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Hong Wang Single-molecule Imaging Laboratory

Publications


Hong Wang Bibliography PUBMED
Hong Wang Google Scholar

2023

    • Liu, M., Kaur, P., Wang, L. J., Jin, M., Detwiler A.C., Opresko, P.L., Tao, Y.J., Wang, H., Riehn, R. (2023) Assembly Path Dependence of Telomeric DNA Compaction by TRF1, TIN2, and SA1. Biophysics J., 122 (10), 1822-1832

      • Biophysics J.

    • Irvin, E.M., Wang, H. (2023) Single-molecule Imaging of Genome Maintenance Proteins Encountering Specific DNA Sequences and Structures DNA repair, Volume 128, 103528

      • DNA repair

    • Kaur, P., Lu, X., Xu, Q., Irvin, E.M., Pappas, C., Zhang, H., Finkelstein, I.J., Shi, Z., Tao, Y.J., Yu, H. & Wang, H. (2023) High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL. J Biol Chem 299, 105296 .

      • JBC

    • Wojtaszek, J.L., Hoff, K.E., Longley, M.J., Kaur, P., Andres, S.N., Wang, H., Williams, R.S., Copeland W.C. (2023) Structure-specific roles for PolG2–DNA complexes in maintenance and replication of mitochondrial DNA. NAR gkad679

      • NAR

    • Laspata, N.K., P., Mersaoui, S.Y.; Muoio D., Liu, Z.S.; Bannister, M.H., Nguyen H.D., Curry, C., Pascal, J.M., Poirier, G.G., Wang, H.; Masson J., Fouquerel, E. (2023) PARP1 associates with R-loops to promote their resolution and genome stability. Nucleic acids research Nucleic Acids Research, gkad066

      • NAR

       

      2022

            • Leighton, G.O., Irvin, E.M., Kaur, P., Liu, M., You, C., Bhattaram, D., Piehler, J., Riehn, R., Wang, H., Pan, H. and Williams, D.C., Jr. (2022) Densely methylated DNA traps Methyl-CpG Binding Domain protein 2 but permits free diffusion by Methyl-CpG Binding Domain protein 3. JBC, 2022 Aug 28;298(10):102428..
              JBC
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            • Li, Z., Kaur, P., Chopra, N., Smith, J., Wang, H. and Gao, Y. (2022) Cryo-EM and HS-AFM Uncover Structural and Dynamic Basis of DNA Capture and Translocation by Mitochondrial Twinkle Helicase. Nucleic Acids Res. 2022 Nov 11;50(20):11965-11978. doi: 10.1093/nar/gkac1089..
              NAR
            • Dangi, S., Liu, M., Azad, Z., Countryman, P., Roushan, M., Livshits, G.I., Kaur, P., Pan, H., Shi, Z., Detwiler, A.C., Opreko, P.L., Yu, H., Wang, H. & Riehn, R. Nanofluidic Device for Manipulation and Modification of DNA by Proteins. BiRxiv 2022.12.29.521498(2022)
              BioRxiv

            2021

                  • Kaur, P., Barnes, R., Pan, H., Detwiler, A.C., Liu, M., Mahn, C., Hall, J., Messenger, Z., You, C., Piehler, J. et al. (2021) TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA. Nucleic Acids Res, 49, 13000-13018.
                    NAR
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                  • Pan, H., Kaur, P., Barnes, R., Detwiler, A.C., Sanford, S.L., Liu, M., Xu, P., Mahn, C., Tang, Q., Hao, P., Bhattaram, D., You, C., Gu, X., Lu, W., Piehler, J., Xu, G., Weninger, K., Riehn, R., Opresko, P.L. and Wang, H. (2021) Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA. J Biol Chem, 297, 101080
                    JBC
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                  • Kaur, P., Pan, H., Longley, M.J., Copeland, W.C. and Wang, H. (2021) Using Atomic Force Microscopy to Study the Real Time Dynamics of DNA Unwinding by Mitochondrial Twinkle Helicase. Bio-protocol, In press.
                    Bio-protocol
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            2020

