Recent publications

# - co-first authors; * - corresponding author(s)

  1. Zajac, M., Mukherjee,S. † , Anees, P. † , Oettinger, D., Henn, K., Srikumar, J., Zou, J., Saminathan. A. * , Krishnan, Y.* “A mechanism of lysosomal calcium entry.” Sci. Adv. 2024, 10, eadk2317.
  2. Anees, P., Saminathan, A., Rozmus, E. R., Di, A., Malik, A. B., Delisle, B. P.*, Krishnan, Y.* “Detecting organelle-specific activity of potassium channels with a DNA nanodevice.” Nat. Biotechnol. 2023 in press.
  3. Zou, J., Mitra, K., Anees, P., Oettinger, D., Ramirez, J., Veetil, A.T., Rao, R., Smith, J.A., Kratsios, P., Krishnan, Y.* “A DNA nanodevice maps sodium at single organelle resolution.” Nat. Biotechnol. 2023, in press.
  4. Rodriguez, R.*, Krishnan, Y.* “The chemistry of Next Generation Sequencing.” Nat. Biotechnol. 2023, 41, 1709-1715.
  5. Mitra, K., Krishnan, Y.* “Lightly counting membrane proteins in native nanodiscs.” Nat. Nanotechnol. 2024, 19, 5-6.
  6. Huang, L. S., Zhou, B., Toth, P. T., Krishnan, Y., Di, A., Malik, A.B.* “Endosomal Trafficking of Two Pore K + Efflux Channel TWIK2 to Plasmalemma Mediates NLRP3 Inflammasome Activation and Inflammatory Injury.” eLife, 2023, 12, e83842.
  7. Zhang, S. J., Anees, P., Krishnan, Y., Fai, T.G.*, Szostak, J. W.*, Wang, A.* “Passive endocytosis in protocells.” Proc. Natl. Acad. Sci. 2023 ,120, e2221064120.
  8. Serulla, M., Anees, P., Trofimenko, E., Kalia, T., Krishnan, Y., Widmann, C.* “Plasma membrane depolarization reveals endosomal escape incapacity of cell-penetrating peptides.” Eur. J. Pharm. Biopharm. 2023, 184, 116-124.
  9. Zajac, M., Modi, S., Krishnan, Y.* “The evolution of organellar calcium mapping technologies” Cell Calcium, 2022, 108, 102658.
  10. Saminathan, A., Zajac, M., Palapuravan, A., Krishnan, Y.* “Achieving Organelle-level Precision with Next- Generation Targeting Technologies.” Nature Reviews Materials, 2022, 7. 355-371.
  11. Suresh, B., Saminathan, A., Chakraborty, K., Cui, C., Becker, L.*, Krishnan, Y.* “Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis.” Proc. Natl. Acad. Sci. U.S.A, 2021, 118, e2113174118.
  12. Cui, C., Chakraborty, K. Tang, X. A., Schoenfelt, K. Q., Hoffman, A., Blank, A., Mcbeth, B., Pulliam, N. Reardon, C. A., Kulkarni, S., Vaisar, T., Ballabio, A., Krishnan, Y.*, Becker, L.* “A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumors.” Nature Nanotechnology, 2021, 16, 1394-1402.
  13. Nachtergaele, S. and Krishnan, Y. ” Cell Surface GlycoRNAs Open New Vistas.” New Engl. J. Med. 2021 385, 658-660.
  14. Chakraborty, K., Palapuravan, A., Surana, S., Martin, S., Aburas, J., Moutel, S., Perez, F., Koushika, S.P., Kratsios, P.* Krishnan, Y.* “Tissue specific targeting of DNA nanodevices in a multicellular living organism.” eLife, 2021, 10, e67830.
  15. Osei-Owusu, J., Yang, J., Leung, K., Ruan, Z., Lü,W. Krishnan, Y., Qiu, Z.*, “Proton-activated chloride channel PAC regulates endosomal acidification and transferrin receptor-mediated endocytosis.” Cell Reports 2021, 34, 108683.
