be rationalized from the different structural features and interactions with other nucleotide excision repair protein factors of the two enzymes.
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Affiliation(s)
- Nicolas Wirth
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Jonas Gross
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Heide M Roth
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Claudia N Buechner
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
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21
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Ma L, Tu C, Le P, Chitoor S, Lim SJ, Zahid MU, Teng KW, Ge P, Selvin PR, Smith AM. Multidentate Polymer Coatings for Compact and Homogeneous Quantum Dots with Efficient Bioconjugation. J Am Chem Soc 2016; 138:3382-94. [PMID: 26863113 DOI: 10.1021/jacs.5b12378] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantum dots are fluorescent nanoparticles used to detect and image proteins and nucleic acids. Compared with organic dyes and fluorescent proteins, these nanocrystals have enhanced brightness, photostability, and wavelength tunability, but their larger size limits their use. Recently, multidentate polymer coatings have yielded stable quantum dots with small hydrodynamic dimensions (≤10 nm) due to high-affinity, compact wrapping around the nanocrystal. However, this coating technology has not been widely adopted because the resulting particles are frequently heterogeneous and clustered, and conjugation to biological molecules is difficult to control. In this article we develop new polymeric ligands and optimize coating and bioconjugation methodologies for core/shell CdSe/Cd(x)Zn(1-x)S quantum dots to generate homogeneous and compact products. We demonstrate that "ligand stripping" to rapidly displace nonpolar ligands with hydroxide ions allows homogeneous assembly with multidentate polymers at high temperature. The resulting aqueous nanocrystals are 7-12 nm in hydrodynamic diameter, have quantum yields similar to those in organic solvents, and strongly resist nonspecific interactions due to short oligoethylene glycol surfaces. Compared with a host of other methods, this technique is superior for eliminating small aggregates identified through chromatographic and single-molecule analysis. We also demonstrate high-efficiency bioconjugation through azide-alkyne click chemistry and self-assembly with hexa-histidine-tagged proteins that eliminate the need for product purification. The conjugates retain specificity of the attached biomolecules and are exceptional probes for immunofluorescence and single-molecule dynamic imaging. These results are expected to enable broad utilization of compact, biofunctional quantum dots for studying crowded macromolecular environments such as the neuronal synapse and cellular cytoplasm.
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Affiliation(s)
| | - Chunlai Tu
- School of Physical Science and Technology, ShanghaiTech University , 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
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22
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DNA-Protein Interactions Studied Directly Using Single Molecule Fluorescence Imaging of Quantum Dot Tagged Proteins Moving on DNA Tightropes. Methods Mol Biol 2016; 1431:141-50. [PMID: 27283307 DOI: 10.1007/978-1-4939-3631-1_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many protein interactions with DNA require specific sequences; however, how these sequences are located remains uncertain. DNA normally appears bundled in solution but, to study DNA-protein interactions, the DNA needs to be elongated. Using fluidics single DNA strands can be efficiently and rapidly elongated between beads immobilized on a microscope slide surface. Such "DNA tightropes" offer a valuable method to study protein search mechanisms. Real-time fluorescence imaging of these interactions provides quantitative descriptions of search mechanism at the single molecule level. In our lab, we use this method to study the complex process of nucleotide excision DNA repair to determine mechanisms of damage detection, lesion removal, and DNA excision.
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23
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Directly interrogating single quantum dot labelled UvrA2 molecules on DNA tightropes using an optically trapped nanoprobe. Sci Rep 2015; 5:18486. [PMID: 26691010 PMCID: PMC4686980 DOI: 10.1038/srep18486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023] Open
Abstract
In this study we describe a new methodology to physically probe individual complexes formed between proteins and DNA. By combining nanoscale, high speed physical force measurement with sensitive fluorescence imaging we investigate the complex formed between the prokaryotic DNA repair protein UvrA2 and DNA. This approach uses a triangular, optically-trapped “nanoprobe” with a nanometer scale tip protruding from one vertex. By scanning this tip along a single DNA strand suspended between surface-bound micron-scale beads, quantum-dot tagged UvrA2 molecules bound to these ‘”DNA tightropes” can be mechanically interrogated. Encounters with UvrA2 led to deflections of the whole nanoprobe structure, which were converted to resistive force. A force histogram from all 144 detected interactions generated a bimodal distribution centered on 2.6 and 8.1 pN, possibly reflecting the asymmetry of UvrA2’s binding to DNA. These observations successfully demonstrate the use of a highly controllable purpose-designed and built synthetic nanoprobe combined with fluorescence imaging to study protein-DNA interactions at the single molecule level.