                  • Pan, H., Jin, M., Ghadiyaram, A., Kaur, P., Miller, H.E. Ta, H.M., Liu, M., Fan, Y., Mahn, C., Gorthi, A., You, C., Piehler, J., Riehr, R., Bishop, A.J.R., Tao, Y.J., and Wang, H. (2020) Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA. Nucleic Acids Research (print pending).
                    NAR
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                  • Kaur, P., Longley, M.J., Pan, H., Wang, W., Countryman, P., Wang, H., and Copeland, W.C. (2020) Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase. Journal of Biological Chemistry, 295(17),5564-5576.
                    JBC
                  • Liu, M., Movahed, S., Dangi, S., Pan, H., Kaur, P., Bilinovich, S.M., Faison, E.M., Leighton, G.O., Wang, H., Williams, D.C., and Riehn, R. (2020) DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices. Epigenetics and Chromatin, 12(18).
                    Epigenetics and Chromatin
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            2019

                  • Fouquerel, E., Barnes, R.P., Wang, H., and Opresko, P.L. (2019) Measuring UV Photoproduct Repair in Isolated Telomeres and Bulk Genomic DNA. DNA Repair, Methods in Molecular Biology, vol 1999. Humana, New York, NY.
                    DNA Repair
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            2018

                  • Kaur, P., Longley, M.J., Pan, H., Wang, H., and Copeland, W.C. (2018) Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein. Nucleic Acids Research, 46(21), 11287-11302.
                    NAR
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            2017

                  • Countryman, P., Fan, Y., Gorthi, A., Pan, H., Strickland, J., Kaur, P., Wang, X., Lin, J., Lei, X., White, C., You, C., Wirth, N., Tessmer, I., Piehler, J., Riehn, R., Bishop, A.J.R., Tao, Y.J. and Wang, H. (2018) Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates. J Biol Chem, 293, 1054-1069
                    JBC
                  • LeBlanc, S., Wilkins, H., Li, Z., Kaur, P., Wang, H., and Erie, D. A. (2017) Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein-DNA Complexes That Carry Out DNA Repair. Methods in enzymology 592, 187-212
                    Methods in Enzymology
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                  • Pan, H., Bilinovich, S. M., Kaur, P., Riehn, R., Wang, H., and Williams, D. C., Jr. (2017) CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic acids research 45, 9164-9177
                    NAR
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                  • Adkins, N.L., Swygert, S.G., Kaur, P., Niu, H., Grigoryev, S.A., Sung, P., Wang, H. and Peterson, C.L. (2017) Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair. J Biol Chem, 292, 5271-5281.
                    Journal of Biological Chemistry
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            2016

                  • Lin, J., Countryman, P., Chen, H., Pan, H., Fan, Y., Jiang, Y., Kaur, P., Miao, W., Gurgel, G., You, C., Piehler, J., Kad, N. M., Riehn, R., Opresko, P. L., Smith, S., Tao, Y. J., and Wang, H. (2016) Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA-DNA pairing. Nucleic Acids Res 44, 6363-6376
                    NAR
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                  • Kaur, P., Wu, D., Lin, J., Countryman, P., Bradford, K.C., Erie, D.A., Riehn, R., Opresko, P.L. and Wang, H. (2016) Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2. Scientific reports, 6, 20513.
                    PUBMED
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                    DREEM in the news
                  • Benarroch-Popivker, D., Pisano, S., Mendez-Bermudez, A., Lototska, L., Kaur, P., Bauwens, S., Djerbi, N., Latrick, C.M., Fraisier, V., Pei, B., Gay, A., Jaune, E., Foucher, K., Cherfils-Vicini, J., Aeby, E., Miron, S., Londono-Vallejo, A., Ye, J., Le Du, M.H., Wang, H., Gilson, E. and Giraud-Panis, M.J.(2016) TRF2-Mediated Control of Telomere DNA Topology as a Mechanism for Chromosome-End Protection. Mol Cell, 61, 274-286.
                    Mol Cell
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                  • Wu, D., Kaur, P., Li, Z.M., Bradford, K.C., Wang, H. and Erie, D.A. (2016)Visualizing the Path of DNA through Proteins Using DREEM Imaging. Mol Cell, 61, 315-323.
                    Mol Cell
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            2015