  16. Saminathan, A., Devany, J., Veetil, A. T., Suresh, B., Pillai, K. S., Schwake, M., Krishnan, Y.* “A DNA- based voltmeter for organelles.” Nature Nanotechnology, 2021, 16, 96-103.
  17. Palapuravan, A., Zajac, M., Krishnan, Y.* “Quantifying phagosomal HOCl at single immune-cell resolution.” Meth. Cell Biol., 2020, 10.1016/bs.mcb.2020.10.006.
  18. Jana, S., Veetil A. T., Telu, S., Krishnan, Y., Pike, V. “Synthesis and Labeling of Potential PET Radioligands for Receptor Interacting Protein Kinase 1” J. Nucl. Med. 2020, 61, 1106.
  19. Krishnan, Y.*, Zou, J., Jani, M.S. “Quantitative imaging of biochemistry in situ and at the nanoscale.” ACS Cent. Sci., 2020, 6, 1938–1954.
  20. Veetil, A.T., Zou, J, Henderson, K. W., Jani, M.S., Shaik, S.M., Sisodia, S. S., Hale, M. E., Krishnan, Y.* “DNA-based fluorescent probes of NOS-2 activity in live brains.” Proc. Natl. Acad. Sci. USA, 2020, 117, 14694-14702.
  21. Jani, M. S., Veetil A. T., Krishnan, Y.* “Controlled release of bioactive signaling molecules.” Meth. Enzymol. 2020, 638, 129-138.
  22. Saminathan, A., Noyola, V., Krishnan, Y.* “Chemically resolving lysosome populations in live cells.” Trends in Biochem. Sci. 2020, 10.1016/j.tibs.2019.12.006.
  23. Jani, M. S., Zou, J., Veetil A.T., Krishnan, Y.* “A DNA-based fluorescent probe maps NOS3 activity with sub-cellular spatial resolution.” Nature Chem. Biol. 2020, 16, 660-666.
  24. Zajac, M., Chakraborty, K., Saha, S., Mahadevan, V., Infield, D., Accardi, A., Qiu, Z., Krishnan, Y.* “What biologists want from their chloride reporters: a conversation between chemists and biologists.” J. Cell Sci., 2020, jcs240390 doi: 10.1242/jcs.240390.
  25. Sayresmith, N., Saminathan, A., Sailer, J., Patberg, S., Sandor, K., Krishnan, Y., Walter, M.* “Photostable Voltage Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles.” J. Am. Chem. Soc., 2019, 10.1021/jacs.9b08959.
  26. Thekkan, S., Jani, M., Cui, C., Dan, K., Zhou, G., Becker, L.*, Krishnan, Y.* "A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome." Nature Chem. Biol. 2019, 15, 1165 –1172.
  27. Jani, M. S., Veetil, A.T., Krishnan, Y.* “Precision immunomodulation with synthetic nucleic acid technologies.” Nature Reviews Materials, 2019, 4, 451-485.
  28. Dan, K., Veetil, A. T., Chakraborty, K., Krishnan, Y.* “DNA nanodevices map enzymatic activity in organelles.” Nature Nanotechnology, 2019, 14, 252-257.
  29. Leung, K.H. # , Chakraborty, K. # , Saminathan, A., Krishnan, Y.* "A DNA nanomachine chemically resolves lysosomes in live cells." Nature Nanotechnology, 2019, 14, 176-183.
  30. Narayanaswamy, N. # , Chakraborty, K. # , Saminathan, A., Leung, K.H., Zeichner, E., Devany, J., Krishnan, Y.* "A pH-correctable, DNA-based fluorescent reporter for organellar Calcium." Nature Methods, 2019, 16, 95-102.
  31. Prakash, V., Tsekouras, K., Venkatachalapathy, M., Heineke, L., Presse, S., Walter, N.*, Krishnan, Y.* "Quantitative maps of endosomal DNA processing by single molecule counting." Angew. Chem. Int. Ed. 2019 58, 3073-77 (invited).