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24
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Yu JS, Lim MC, Huynh DTN, Kim HJ, Kim HM, Kim YR, Kim KB. Identifying the Location of a Single Protein along the DNA Strand Using Solid-State Nanopores. ACS NANO 2015; 9:5289-98. [PMID: 25938865 DOI: 10.1021/acsnano.5b00784] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Solid-state nanopore has been widely studied as an effective tool to detect and analyze small biomolecules, such as DNA, RNA, and proteins, at a single molecule level. In this study, we demonstrate a rapid identification of the location of zinc finger protein (ZFP), which is bound to a specific locus along the length of a double-stranded DNA (dsDNA) to a single protein resolution using a low noise solid-state nanopore. When ZFP labeled DNAs were driven through a nanopore by an externally applied electric field, characteristic ionic current signals arising from the passage of the DNA/ZFP complex and bare DNA were detected, which enabled us to identify the locations of ZFP binding site. We examined two DNAs with ZFP binding sites at different positions and found that the location of the additional current drop derived from the DNA/ZFP complex is well-matched with a theoretical one along the length of the DNA molecule. These results suggest that the protein binding site on DNA can be mapped or that genetic information can be read at a single molecule level using solid-state nanopores.
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Affiliation(s)
- Jae-Seok Yu
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Min-Cheol Lim
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Duyen Thi Ngoc Huynh
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Hyung-Jun Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Hyun-Mi Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Young-Rok Kim
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Ki-Bum Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
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25
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Hughes CD, Simons M, Mackenzie CE, Van Houten B, Kad NM. Single molecule techniques in DNA repair: a primer. DNA Repair (Amst) 2014; 20:2-13. [PMID: 24819596 DOI: 10.1016/j.dnarep.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.
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Affiliation(s)
- Craig D Hughes
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Cassidy E Mackenzie
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil M Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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26
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Van Houten B, Kad N. Investigation of bacterial nucleotide excision repair using single-molecule techniques. DNA Repair (Amst) 2014; 20:41-48. [PMID: 24472181 PMCID: PMC5053424 DOI: 10.1016/j.dnarep.2013.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 12/23/2022]
Abstract
Despite three decades of biochemical and structural analysis of the prokaryotic nucleotide excision repair (NER) system, many intriguing questions remain with regard to how the UvrA, UvrB, and UvrC proteins detect, verify and remove a wide range of DNA lesions. Single-molecule techniques have begun to allow more detailed understanding of the kinetics and action mechanism of this complex process. This article reviews how atomic force microscopy and fluorescence microscopy have captured new glimpses of how these proteins work together to mediate NER.