                  • Roushan, M., Azad, Z., Lim, S. F., Wang, H., and Riehn, R. (2015) Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels. Microchim Acta 182, 1561-1565
                    Microchim Acta
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                  • Parikh, D., Fouquerel, E., Murphy, C.T., Wang, H. and Opresko, P.L.(2015) Telomeres are partly shielded from ultraviolet-induced damage and proficient for nucleotide excision repair of photoproducts. Nature communications, 6, 8214.
                    Nature Communications
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            2014

                  • Roushan, M., Kaur, P., Karpusenko, A., Peston J. C., Ortiz, C. P. Lim, S. F.,Wang, H. and Riehn, R.(2014) Probing transient protein-mediated DNA linkages using nanoconfinement, Biomicrofluidics
                    Biomicrofluidics
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                  • Lin, J., Kaur, P., Countryman, P., Opresko, P. L., and Wang, H. (2014) Unraveling secrets of telomeres: one molecule at a time. DNA repair 20, 142-153
                    PUBMED
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                  • Ghodke, H., Wang, H., Hsieh, C.L., Woldemeskel, S., Watkins, S.C., Rapic-Otrin, V. and Van Houten, B.(2014) Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates. Proceedings of the National Academy of Sciences of the United States of America, 111, E1862-1871.
                    NCBI
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                    UV-DBB in the news
                  • Lin, J., Countryman, P., Buncher, N., Kaur, P., E, L., Zhang, Y., Gibson, G., You, C., Watkins, S.C., Piehler, Opesko, L. P., Kad, N., Wang, H.(2014) 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, 42, 2493-2504.
                    NAR
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            BEFORE 2014

