@article{neikirk_marshall_kula_smith_leblanc_hinton_2023, title={MitoTracker: A useful tool in need of better alternatives}, volume={102}, ISSN={["1618-1298"]}, DOI={10.1016/j.ejcb.2023.151371}, abstractNote={The fluorescence viewing of mitochondria is commonly performed by MitoTracker, a lipophilic cationic dye that is taken up by the mitochondria. In this forum, we highlight several issues that may occur with MitoTracker, including staining of other organelles. Our aim is to offer alternative dyes and discuss their advantages and disadvantages. We also offer options for software with alternatives to MitoTracker to expedite future experimental design.}, number={4}, journal={EUROPEAN JOURNAL OF CELL BIOLOGY}, author={Neikirk, Kit and Marshall, Andrea G. and Kula, Bartosz and Smith, Nathan and Leblanc, Sharonda and Hinton, Antentor}, year={2023}, month={Dec} }
 @article{hao_leblanc_case_elston_hingorani_erie_weninger_2020, title={Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby}, volume={117}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1918517117}, abstractNote={Significance}, number={30}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Hao, Pengyu and LeBlanc, Sharonda J. and Case, Brandon C. and Elston, Timothy C. and Hingorani, Manju M. and Erie, Dorothy A. and Weninger, Keith R.}, year={2020}, month={Jul}, pages={17775–17784} }
 @article{leblanc_gauer_hao_case_hingorani_weninger_erie_2018, title={Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS}, volume={46}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gky865}, abstractNote={Abstract MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein–DNA and DNA–DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.}, number={20}, journal={NUCLEIC ACIDS RESEARCH}, author={LeBlanc, Sharonda J. and Gauer, Jacob W. and Hao, Pengyu and Case, Brandon C. and Hingorani, Manju M. and Weninger, Keith R. and Erie, Dorothy A.}, year={2018}, month={Nov}, pages={10782–10795} }
 @misc{leblanc_kulkarni_weninger_2018, title={Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins}, volume={8}, ISSN={["2218-273X"]}, DOI={10.3390/biom8040140}, abstractNote={Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.}, number={4}, journal={BIOMOLECULES}, author={LeBlanc, Sharonda J. and Kulkarni, Prakash and Weninger, Keith R.}, year={2018}, month={Dec} }