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  4. Yamuna Krishnan

Yamuna Krishnan

Professor
yamuna@uchicago.edu
Biosciences Graduate Program Association
Publications

  1. Plasma membrane depolarization reveals endosomal escape incapacity of cell-penetrating peptides. Eur J Pharm Biopharm. 2023 Mar; 184:116-124. View in: PubMed

  2. The evolution of organellar calcium mapping technologies. Cell Calcium. 2022 12; 108:102658. View in: PubMed

  3. A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours. Nat Nanotechnol. 2021 12; 16(12):1394-1402. View in: PubMed

  4. Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis. Proc Natl Acad Sci U S A. 2021 10 12; 118(41). View in: PubMed

  5. New Vistas for Cell-Surface GlycoRNAs. N Engl J Med. 2021 Aug 12; 385(7):658-660. View in: PubMed

  6. Tissue-specific targeting of DNA nanodevices in a multicellular living organism. Elife. 2021 07 28; 10. View in: PubMed

  7. Quantifying phagosomal HOCl at single immune-cell resolution. Methods Cell Biol. 2021; 164:119-136. View in: PubMed

  8. Proton-activated chloride channel PAC regulates endosomal acidification and transferrin receptor-mediated endocytosis. Cell Rep. 2021 01 26; 34(4):108683. View in: PubMed

  9. Quantitative Imaging of Biochemistry in Situ and at the Nanoscale. ACS Cent Sci. 2020 Nov 25; 6(11):1938-1954. View in: PubMed

  10. A DNA-based voltmeter for organelles. Nat Nanotechnol. 2021 01; 16(1):96-103. View in: PubMed

  11. DNA-based fluorescent probes of NOS2 activity in live brains. Proc Natl Acad Sci U S A. 2020 06 30; 117(26):14694-14702. View in: PubMed

  12. Controlled release of bioactive signaling molecules. Methods Enzymol. 2020; 638:129-138. View in: PubMed

  13. Chemically Resolving Lysosome Populations in Live Cells. Trends Biochem Sci. 2020 04; 45(4):365-366. View in: PubMed

  14. A DNA-based fluorescent probe maps NOS3 activity with subcellular spatial resolution. Nat Chem Biol. 2020 06; 16(6):660-666. View in: PubMed

  15. What biologists want from their chloride reporters - a conversation between chemists and biologists. J Cell Sci. 2020 01 23; 133(2). View in: PubMed

  16. Correction to "Photostable Voltage-Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles". J Am Chem Soc. 2020 Jan 29; 142(4):2083. View in: PubMed

  17. Photostable Voltage-Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles. J Am Chem Soc. 2019 11 27; 141(47):18780-18790. View in: PubMed

  18. Dynamic RNA Nanotechnology Enters the CRISPR Toolbox. ACS Cent Sci. 2019 Jul 24; 5(7):1111-1113. View in: PubMed

  19. Introduction: Nucleic Acid Nanotechnology. Chem Rev. 2019 05 22; 119(10):6271-6272. View in: PubMed

  20. A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition. Chembiochem. 2020 01 15; 21(1-2):157-162. View in: PubMed

  21. DNA nanodevices map enzymatic activity in organelles. Nat Nanotechnol. 2019 03; 14(3):252-259. View in: PubMed

  22. Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting. Angew Chem Int Ed Engl. 2019 03 04; 58(10):3073-3076. View in: PubMed

  23. Author Correction: A pH-correctable, DNA-based fluorescent reporter for organellar calcium. Nat Methods. 2019 Feb; 16(2):205. View in: PubMed

  24. A pH-correctable, DNA-based fluorescent reporter for organellar calcium. Nat Methods. 2019 01; 16(1):95-102. View in: PubMed

  25. A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome. Nat Chem Biol. 2019 12; 15(12):1165-1172. View in: PubMed

  26. A DNA nanomachine chemically resolves lysosomes in live cells. Nat Nanotechnol. 2019 02; 14(2):176-183. View in: PubMed

  27. Visualization of Calcium Ion Loss from Rotavirus during Cell Entry. J Virol. 2018 12 15; 92(24). View in: PubMed

  28. Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chem Sci. 2016 Mar 01; 7(3):1946-1953. View in: PubMed

  29. Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule. Proc Natl Acad Sci U S A. 2018 09 18; 115(38):9432-9437. View in: PubMed

  30. Subcellular Nanorheology Reveals Lysosomal Viscosity as a Reporter for Lysosomal Storage Diseases. Nano Lett. 2018 02 14; 18(2):1351-1359. View in: PubMed

  31. A novel type of quantum dot-transferrin conjugate using DNA hybridization mimics intracellular recycling of endogenous transferrin. Nanoscale. 2017 Oct 19; 9(40):15453-15460. View in: PubMed

  32. A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Res. 2017 Sep 19; 45(16):9694-9705. View in: PubMed

  33. Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nat Nanotechnol. 2017 12; 12(12):1183-1189. View in: PubMed

  34. High lumenal chloride in the lysosome is critical for lysosome function. Elife. 2017 07 25; 6. View in: PubMed

  35. ATP as a biological hydrotrope. Science. 2017 05 19; 356(6339):753-756. View in: PubMed

  36. Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations. Nanoscale. 2017 Mar 30; 9(13):4467-4477. View in: PubMed