                • Tessmer, I., Kaur, P., Lin, J. and Wang, H. (2013) Investigating bioconjugation by atomic force microscopy. Journal of nanobiotechnology, 11, 25.
                  PUBMED
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                • Lormand, J.D., Buncher, N., Murphy, C.T., Kaur, P., Lee, M.Y., Burgers, P., Wang, H., Kunkel, T.A. and Opresko, P.L. (2013) DNA polymerase delta stalls on telomeric lagging strand templates independently from G-quadruplex formation. Nucleic Acids Res, 41, 10323-10333.
                  PUBMED 
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                • Hughes, C.D., Wang, H., Ghodke, H., Simons, M., Towheed, A., Peng, Y., Van Houten, B. and Kad, N.M. (2013) Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes. Nucleic Acids Res, 41, 4901-4912.
                  NAR 
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                • Yeh, J.I., Levine, A.S., Du, S., Chinte, U., Ghodke, H., Wang, H., Shi, H., Hsieh, C.L., Conway, J.F., Van Houten, B. et al. (2012) Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Proceedings of the National Academy of Sciences of the United States of America, 109, E2737-2746.
                  PUBMED
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                • Damerla, R.R., Knickelbein, K.E., Strutt, S., Liu, F.J., Wang, H. and Opresko, P.L. (2012) Werner syndrome protein suppresses the formation of large deletions during the replication of human telomeric sequences. Cell cycle, 11, 3036-3044.
                  PUBMED
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                • Wang, H., Nora, G.J., Ghodke, H. and Opresko, P.L. (2011) Single molecule studies of physiologically relevant telomeric tails reveal POT1 mechanism for promoting G-quadruplex unfolding. J Biol Chem, 286, 7479-7489.
                  PUBMED
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                • Fronczek, D.N., Quammen, C., Wang, H., Kisker, C., Superfine, R., Taylor, R., Erie, D.A. and Tessmer, I. (2011) High accuracy FIONA-AFM hybrid imaging. Ultramicroscopy, 111, 350-355.
                  PUBMED
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                • Peng, Y., Wang, H., Santana-Santos, L., Kisker, C., and Van Houten, B. (2011) Nucleotide Excision Repair from Bacteria to Humans: Structure-Function Studies Current Cancer Research, 267-296
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                • Kad, N.M., Wang, H., Kennedy, G.G., Warshaw, D.M. and Van Houten, B. (2010) Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single- molecule imaging of quantum-dot-labeled proteins. Mol Cell, 37, 702-713.
                  PUBMED
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                • Sowd, G., Wang, H., Pretto, D., Chazin, W.J. and Opresko, P.L. (2009) Replication protein a stimulates the werner syndrome protein branch migration activity. J Biol Chem, 284, 34682-34691.
                  PUBMED
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                • Opresko, P.L., Sowd, G. and Wang, H. (2009) The Werner syndrome helicase/exonuclease processes mobile D-loops through branch migration and degradation. PLoS ONE, 4, e4825.
                  PUBMED
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                • Wang, H., Tessmer, I., Croteau, D.L., Erie, D.A. and Van Houten, B. (2008) Functional characterization and atomic force microscopy of a DNA repair protein conjugated to a quantum dot. Nano Lett, 8, 1631-1637.
                  PUBMED
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                • Christensen, L.A., Wang, H., Van Houten, B. and Vasquez, K.M. (2008) Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease. Nucleic Acids Res, 36, 7136-7145.PUBMED 
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                • Wang, H., Yang, Y. and Erie, D.A. (2007) Characterization of Protein-protein Interactions Using Atomic Force Microscopy. Protein Interactions-Biophysical methodology for multi-component systems (Kluwer/Plenum).
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                • Christensen, L. A., Wang, H., Van Houten, B., and Vasquez, K. M. (2008) Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease. Nucleic Acids Res 36, 7136-7145
                  NAR
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                • Wang, H., DellaVecchia, M.J., Skorvaga, M., Croteau, D.L., Erie, D.A. and Van Houten, B. (2006) UvrB domain 4, an autoinhibitory gate for regulation of DNA binding and ATPase activity. J Biol Chem, 281, 15227-15237.
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                • Truglio, J.J., Karakas, E., Rhau, B., Wang, H., DellaVecchia, M.J., Van Houten, B. and Kisker, C. (2006) Structural basis for DNA recognition and processing by UvrB. Nat Struct Mol Biol, 13, 360-364.
                  PUBMED
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                • Croteau, D.L., DellaVecchia, M.J., Wang, H., Bienstock, R.J., Melton, M.A. and Van Houten, B. (2006) The C-terminal zinc finger of UvrA does not bind DNA directly but regulates damage-specific DNA binding. J Biol Chem, 281, 26370-26381.
                  PUBMED
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                • Van Houten, B., Croteau, D.L., Dellavecchia, M.J., Wang, H. and Kisker, C. (2005) ‘Close-fitting sleeves’: DNA damage recognition by the UvrABC nuclease system. Mutat Res, 577, 92-117.
                  PUBMED
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                • Truglio, J.J., Rhau, B., Croteau, D.L., Wang, L., Skorvaga, M., Karakas, E., DellaVecchia, M.J., Wang, H., Van Houten, B. and Kisker, C. (2005) Structural insights into the first incision reaction during nucleotide excision repair. EMBO J, 24, 885-894.
                  PUBMED
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                • Yang, Y., Wang, H. and Erie, D.A. (2003) Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy. Methods, 29, 175-187.
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                • Wang, H., Yang, Y., Schofield, M.J., Du, C., Fridman, Y., Lee, S.D., Larson, E.D., Drummond, J.T., Alani, E., Hsieh, P. et al. (2003) DNA bending and unbending by MutS govern mismatch recognition and specificity. Proceedings of the National Academy of Sciences of the United States of America, 100, 14822-14827.
                  PNAS
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                • Bao, K. K., Wang, H., Miller, J. K., Erie, D. A., Skalka, A. M., and Wong, I. (2003) Functional oligomeric state of avian sarcoma virus integrase. J Biol Chem 278, 1323-1327
                  JBC
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                • Xue, Y., Ratcliff, G.C., Wang, H., Davis-Searles, P.R., Gray, M.D., Erie, D.A. and Redinbo, M.R. (2002) A minimal exonuclease domain of WRN forms a hexamer on DNA and possesses both 3′- 5′ exonuclease and 5′-protruding strand endonuclease activities. Biochemistry, 41, 2901-2912.
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                • Drotschmann, K., Hall, M.C., Shcherbakova, P.V., Wang, H., Erie, D.A., Brownewell, F.R., Kool, E.T. and Kunkel, T.A. (2002) DNA binding properties of the yeast Msh2-Msh6 and Mlh1-Pms1 heterodimers. Biol Chem, 383, 969-975.
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                • Hall, M. C., Wang, H., Erie, D. A., and Kunkel, T. A. (2001) High affinity cooperative DNA binding by the yeast Mlh1-Pms1 heterodimer. J Mol Biol 312, 637-647
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