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DNA

  • 1.
    King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887
    Reference Link
  • 1.
    Lukasak B, Mitchener M, Kong L, Dul B, Lazarus C, Ramakrishnan A, Ni J, Shen L, Maze I, Muir T. TGM2-mediated histone transglutamination is dictated by steric accessibility. Proc Natl Acad Sci U S A. 2022;119(43):e2208672119. PMCID: PMC9618071
    Reference Link
  • 1.
    Landajuela A, Braun M, Martínez-Calvo A, Rodrigues C, Perez C, Doan T, Rudner D, Wingreen N, Karatekin E. Membrane fission during bacterial spore development requires cellular inflation driven by DNA translocation. Curr Biol. 2022;32(19):4186–4200.e8. PMCID: PMC9730832
    Reference Link
  • 1.
    Justice J, Cristea I. Nuclear antiviral innate responses at the intersection of DNA sensing and DNA repair. Trends Microbiol. 2022;30(11):1056–1071. PMCID: PMC9560981
    Reference Link
  • 1.
    Jack A, Kim Y, Strom A, Lee D, Williams B, Schaub J, Kellogg E, Finkelstein I, Ferro L, Yildiz A, Brangwynne C. Compartmentalization of telomeres through DNA-scaffolded phase separation. Dev Cell. 2022;57(2):277–290.e9. PMCID: PMC8988007
    Reference Link
  • 1.
    Dao H, Liu H, Mashtalir N, Kadoch C, Muir T. Synthesis of Oriented Hexasomes and Asymmetric Nucleosomes Using a Template Editing Process. J Am Chem Soc. 2022;144(5):2284–2291. PMCID: PMC8935522
    Reference Link
  • 1.
    Chen P, Hussmann J, Yan J, Knipping F, Ravisankar P, Chen P-F, Chen C, Nelson J, Newby G, Sahin M, Osborn M, Weissman J, Adamson B, Liu D. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22):5635–5652.e29. PMCID: PMC8584034
    Reference Link
  • 1.
    Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948
    Reference Link
  • 1.
    Mitchener M, Muir T. Janus Bioparticles: Asymmetric Nucleosomes and Their Preparation Using Chemical Biology Approaches. Acc Chem Res. 2021;54(16):3215–3227. PMCID: PMC8411803
    Reference Link
  • 1.
    Anlas A, Nelson C. Living under Strain: How Epithelia Protect Their Genomes from Repeated Stretching. Biochemistry. 2020;59(30):2761–2763. PMID: 32702973
    Reference Link
  • 1.
    Valastyan J, Tota M, Taylor I, Stergioula V, Hone G, Smith C, Henke B, Carson K, Bassler B. Discovery of PqsE Thioesterase Inhibitors for Using DNA-Encoded Small Molecule Library Screening. ACS Chem Biol. 2020;15(2):446–456. PMCID: PMC7036018
    Reference Link
  • 1.
    Huang X, Duddy O, Silpe J, Paczkowski J, Cong J, Henke B, Bassler B. Mechanism underlying autoinducer recognition in the DPO-VqmA quorum-sensing pathway. J Biol Chem. 2020;295(10):2916–2931. PMCID: PMC7062168
    Reference Link
  • 1.
    Yan J, Cirincione A, Adamson B. Prime Editing: Precision Genome Editing by Reverse Transcription. Mol Cell. 2020;77(2):210–212. PMID: 31951546
    Reference Link
  • 1.
    Howard T, Song B, Cristea I. Workflows and considerations for investigating protein interactions of viral DNA sensors. Methods Enzymol. 2019;625:309–338. PMCID: PMC6889811
    Reference Link
  • 1.
    DeCandia A, Leverett K, vonHoldt B. Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites. Parasit Vectors. 2019;12(1):488. PMCID: PMC6796464
    Reference Link
  • 1.
    Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845
    Reference Link
  • 1.
    Kachaev Z, Lebedeva L, Shaposhnikov A, Moresco J, Yates J, Schedl P, Shidlovskii Y. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett. 2019;593(10):1102–1112. PMCID: PMC6538421
    Reference Link
  • 1.
    Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol. 2018;14(6):e1006290. PMCID: PMC6040777
    Reference Link
  • 1.
    Liszczak G, Diehl K, Dann G, Muir T. Acetylation blocks DNA damage-induced chromatin ADP-ribosylation. Nat Chem Biol. 2018;14(9):837–840. PMCID: PMC6505472
    Reference Link
  • 1.
    Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu J-K, Shi Y, Yan N. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 2012;335(6069):720–3. PMCID: PMC3586824
    Reference Link
  • 1.
    Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu J-K, Yan N, Shi Y. Recognition of methylated DNA by TAL effectors. Cell Res. 2012;22(10):1502–4. PMCID: PMC3463267
    Reference Link
  • 1.
    Yin P, Deng D, Yan C, Pan X, Xi J, Yan N, Shi Y. Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep. 2012;2(4):707–13. PMID: 23022487
    Reference Link
  • 1.
    Deng D, Yan C, Wu J, Pan X, Yan N. Revisiting the TALE repeat. Protein Cell. 2014;5(4):297–306. PMCID: PMC3978159
    Reference Link
  • 1.
    Wang X, Paucek R, Gooding A, Brown Z, Ge E, Muir T, Cech T. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017;24(12):1028–1038. PMCID: PMC5771497
    Reference Link
  • 1.
    Webb C, Zakian V. Telomerase RNA is more than a DNA template. RNA Biol. 2016;13(8):683–9. PMCID: PMC4993324
    Reference Link
  • 1.
    Garcia H, Gregor T. Live Imaging of mRNA Synthesis in Drosophila. Methods Mol Biol. 2018;1649:349–357. PMCID: PMC5909709
    Reference Link
  • 1.
    David Y, Muir T. Emerging Chemistry Strategies for Engineering Native Chromatin. J Am Chem Soc. 2017;139(27):9090–9096. PMCID: PMC5752102
    Reference Link
  • 1.
    Geronimo C, Zakian V. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst). 2016;44:151–158. PMCID: PMC5441554
    Reference Link
  • 1.
    Snir S, vonHoldt B, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016;12(11):e1005183. PMCID: PMC5106012
    Reference Link
  • 1.
    Persikov A, Wetzel J, Rowland E, Oakes B, Xu D, Singh M, Noyes M. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 2015;43(3):1965–84. PMCID: PMC4330361
    Reference Link
  • 1.
    Su X, Wellen K, Rabinowitz J. Metabolic control of methylation and acetylation. Curr Opin Chem Biol. 2016;30:52–60. PMCID: PMC4731252
    Reference Link
  • 1.
    Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol. 2010;6(6):e1000801. PMCID: PMC2880562
    Reference Link
  • 1.
    Chen G, Swem L, Swem D, Stauff D, O’Loughlin C, Jeffrey P, Bassler B, Hughson F. A strategy for antagonizing quorum sensing. Mol Cell. 2011;42(2):199–209. PMCID: PMC3092643
    Reference Link

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