Yamuna Krishnan

Biosciences Graduate Program Association
Publications
  1. Veetil AT, Zou J, Henderson KW, Jani MS, Shaik SM, Sisodia SS, Hale ME, Krishnan Y. DNA-based fluorescent probes of NOS2 activity in live brains. Proc Natl Acad Sci U S A. 2020 Jun 30; 117(26):14694-14702. View in: PubMed

  2. Jani MS, Veetil AT, Krishnan Y. Controlled release of bioactive signaling molecules. Methods Enzymol. 2020; 638:129-138. View in: PubMed

  3. Saminathan A, Noyola VS, Krishnan Y. Chemically Resolving Lysosome Populations in Live Cells. Trends Biochem Sci. 2020 Apr; 45(4):365-366. View in: PubMed

  4. Jani MS, Zou J, Veetil AT, Krishnan Y. A DNA-based fluorescent probe maps NOS3 activity with subcellular spatial resolution. Nat Chem Biol. 2020 Jun; 16(6):660-666. View in: PubMed

  5. Zajac M, Chakraborty K, Saha S, Mahadevan V, Infield DT, Accardi A, Qiu Z, Krishnan Y. What biologists want from their chloride reporters - a conversation between chemists and biologists. J Cell Sci. 2020 01 23; 133(2). View in: PubMed

  6. Sayresmith NA, Saminathan A, Sailer JK, Patberg SM, Sandor K, Krishnan Y, Walter MG. 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

  7. Sayresmith NA, Saminathan A, Sailer JK, Patberg SM, Sandor K, Krishnan Y, Walter MG. Photostable Voltage-Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles. J Am Chem Soc. 2019 11 27; 141(47):18780-18790. View in: PubMed

  8. Leung K, Krishnan Y. Dynamic RNA Nanotechnology Enters the CRISPR Toolbox. ACS Cent Sci. 2019 Jul 24; 5(7):1111-1113. View in: PubMed

  9. Krishnan Y, Seeman NC. Introduction: Nucleic Acid Nanotechnology. Chem Rev. 2019 05 22; 119(10):6271-6272. View in: PubMed

  10. Sharma S, Zajac M, Krishnan Y. A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition. Chembiochem. 2020 01 15; 21(1-2):157-162. View in: PubMed

  11. Dan K, Veetil AT, Chakraborty K, Krishnan Y. DNA nanodevices map enzymatic activity in organelles. Nat Nanotechnol. 2019 03; 14(3):252-259. View in: PubMed

  12. Prakash V, Tsekouras K, Venkatachalapathy M, Heinicke L, Pressé S, Walter NG, Krishnan Y. 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

  13. Narayanaswamy N, Chakraborty K, Saminathan A, Zeichner E, Leung K, Devany J, Krishnan Y. Author Correction: A pH-correctable, DNA-based fluorescent reporter for organellar calcium. Nat Methods. 2019 Feb; 16(2):205. View in: PubMed

  14. Narayanaswamy N, Chakraborty K, Saminathan A, Zeichner E, Leung K, Devany J, Krishnan Y. A pH-correctable, DNA-based fluorescent reporter for organellar calcium. Nat Methods. 2019 01; 16(1):95-102. View in: PubMed

  15. Thekkan S, Jani MS, Cui C, Dan K, Zhou G, Becker L, Krishnan Y. A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome. Nat Chem Biol. 2019 12; 15(12):1165-1172. View in: PubMed

  16. Leung K, Chakraborty K, Saminathan A, Krishnan Y. A DNA nanomachine chemically resolves lysosomes in live cells. Nat Nanotechnol. 2019 02; 14(2):176-183. View in: PubMed

  17. Salgado EN, Garcia Rodriguez B, Narayanaswamy N, Krishnan Y, Harrison SC. Visualization of Calcium Ion Loss from Rotavirus during Cell Entry. J Virol. 2018 12 15; 92(24). View in: PubMed

  18. Prakash V, Saha S, Chakraborty K, Krishnan Y. 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

  19. Veetil AT, Jani MS, Krishnan Y. 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

  20. Devany J, Chakraborty K, Krishnan Y. Subcellular Nanorheology Reveals Lysosomal Viscosity as a Reporter for Lysosomal Storage Diseases. Nano Lett. 2018 02 14; 18(2):1351-1359. View in: PubMed

  21. Banerjee A, Grazon C, Pons T, Bhatia D, Valades-Cruz CA, Johannes L, Krishnan Y, Dubertret B. 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

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

  23. Veetil AT, Chakraborty K, Xiao K, Minter MR, Sisodia SS, Krishnan Y. Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nat Nanotechnol. 2017 12; 12(12):1183-1189. View in: PubMed

  24. Chakraborty K, Leung K, Krishnan Y. High lumenal chloride in the lysosome is critical for lysosome function. Elife. 2017 07 25; 6. View in: PubMed

  25. Patel A, Malinovska L, Saha S, Wang J, Alberti S, Krishnan Y, Hyman AA. ATP as a biological hydrotrope. Science. 2017 05 19; 356(6339):753-756. View in: PubMed