  32. Sharma, S., Zajac, M., Krishnan, Y.* “A DNA aptamer for cyclic adenosine monophosphate that shows adaptive recognition.” ChemBioChem, 2019, 10.1002/cbic.201900259. (invited)
  33. Krishnan, Y.,* Seeman, N. C.* “Introduction: Nucleic Acid Nanotechnology.” Chem. Rev. 2019, 119, 6271- 6272. (Foreword by the Editors for a Special Issue on Nucleic Acid Nanotechnology)
  34. Leung, K.H., Krishnan, Y.,* “Dynamic RNA nanotechnology enters the CRISPR toolbox.” ACS Cent. Sci.. 2019, 5, 1111. (News & Views)
  35. Veetil, A., Jani, M., Krishnan, Y.* “Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule” Proc. Natl. Acad. Sci. U.S.A. 2018, 115, 9432–9437. (invited)
  36. Salgado, E., Rodriguez, B. G., Narayanaswamy, N., Krishnan, Y., Harrison, S.C.* "Visualization of Ca 2+ loss from rotavirus during cell entry." J. Virol. 2018, 92, e01327-18.
  37. Devany, J., Chakraborty, K., Krishnan, Y.* "Sub-cellular nanorheology reveals lysosomal viscosity as a reporter of lysosomal storage diseases." Nano Letters 2018, 18, 1351-1359.
  38. Banerjee, A., Grazon, C., Pons, T., Bhatia, D., Valades-Cruz, C. A., 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, 9, 15453-60.
  39. Chakraborty, S., Krishnan, Y.* "A structural map of oncomiR-1 at single-nucleotide resolution." Nucleic Acids Res. 2017, 45, 9694–9705.
  40. Chakraborty, K., Leung, K., Krishnan, Y.* "High lumenal chloride in the lysosome is critical for lysosome function." eLife, 2017, 6, e28862.
  41. Patel, A., Malinovska, L, Saha, S., Wang, J., Alberti, S., Krishnan, Y.*, Hyman, A. A.*, “ATP is a biological hydrotrope.” Science, 2017, 356, 753-756.
  42. Veetil, A., Chakraborty, K., Xiao, K., Minter, M. R., Sisodia, S.S., Krishnan, Y.* "Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules." Nature Nanotechnology, 2017, 12, 1183–1189.
  43. Joshi, H., Bhatia, D., Krishnan, Y., Maiti, P.K.* "Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations." Nanoscale, 2017, 9, 4467-4477.
  44. Krishnan, Y. "Nano on Reflection." 10th anniversary issue. Nature Nanotechnology, 2016, 11, 831-832. (invited)
  45. Amit, I.; Baker, D.; Barker, R.; Berger, B., Bertozzi, C., et. al. "Voices of Biotech" 25th anniversary issue Nature Biotechnology, 2016, 34, 270-275. (invited)
  46. Bhatia, D., Arumugam, S., Nasilowski, M., Joshi, H., Wunder, C., Chambon, V., Prakash, V., Grazon, C., Nadal, B., Maiti, P.K., Johannes, L.*, Dubertret, B.*, Krishnan, Y.* "Quantum dot-loaded monofunctionalized DNA Icosahedra for single particle tracking of endocytic pathways." Nature Nanotechnology, 2016, 11, 1112-1119.
  47. Prakash, V., Saha, S., Chakraborty, K., Krishnan, Y.* Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chemical Science, 2016, 7, 1946 - 1953.
  48. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.,* Krishnan, Y.* Nucleic acid-based nanodevices in biological imaging. Ann. Rev. Biochem., 2016, 85, 349-73.
  49. Surana, S., Shenoy, A. R.*, Krishnan, Y.* Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 2015, 10, 734-747.
  50. Krishnan, Y.* Crack the cliques, enable visionaries. Nature, 2015, 521, 152.
  51. 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. Bioconjugate Chem. 2015, 26, 1582-89.