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Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Neil Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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27
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Comparison of quantum dot-binding protein tags: affinity determination by ultracentrifugation and FRET. Biochim Biophys Acta Gen Subj 2013; 1840:1651-6. [PMID: 24361618 DOI: 10.1016/j.bbagen.2013.11.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 11/20/2022]
Abstract
BACKGROUND Hybrid complexes of proteins and colloidal semiconductor nanocrystals (quantum dots, QDs) are of increasing interest in various fields of biochemistry and biomedicine, for instance for biolabeling or drug transport. The usefulness of protein-QD complexes for such applications is dependent on the binding specificity and strength of the components. Often the binding properties of these components are difficult and time consuming to assess. METHODS In this work we characterized the interaction between recombinant light harvesting chlorophyll a/b complex (LHCII) and CdTe/CdSe/ZnS QDs by using ultracentrifugation and fluorescence resonance energy transfer (FRET) assay experiments. Ultracentrifugation was employed as a fast method to compare the binding strength between different protein tags and the QDs. Furthermore the LHCII:QD stoichiometry was determined by separating the protein-QD hybrid complexes from unbound LHCII via ultracentrifugation through a sucrose cushion. RESULTS One trimeric LHCII was found to be bound per QD. Binding constants were evaluated by FRET assays of protein derivatives carrying different affinity tags. A new tetra-cysteine motif interacted more strongly (Ka=4.9±1.9nM(-1)) with the nanoparticles as compared to a hexahistidine tag (His6 tag) (Ka~1nM(-1)). CONCLUSION Relative binding affinities and binding stoichiometries of hybrid complexes from LHCII and quantum dots were identified via fast ultracentrifugation, and binding constants were determined via FRET assays. GENERAL SIGNIFICANCE The combination of rapid centrifugation and fluorescence-based titration will be useful to assess the binding strength between different types of nanoparticles and a broad range of proteins.
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28
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Lin J, Countryman P, Buncher N, Kaur P, E L, Zhang Y, Gibson G, You C, Watkins SC, Piehler J, Opresko PL, Kad NM, Wang H. TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres. Nucleic Acids Res 2013; 42:2493-504. [PMID: 24271387 PMCID: PMC3936710 DOI: 10.1093/nar/gkt1132] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Human telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1’s 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼9–17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼2.8–3.6 κBT greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This ‘tag-team proofreading’ represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.
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Affiliation(s)
- Jiangguo Lin
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA, Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA, Electric and Computer Engineering Department, University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Department of Industrial and System Engineering, North Carolina State University, Raleigh, NC 27695, USA, Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA, Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076, Osnabrück, Germany and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ UK
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29
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Tessmer I, Kaur P, Lin J, Wang H. Investigating bioconjugation by atomic force microscopy. J Nanobiotechnology 2013; 11:25. [PMID: 23855448 PMCID: PMC3723498 DOI: 10.1186/1477-3155-11-25] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 07/05/2013] [Indexed: 12/15/2022] Open
Abstract
Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str, 2, 97080, Würzburg, Germany.
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30
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Hughes CD, Wang H, Ghodke H, Simons M, Towheed A, Peng Y, Van Houten B, Kad NM. Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes. Nucleic Acids Res 2013; 41:4901-12. [PMID: 23511970 PMCID: PMC3643590 DOI: 10.1093/nar/gkt177] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA–D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB–DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with different colored quantum dots and quantitatively observed their interactions with DNA tightropes under a variety of solution conditions using oblique angle fluorescence imaging. Alone, UvrC predominantly interacts statically with DNA at low salt. Surprisingly, however, UvrC and UvrB together in solution bind to form the previously unseen UvrBC complex on duplex DNA. This UvrBC complex is highly motile and engages in unbiased one-dimensional diffusion. To test whether UvrB makes direct contact with the DNA in the UvrBC–DNA complex, we investigated three UvrB mutants: Y96A, a β-hairpin deletion and D338N. These mutants affected the motile properties of the UvrBC complex, indicating that UvrB is in intimate contact with the DNA when bound to UvrC. Given the in vivo excess of UvrB and the abundance of UvrBC in our experiments, this newly identified complex is likely to be the predominant form of UvrC in the cell.
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Affiliation(s)
- Craig D Hughes
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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31
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Abstract
Nucleotide excision repair (NER) has allowed bacteria to flourish in many different niches around the globe that inflict harsh environmental damage to their genetic material. NER is remarkable because of its diverse substrate repertoire, which differs greatly in chemical composition and structure. Recent advances in structural biology and single-molecule studies have given great insight into the structure and function of NER components. This ensemble of proteins orchestrates faithful removal of toxic DNA lesions through a multistep process. The damaged nucleotide is recognized by dynamic probing of the DNA structure that is then verified and marked for dual incisions followed by excision of the damage and surrounding nucleotides. The opposite DNA strand serves as a template for repair, which is completed after resynthesis and ligation.