  37. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nat Nanotechnol. 2016 12; 11(12):1112-1119. View in: PubMed

  38. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem. 2016 Jun 02; 85:349-73. View in: PubMed

  39. Voices of biotech. Nat Biotechnol. 2016 Mar; 34(3):270-5. View in: PubMed

  40. Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nat Nanotechnol. 2015 Sep; 10(9):741-7. View in: PubMed

  41. A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells. Nat Nanotechnol. 2015 Jul; 10(7):645-51. View in: PubMed

  42. Tuning the pH Response of i-Motif DNA Oligonucleotides. Chembiochem. 2015 Jul 27; 16(11):1647-56. View in: PubMed

  43. Fast, Efficient, and Stable Conjugation of Multiple DNA Strands on Colloidal Quantum Dots. Bioconjug Chem. 2015 Aug 19; 26(8):1582-9. View in: PubMed

  44. Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. Nanoscale. 2015 Jun 14; 7(22):10008-12. View in: PubMed

  45. A fluorescent nucleic acid nanodevice quantitatively images elevated cyclic adenosine monophosphate in membrane-bound compartments. Small. 2014 Nov 12; 10(21):4276-80. View in: PubMed

  46. At a long-awaited turning point. Nat Nanotechnol. 2014 Jul; 9(7):491-4. View in: PubMed

  47. The predictive power of synthetic nucleic acid technologies in RNA biology. Acc Chem Res. 2014 Jun 17; 47(6):1710-9. View in: PubMed

  48. Nucleic acids--chemistry and applications. J Org Chem. 2013 Dec 20; 78(24):12283-7. View in: PubMed

  49. Nucleic acids--chemistry and applications. Org Lett. 2013 Dec 20; 15(24):6115. View in: PubMed

  50. Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale. 2014 Jan 21; 6(2):1144-52. View in: PubMed

  51. Controlled release of encapsulated cargo from a DNA icosahedron using a chemical trigger. Angew Chem Int Ed Engl. 2013 Jul 01; 52(27):6854-7. View in: PubMed

  52. Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nat Nanotechnol. 2013 Jun; 8(6):459-67. View in: PubMed

  53. A method to study in vivo stability of DNA nanostructures. Methods. 2013 Nov; 64(1):94-100. View in: PubMed

  54. A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol Biol. 2013; 991:65-80. View in: PubMed

  55. A method to map spatiotemporal pH changes in a multicellular living organism using a DNA nanosensor. Methods Mol Biol. 2013; 991:9-23. View in: PubMed

  56. Designer nucleic acids to probe and program the cell. Trends Cell Biol. 2012 Dec; 22(12):624-33. View in: PubMed

  57. Gene delivery: Designer DNA give RNAi more spine. Nat Nanotechnol. 2012 Jun 03; 7(6):344-6. View in: PubMed

  58. Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing. RNA. 2012 May; 18(5):1014-28. View in: PubMed

  59. Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation. Chem Commun (Camb). 2012 Mar 04; 48(19):2513-5. View in: PubMed

  60. A method to map spatiotemporal pH changes inside living cells using a pH-triggered DNA nanoswitch. Methods Mol Biol. 2011; 749:61-77. View in: PubMed

  61. An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism. Nat Commun. 2011 Jun 07; 2:340. View in: PubMed

  62. A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Nat Commun. 2011 Jun 07; 2:339. View in: PubMed

  63. Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol. 2011 Aug; 22(4):475-84. View in: PubMed

  64. Nucleic acid based molecular devices. Angew Chem Int Ed Engl. 2011 Mar 28; 50(14):3124-56. View in: PubMed

  65. pH-Toggled DNA architectures: reversible assembly of three-way junctions into extended 1D architectures through A-motif formation. Small. 2010 Jun 21; 6(12):1288-92. View in: PubMed

  66. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol. 2009 May; 4(5):325-30. View in: PubMed

  67. The poly dA helix: a new structural motif for high performance DNA-based molecular switches. Nucleic Acids Res. 2009 May; 37(9):2810-7. View in: PubMed

  68. Icosahedral DNA nanocapsules by modular assembly. Angew Chem Int Ed Engl. 2009; 48(23):4134-7. View in: PubMed

  69. Combining G-quadruplex targeting motifs on a single peptide nucleic acid scaffold: a hybrid (3+1) PNA-DNA bimolecular quadruplex. Chemistry. 2008; 14(28):8682-9. View in: PubMed

  70. The RNA2-PNA2 hybrid i-motif-a novel RNA-based building block. Chem Commun (Camb). 2008 Jan 07; (1):70-2. View in: PubMed

  71. Kinetic hybrid i-motifs: intercepting DNA with RNA to form a DNA(2)-RNA(2) i-motif. Biochimie. 2008 Jul; 90(7):1088-95. View in: PubMed

  72. The I-tetraplex building block: rational design and controlled fabrication of robust 1D DNA scaffolds through non-Watson-Crick interactions. Angew Chem Int Ed Engl. 2007; 46(15):2646-9. View in: PubMed

  73. First blueprint, now bricks: DNA as construction material on the nanoscale. Chem Soc Rev. 2006 Nov; 35(11):1111-21. View in: PubMed

  74. The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization. Nucleic Acids Res. 2006; 34(16):4354-63. View in: PubMed
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