  52. Halder, S., Krishnan, Y.* Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices Nanoscale 2015, 7, 10008-10012.
  53. Lannes, L., Halder, S., Krishnan, Y., Schwalbe, H.* Tuning the pH-response of i-motif DNA oligonucleotides. ChemBioChem, 2015, 16, 1647-1656.
  54. Saha, S., Prakash, V., Halder, S., Chakraborty, K., Krishnan, Y.* A pH independent DNA nanodevice for quantifying chloride transport in organelles of living cells. Nature Nanotechnology, 2015, 10, 645-51.
  55. Ghosh, A., Krishnan, Y. At a long awaited turning point. Nature Nanotechnology, 2014, 9, 491-4.
  56. Sharma, S., Zaveri, A., Visweswariah, S. S., Krishnan, Y.* A fluorescent nucleic acid nanodevice quantitatively images elevated cyclic AMP in membrane-bound compartments. Small, 2014, 10, 4276- 80.
  57. Chakraborty, S., Mehtab, S., Krishnan, Y.* The predictive power of synthetic nucleic acid technologies in RNA biology. Accounts of Chemical Research, 2014, 47, 1710-1719.
  58. Modi, S., Halder, S., Nizak, C.,* Krishnan, Y.* Recombinant antibody mediated delivery of organelle- specific DNA pH sensors along endocytic pathways. Nanoscale, 2014, 6, 1144-1152.
  59. Ganesh, K. N.*, Krishnan, Y. Nucleic Acids – Chemistry and Applications. J. Org. Chem. 2013, 78, 12283- 12287.
  60. 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. 2013, 52, 6854- 6857.
  61. Surana, S., Bhatia, D., Krishnan, Y.* A method to study in vivo stability of DNA nanostructures. Methods, 2013, 64, 94-100.
  62. Modi, S., Nizak, C., Surana, S., Halder, S., Krishnan, Y.* Two DNA nanomachines map pH of intersecting endocytic pathways. Nature Nanotechnology, 2013, 8, 459-467.
  63. Bhatia, D., Chakraborty, S., Mehtab, S., Krishnan, Y.* A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol. Biol. 2013, 991, 65-80.
  64. 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.
  65. Krishnan, Y., Bathe, M. Designer Nucleic Acids to probe and program the Cell. Trends in Cell Biol. 2012, 22, 624-633.
  66. Bhatia, D., Chakraborty, S., Krishnan, Y.* Designer DNA gives RNAi more spine. Nature Nanotechnology, 2012, 7, 344-346.
  67. Chakraborty, S., Mehtab, S., Patwardhan, A.R., Krishnan, Y.* Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing. RNA, 2012, 18, 1014-1028.
  68. Tunable, colorimetric DNA based pH sensors mediated by A-motif formation. Saha, S., Chakraborty, K., Krishnan, Y.* Chem. Commun. 2012, 48, 2513-2515.
  69. A Method to Map Spatiotemporal pH Changes Inside Living Cells using a pH Triggered DNA Nanoswitch. Modi, S., Krishnan, Y.* Methods Mol. Biol. 2011, 749, 61-77.
  70. Synthetic, biofunctional nucleic acid based molecular devices. Bhatia, D., Sharma, S., Krishnan, Y.* Curr. Opin. Biotechnol. 2011, 22, 475-484.
  71. A DNA nanomachine maps spatial and temporal pH changes in a multicellular living organism. Surana, S., Bhatt, J. M., Koushika, S.P.*, Krishnan, Y.* Nature Communications, 2011, 2, 339.
  72. A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Bhatia, D., Surana, S., Chakraborty, S., Koushika, S. P., Krishnan, Y.* Nature Communications, 2011, 2, 340.
  73. Nucleic Acid Based Molecular Devices. Krishnan, Y., Simmel. F. C. Angew. Chem. Int. Ed., 2011, 50, 3124 – 3156.
  74. Structural DNA Nanotechnology: From bases to bricks, from structure to function. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* J. Phys. Chem. Lett., 2010, 1,1999-2005.