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Affiliation(s)
- Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, 97080 Wuerzburg, Germany.
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32
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Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Proc Natl Acad Sci U S A 2012; 109:E2737-46. [PMID: 22822215 DOI: 10.1073/pnas.1110067109] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
UV light-induced photoproducts are recognized and removed by the nucleotide-excision repair (NER) pathway. In humans, the UV-damaged DNA-binding protein (UV-DDB) is part of a ubiquitin E3 ligase complex (DDB1-CUL4A(DDB2)) that initiates NER by recognizing damaged chromatin with concomitant ubiquitination of core histones at the lesion. We report the X-ray crystal structure of the human UV-DDB in a complex with damaged DNA and show that the N-terminal domain of DDB2 makes critical contacts with two molecules of DNA, driving N-terminal-domain folding and promoting UV-DDB dimerization. The functional significance of the dimeric UV-DDB [(DDB1-DDB2)(2)], in a complex with damaged DNA, is validated by electron microscopy, atomic force microscopy, solution biophysical, and functional analyses. We propose that the binding of UV-damaged DNA results in conformational changes in the N-terminal domain of DDB2, inducing helical folding in the context of the bound DNA and inducing dimerization as a function of nucleotide binding. The temporal and spatial interplay between domain ordering and dimerization provides an elegant molecular rationale for the unprecedented binding affinities and selectivities exhibited by UV-DDB for UV-damaged DNA. Modeling the DDB1-CUL4A(DDB2) complex according to the dimeric UV-DDB-AP24 architecture results in a mechanistically consistent alignment of the E3 ligase bound to a nucleosome harboring damaged DNA. Our findings provide unique structural and conformational insights into the molecular architecture of the DDB1-CUL4A(DDB2) E3 ligase, with significant implications for the regulation and overall organization of the proteins responsible for initiation of NER in the context of chromatin and for the consequent maintenance of genomic integrity.
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33
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Dynamics of lesion processing by bacterial nucleotide excision repair proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:1-24. [PMID: 22749140 DOI: 10.1016/b978-0-12-387665-2.00001-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Single-molecule approaches permit an unrivalled view of how complex systems operate and have recently been used to understand DNA-protein interactions. These tools have enabled advances in a particularly challenging problem, the search for damaged sites on DNA. DNA repair proteins are present at the level of just a few hundred copies in bacterial cells to just a few thousand in human cells, and they scan the entire genome in search of their specific substrates. How do these proteins achieve this herculean task when their targets may differ from undamaged DNA by only a single hydrogen bond? Here we examine, using single-molecule approaches, how the prokaryotic nucleotide excision repair system balances the necessity for speed against specificity. We discuss issues at a theoretical, biological, and technical level and finally pose questions for future research.
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34
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Bruchez MP. Quantum dots find their stride in single molecule tracking. Curr Opin Chem Biol 2011; 15:775-80. [PMID: 22055494 DOI: 10.1016/j.cbpa.2011.10.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 09/30/2011] [Accepted: 10/17/2011] [Indexed: 01/01/2023]
Abstract
Thirteen years after the demonstration of quantum dots as biological imaging agents, and nine years after the initial commercial introduction of bioconjugated quantum dots, the brightness and photostability of the quantum dots has enabled a range of investigations using single molecule tracking. These materials are being routinely utilized by a number of groups to track the dynamics of single molecules in reconstituted biophysical systems and on living cells, and are especially powerful for investigations of single molecules over long timescales with short exposure times and high pointing accuracy. New approaches are emerging where the quantum dots are used as 'hard-sphere' probes for intracellular compartments. Innovations in quantum dot surface modification are poised to substantially expand the utility of these materials.
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Affiliation(s)
- Marcel P Bruchez
- Carnegie Mellon University, Department of Chemistry, Pittsburgh, PA 15213, USA.