  26. Joshi H, Bhatia D, Krishnan Y, Maiti PK. 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

  27. Bhatia D, Arumugam S, Nasilowski M, Joshi H, Wunder C, Chambon V, Prakash V, Grazon C, Nadal B, Maiti PK, Johannes L, Dubertret B, Krishnan Y. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nat Nanotechnol. 2016 12; 11(12):1112-1119. View in: PubMed

  28. Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem. 2016 Jun 02; 85:349-73. View in: PubMed

  29. Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T. Voices of biotech. Nat Biotechnol. 2016 Mar; 34(3):270-5. View in: PubMed

  30. Surana S, Shenoy AR, Krishnan Y. Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nat Nanotechnol. 2015 Sep; 10(9):741-7. View in: PubMed

  31. Saha S, Prakash V, Halder S, Chakraborty K, Krishnan Y. 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

  32. Lannes L, Halder S, Krishnan Y, Schwalbe H. Tuning the pH Response of i-Motif DNA Oligonucleotides. Chembiochem. 2015 Jul 27; 16(11):1647-56. View in: PubMed

  33. Banerjee A, Grazon C, Nadal B, Pons T, Krishnan Y, Dubertret B. 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

  34. Halder S, Krishnan Y. Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. Nanoscale. 2015 Jun 14; 7(22):10008-12. View in: PubMed

  35. Sharma S, Zaveri A, Visweswariah SS, Krishnan Y. 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

  36. Ghosh A, Krishnan Y. At a long-awaited turning point. Nat Nanotechnol. 2014 Jul; 9(7):491-4. View in: PubMed

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

  38. Ganesh KN, Krishnan Y. Nucleic acids--chemistry and applications. J Org Chem. 2013 Dec 20; 78(24):12283-7. View in: PubMed

  39. Ganesh KN, Krishnan Y. Nucleic acids--chemistry and applications. Org Lett. 2013 Dec 20; 15(24):6115. View in: PubMed

  40. Modi S, Halder S, Nizak C, Krishnan Y. Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale. 2014 Jan 21; 6(2):1144-52. View in: PubMed

  41. Banerjee A, Bhatia D, Saminathan A, Chakraborty S, Kar S, Krishnan Y. 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

  42. Modi S, Nizak C, Surana S, Halder S, Krishnan Y. 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

  43. Surana S, Bhatia D, Krishnan Y. A method to study in vivo stability of DNA nanostructures. Methods. 2013 Nov; 64(1):94-100. View in: PubMed

  44. Bhatia D, Chakraborty S, Mehtab S, Krishnan Y. A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol Biol. 2013; 991:65-80. View in: PubMed

  45. Surana S, Krishnan Y. 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

  46. Krishnan Y, Bathe M. Designer nucleic acids to probe and program the cell. Trends Cell Biol. 2012 Dec; 22(12):624-33. View in: PubMed

  47. Bhatia D, Chakraborty S, Krishnan Y. Gene delivery: Designer DNA give RNAi more spine. Nat Nanotechnol. 2012 Jun 03; 7(6):344-6. View in: PubMed

  48. Chakraborty S, Mehtab S, Patwardhan A, Krishnan Y. Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing. RNA. 2012 May; 18(5):1014-28. View in: PubMed

  49. Saha S, Chakraborty K, Krishnan Y. Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation. Chem Commun (Camb). 2012 Mar 04; 48(19):2513-5. View in: PubMed

  50. Modi S, Krishnan Y. 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

  51. Surana S, Bhat JM, Koushika SP, Krishnan Y. An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism. Nat Commun. 2011 Jun 07; 2:340. View in: PubMed

  52. Bhatia D, Surana S, Chakraborty S, Koushika SP, Krishnan Y. A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Nat Commun. 2011 Jun 07; 2:339. View in: PubMed

  53. Bhatia D, Sharma S, Krishnan Y. Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol. 2011 Aug; 22(4):475-84. View in: PubMed

  54. Krishnan Y, Simmel FC. Nucleic acid based molecular devices. Angew Chem Int Ed Engl. 2011 Mar 28; 50(14):3124-56. View in: PubMed

  55. Saha S, Bhatia D, Krishnan Y. 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

  56. Modi S, M G S, Goswami D, Gupta GD, Mayor S, Krishnan Y. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol. 2009 May; 4(5):325-30. View in: PubMed

  57. Chakraborty S, Sharma S, Maiti PK, Krishnan Y. 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

  58. Bhatia D, Mehtab S, Krishnan R, Indi SS, Basu A, Krishnan Y. Icosahedral DNA nanocapsules by modular assembly. Angew Chem Int Ed Engl. 2009; 48(23):4134-7. View in: PubMed

  59. Paul A, Sengupta P, Krishnan Y, Ladame S. 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

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

  61. Chakraborty S, Krishnan Y. 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

  62. Ghodke HB, Krishnan R, Vignesh K, Kumar GV, Narayana C, Krishnan Y. 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

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

  64. Modi S, Wani AH, Krishnan Y. 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