@article{kaur_longley_pan_wang_countryman_wang_copeland_2020, title={Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase}, volume={295}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.RA120.012795}, abstractNote={Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA–binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.}, number={17}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Kaur, Parminder and Longley, Matthew J. and Pan, Hai and Wang, Wendy and Countryman, Preston and Wang, Hong and Copeland, William C.}, year={2020}, month={Apr}, pages={5564–5576} }
 @article{kaur_wu_lin_countryman_bradford_erie_riehn_opresko_wang_2016, title={Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2}, volume={6}, journal={Scientific Reports}, author={Kaur, P. and Wu, D. and Lin, J. G. and Countryman, P. and Bradford, K. C. and Erie, D. A. and Riehn, R. and Opresko, P. L. and Wang, H.}, year={2016} }
 @article{lin_countryman_chen_pan_fan_jiang_kaur_miao_gurgel_you_et al._2016, title={Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA-DNA pairing}, volume={44}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkw518}, abstractNote={Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids. Cohesion is thought to occur through the entrapment of DNA within the tripartite ring (Smc1, Smc3 and Rad21) with enforcement from a fourth subunit (SA1/SA2). Surprisingly, cohesin rings do not play a major role in sister telomere cohesion. Instead, this role is replaced by SA1 and telomere binding proteins (TRF1 and TIN2). Neither the DNA binding property of SA1 nor this unique telomere cohesion mechanism is understood. Here, using single-molecule fluorescence imaging, we discover that SA1 displays two-state binding on DNA: searching by one-dimensional (1D) free diffusion versus recognition through subdiffusive sliding at telomeric regions. The AT-hook motif in SA1 plays dual roles in modulating non-specific DNA binding and subdiffusive dynamics over telomeric regions. TRF1 tethers SA1 within telomeric regions that SA1 transiently interacts with. SA1 and TRF1 together form longer DNA–DNA pairing tracts than with TRF1 alone, as revealed by atomic force microscopy imaging. These results suggest that at telomeres cohesion relies on the molecular interplay between TRF1 and SA1 to promote DNA–DNA pairing, while along chromosomal arms the core cohesin assembly might also depend on SA1 1D diffusion on DNA and sequence-specific DNA binding.}, number={13}, journal={NUCLEIC ACIDS RESEARCH}, author={Lin, Jiangguo and Countryman, Preston and Chen, Haijiang and Pan, Hai and Fan, Yanlin and Jiang, Yunyun and Kaur, Parminder and Miao, Wang and Gurgel, Gisele and You, Changjiang and et al.}, year={2016}, month={Jul}, pages={6363–6376} }
 @article{roushan_kaur_karpusenko_countryman_ortiz_lim_wang_riehn_2014, title={Probing transient protein-mediated DNA linkages using nanoconfinement}, volume={8}, number={3}, journal={Biomicrofluidics}, author={Roushan, M. and Kaur, P. and Karpusenko, A. and Countryman, P. J. and Ortiz, C. P. and Lim, S. F. and Wang, H. and Riehn, R.}, year={2014} }
 @inproceedings{lin_kaur_chen_countryman_roushan_flaherty_brennan_you_piehler_riehn_et al._2014, title={Single-molecule imaging reveals DNA-binding properties of cohesin proteins SA1 and SA2.}, volume={55}, booktitle={Environmental and Molecular Mutagenesis}, author={Lin, J. and Kaur, P. and Chen, H. and Countryman, P. and Roushan, M. and Flaherty, D. and Brennan, E. and You, C. and Piehler, J. and Riehn, R. and et al.}, year={2014}, pages={S29–29} }
 @article{lin_countryman_buncher_kaur_longjiang_zhang_gibson_you_watkins_piehler_et al._2014, title={TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres}, volume={42}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkt1132}, abstractNote={Abstract}, number={4}, journal={NUCLEIC ACIDS RESEARCH}, author={Lin, Jiangguo and Countryman, Preston and Buncher, Noah and Kaur, Parminder and Longjiang, E. and Zhang, Yiyun and Gibson, Greg and You, Changjiang and Watkins, Simon C. and Piehler, Jacob and et al.}, year={2014}, month={Feb}, pages={2493–2504} }
 @article{lin_kaur_countryman_opresko_wang_2014, title={Unraveling secrets of telomeres: One molecule at a time}, volume={20}, ISSN={["1568-7856"]}, DOI={10.1016/j.dnarep.2014.01.012}, abstractNote={Telomeres play important roles in maintaining the stability of linear chromosomes. Telomere maintenance involves dynamic actions of multiple proteins interacting with long repetitive sequences and complex dynamic DNA structures, such as G-quadruplexes, T-loops and t-circles. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure-function relationships that govern telomere maintenance. In this review, we present a brief overview of the principles of single-molecule imaging and manipulation techniques. We then highlight results obtained from applying these single-molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins.}, journal={DNA REPAIR}, author={Lin, Jiangguo and Kaur, Parminder and Countryman, Preston and Opresko, Patricia L. and Wang, Hong}, year={2014}, month={Aug}, pages={142–153} }