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35
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Sapsford KE, Tyner KM, Dair BJ, Deschamps JR, Medintz IL. Analyzing nanomaterial bioconjugates: a review of current and emerging purification and characterization techniques. Anal Chem 2011; 83:4453-88. [PMID: 21545140 DOI: 10.1021/ac200853a] [Citation(s) in RCA: 278] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kim E Sapsford
- Division of Biology, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA.
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36
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Li S, Xiong X, Li W. The breakage and damage of plasmid DNA photocatalized by TiO2
/carbon nanotube composites. SURF INTERFACE ANAL 2011. [DOI: 10.1002/sia.3775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Fronczek DN, Quammen C, Wang H, Kisker C, Superfine R, Taylor R, Erie DA, Tessmer I. High accuracy FIONA-AFM hybrid imaging. Ultramicroscopy 2011; 111:350-5. [PMID: 21329649 DOI: 10.1016/j.ultramic.2011.01.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 11/03/2010] [Accepted: 01/11/2011] [Indexed: 11/24/2022]
Abstract
Multi-protein complexes are ubiquitous and play essential roles in many biological mechanisms. Single molecule imaging techniques such as electron microscopy (EM) and atomic force microscopy (AFM) are powerful methods for characterizing the structural properties of multi-protein and multi-protein-DNA complexes. However, a significant limitation to these techniques is the ability to distinguish different proteins from one another. Here, we combine high resolution fluorescence microscopy and AFM (FIONA-AFM) to allow the identification of different proteins in such complexes. Using quantum dots as fiducial markers in addition to fluorescently labeled proteins, we are able to align fluorescence and AFM information to ≥8nm accuracy. This accuracy is sufficient to identify individual fluorescently labeled proteins in most multi-protein complexes. We investigate the limitations of localization precision and accuracy in fluorescence and AFM images separately and their effects on the overall registration accuracy of FIONA-AFM hybrid images. This combination of the two orthogonal techniques (FIONA and AFM) opens a wide spectrum of possible applications to the study of protein interactions, because AFM can yield high resolution (5-10nm) information about the conformational properties of multi-protein complexes and the fluorescence can indicate spatial relationships of the proteins in the complexes.
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Affiliation(s)
- D N Fronczek
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
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38
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Wagner K, Moolenaar GF, Goosen N. Role of the two ATPase domains of Escherichia coli UvrA in binding non-bulky DNA lesions and interaction with UvrB. DNA Repair (Amst) 2010; 9:1176-86. [PMID: 20864419 DOI: 10.1016/j.dnarep.2010.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/24/2010] [Accepted: 08/27/2010] [Indexed: 01/20/2023]
Abstract
The UvrA protein is the initial DNA damage-sensing protein in bacterial nucleotide excision repair and detects a wide variety of structurally unrelated lesions. After initial recognition of DNA damage, UvrA loads the UvrB protein onto the DNA. This protein then verifies the presence of a lesion, after which UvrA is released from the DNA. UvrA contains two ATPase domains, both belonging to the ABC ATPase superfamily. We have determined the activities of two mutants, in which a single domain was deactivated. Inactivation of either one ATPase domain in Escherichia coli UvrA results in a complete loss of ATPase activity, indicating that both domains function in a cooperative way. We could show that this ATPase activity is not required for the recognition of bulky lesions by UvrA, but it does promote the specific binding to the less distorting cyclobutane-pyrimidine dimer (CPD). The two ATPase mutants also show a difference in UvrB-loading, depending on the length of the DNA substrate. The ATPase domain I mutant was capable of loading UvrB on a lesion in a 50 bp fragment, but this loading was reduced on a longer substrate. For the ATPase domain II mutant the opposite was found: UvrB could not be loaded on a 50 bp substrate, but this loading was rescued when the length of the fragment was increased. This differential loading of UvrB by the two ATPase mutants could be related to different interactions between the UvrA and UvrB subunits.
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Affiliation(s)
- Koen Wagner
- Leiden Institute of Chemistry, Leiden University, The Netherlands
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39
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Kad NM, Wang H, Kennedy GG, Warshaw DM, Van Houten B. Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single- molecule imaging of quantum-dot-labeled proteins. Mol Cell 2010; 37:702-13. [PMID: 20227373 DOI: 10.1016/j.molcel.2010.02.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 10/14/2009] [Accepted: 12/23/2009] [Indexed: 11/29/2022]
Abstract
How DNA repair proteins sort through a genome for damage is one of the fundamental unanswered questions in this field. To address this problem, we uniquely labeled bacterial UvrA and UvrB with differently colored quantum dots and visualized how they interacted with DNA individually or together using oblique-angle fluorescence microscopy. UvrA was observed to utilize a three-dimensional search mechanism, binding transiently to the DNA for short periods (7 s). UvrA also was observed jumping from one DNA molecule to another over approximately 1 microm distances. Two UvrBs can bind to a UvrA dimer and collapse the search dimensionality of UvrA from three to one dimension by inducing a substantial number of UvrAB complexes to slide along the DNA. Three types of sliding motion were characterized: random diffusion, paused motion, and directed motion. This UvrB-induced change in mode of searching permits more rapid and efficient scanning of the genome for damage.
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Affiliation(s)
- Neil M Kad
- Department of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK.
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40
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Hu M, He Y, Song S, Yan J, Lu HT, Weng LX, Wang LH, Fan C. DNA-bridged bioconjugation of fluorescent quantum dots for highly sensitive microfluidic protein chips. Chem Commun (Camb) 2010; 46:6126-8. [DOI: 10.1039/c0cc01608j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Ebenstein Y, Gassman N, Kim S, Weiss S. Combining atomic force and fluorescence microscopy for analysis of quantum-dot labeled protein-DNA complexes. J Mol Recognit 2009; 22:397-402. [PMID: 19452448 DOI: 10.1002/jmr.956] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Atomic force microscopy (AFM) and fluorescence microscopy are widely used for the study of protein-DNA interactions. While AFM excels in its ability to elucidate structural detail and spatial arrangement, it lacks the ability to distinguish between similarly sized objects in a complex system. This information is readily accessible to optical imaging techniques via site-specific fluorescent labels, which enable the direct detection and identification of multiple components simultaneously. Here, we show how the utilization of semiconductor quantum dots (QDs), serving as contrast agents for both AFM topography and fluorescence imaging, facilitates the combination of both imaging techniques, and with the addition of a flow based DNA extension method for sample deposition, results in a powerful tool for the study of protein-DNA complexes. We demonstrate the inherent advantages of this novel combination of techniques by imaging individual RNA polymerases (RNAP) on T7 genomic DNA.
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Affiliation(s)
- Yuval Ebenstein
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
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42
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Destainville N, Manghi M, Palmeri J. Microscopic mechanism for experimentally observed anomalous elasticity of DNA in two dimensions. Biophys J 2009; 96:4464-9. [PMID: 19486670 DOI: 10.1016/j.bpj.2009.03.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 02/26/2009] [Accepted: 03/10/2009] [Indexed: 11/27/2022] Open
Abstract
By exploring a recent model in which DNA bending elasticity, described by the wormlike chain model, is coupled to basepair denaturation, we demonstrate that small denaturation bubbles lead to anomalies in the flexibility of DNA at the nanometric scale, when confined in two dimensions (2D), as reported in atomic-force microscopy experiments. Our model yields very good fits to experimental data and quantitative predictions that can be tested experimentally. Although such anomalies exist when DNA fluctuates freely in three dimensions (3D), they are too weak to be detected. Interactions between bases in the helical double-stranded DNA are modified by electrostatic adsorption on a 2D substrate, which facilitates local denaturation. This work reconciles the apparent discrepancy between observed 2D and 3D DNA elastic properties and points out that conclusions about the 3D properties of DNA (and its companion proteins and enzymes) do not directly follow from 2D experiments by atomic-force microscopy.
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Affiliation(s)
- Nicolas Destainville
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Physique Théorique (Institut de Recherche sur Systèmes Atomiques et Moléculaires Complexes), Toulouse, France.
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43
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Zeng G, Chen J, Zhong L, Wang R, Jiang L, Cai J, Yan L, Huang D, Chen CY, Chen ZW. NSOM- and AFM-based nanotechnology elucidates nano-structural and atomic-force features of a Y. pestis V immunogen-containing particle vaccine capable of eliciting robust response. Proteomics 2009; 9:1538-47. [PMID: 19253301 DOI: 10.1002/pmic.200800528] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
It is postulated that unique nanoscale proteomic features of immunogen on vaccine particles may determine immunogen-packing density, stability, specificity, and pH-sensitivity on the vaccine particle surface and thus impact the vaccine-elicited immune responses. To test this presumption, we employed near-filed scanning optical microscopy (NSOM)- and atomic force microscopy (AFM)-based nanotechnology to study nano-structural and single-molecule force bases of Yersinia pestis (Y. pestis) V immunogen fused with protein anchor (V-PA) loaded on gram positive enhancer matrix (GEM) vaccine particles. Surprisingly, the single-molecule sensitive NSOM revealed that approximately 90% of V-PA immunogen molecules were packed as high-density nanoclusters on GEM particle. AFM-based single-molecule force analyses indicated a highly stable and specific binding between V-PA and GEM at the physiological pH. In contrast, this specific binding was mostly abrogated at the acidic pH equivalent to the biochemical pH in phagolysosomes of antigen-presenting-cells in which immunogen protein is processed for antigen presentation. Intranasal mucosal vaccination of mice with such immunogen loaded on vaccine particles elicited robust antigen-specific immune response. This study indicated that high-density, high-stability, specific, and immunological pH-responsive loading of immunogen nanoclusters on vaccine particles could readily be presented to the immune system for induction of strong antigen-specific immune responses.
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Affiliation(s)
- Gucheng Zeng
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL 60612, USA
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44
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Wagner K, Moolenaar G, van Noort J, Goosen N. Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer. Nucleic Acids Res 2009; 37:1962-72. [PMID: 19208636 PMCID: PMC2665241 DOI: 10.1093/nar/gkp071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The UvrA protein is the initial damage-recognizing factor in bacterial nucleotide excision repair. Each monomer of the UvrA dimer contains two ATPase sites. Using single-molecule analysis we show that dimerization of UvrA in the presence of ATP is significantly higher than with ADP or nonhydrolyzable ATPγS, suggesting that the active UvrA dimer contains a mixture of ADP and ATP. We also show that the UvrA dimer has a high preference of binding the end of a linear DNA fragment, independent on the presence or type of cofactor. Apparently ATP binding or hydrolysis is not needed to discriminate between DNA ends and internal sites. A significant number of complexes could be detected where one UvrA dimer bridges two DNA ends implying the presence of two separate DNA-binding domains, most likely present in each monomer. On DNA containing a site-specific lesion the damage-specific binding is much higher than DNA-end binding, but only in the absence of cofactor or with ATP. With ATPγS no discrimination between a DNA end and a DNA damage could be observed. We present a model where damage recognition of UvrA depends on the ability of both UvrA monomers to interact with the DNA flanking the lesion.
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Affiliation(s)
- Koen Wagner
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
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45
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Ray PC, Yu H, Fu PP. Toxicity and environmental risks of nanomaterials: challenges and future needs. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2009; 27:1-35. [PMID: 19204862 PMCID: PMC2844666 DOI: 10.1080/10590500802708267] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nanotechnology has gained a great deal of public interest because of the needs and applications of nanomaterials in many areas of human endeavors including industry, agriculture, business, medicine, and public health. Environmental exposure to nanomaterials is inevitable as nanomaterials become part of our daily life, and, as a result, nanotoxicity research is gaining attention. This review presents a summary of recent research efforts on fate, behavior, and toxicity of different classes of nanomaterials in the environment. A critical evaluation of challenges and future needs for the safe environmental nanotechnology are discussed.
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Affiliation(s)
- Paresh Chandra Ray
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA.
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