  75. pH Toggled DNA Architectures: Reversible Assembly of 3WJs into Extended 1D Architectures through A- motif Formation. Saha, S., Bhatia, D., Krishnan, Y.* Small, 2010, 6, 1288-1292.
  76. The poly dA helix: A new structural motif for high-performance DNA-based molecular switches. Chakraborty, S., Sharma, S., Maiti, P.K., Krishnan, Y.* Nucleic Acids Res., 2009, 37, 2810-2817.
  77. A DNA nanomachine that maps spatial and temporal pH changes in living cells. Modi, S., Swetha, M. G., Goswami, D., Gupta, G. D., Mayor, S., Krishnan, Y.* Nature Nanotechnology, 2009, 4, 325-330.
  78. Icosahedral DNA nanocapsules via modular assembly. Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A., Krishnan, Y.* Angew. Chem. Int. Ed., 2009, 48, 4134 - 4137.
  79. Combining G-quadruplex targeting motifs on a single PNA scaffold: A hybrid (3+1) PNA-DNA bimolecular quadruplex. Paul, A., Sengupta, P., Krishnan, Y., Ladame, S.* Chem. Eur. J., 2008, 14, 8682-8689.
  80. Kinetic Hybrid I-motifs: Intercepting DNA with RNA to form a DNA 2 RNA 2 hybrid i-motif. Chakraborty, S., Krishnan, Y.* Biochimie, 2008, 90, 1088-1095.
  81. The RNA 2 -PNA 2 Hybrid I-motif - A novel RNA-based building block. Chakraborty, S., Modi, S., Krishnan, Y.*, Chem. Commun., 2008, 70-72.
  82. Molecular mechanism of physical gelation of hydrocarbons by fatty acid amides of natural amino acids. Pal, A.; Ghosh, Y. K.; Bhattacharya, S. Tetrahedron, 2007, 63, 7334-7348.
  83. The I-tetraplex building block: Rational Design and Controlled Fabrication of robust 1D DNA Scaffolds via non-Watson Crick self assembly. Ghodke, H. B., Krishnan, R., Vignesh, K., Kumar, G. V. P., Narayana, C., Krishnan, Y.* Angew. Chem. Int. Ed. 2007, 46, 2646-2649.
  84. Structural Analysis of the Catalytic Core of Human Telomerase RNA by FRET and Molecular Modeling. Gavory, G.; Symmons, M. F.; Krishnan-Ghosh, Y.; Klenerman, D.; Balasubramanian, S.*, Biochemistry, 2006, 45, 13304-13311.
  85. First Blueprint, Now Bricks: DNA as construction material on the nanoscale. Pitchiaya, S.; Krishnan, Y.*; Chem. Soc. Rev., 2006, 35, 1111-1121.
  86. The PNA-DNA hybrid I-motif: Implications for sugar-sugar contacts in i-motif tetramerization. Modi, S., Wani, A. H., Krishnan, Y.* Nucleic Acids Res., 2006, 34, 4354-4363.
  87. PNA forms an I-motif. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* Chem. Commun. 2005, 5278-5280.
  88. Dynamic covalent chemistry on self-templating PNA oligomers: Formation of a bimolecular PNA quadruplex. Krishnan-Ghosh, Y.; Whitney, A. M.; Balasubramanian, S.* Chem. Commun. 2005, 3068-3070.
  89. A PNA 4 quadruplex. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* J. Am. Chem. Soc. 2004, 126, 5944-5945.
  90. Formation of an interlocked quadruplex dimer by d(GGGT). Krishnan-Ghosh, Y.; Liu, D.; Balasubramanian, S.* J. Am. Chem. Soc. 2004, 126, 11009-11016.
  91. Dynamic covalent chemistry on self-templating peptides: Formation of a disulfide-linked beta-hairpin mimic. Krishnan-Ghosh, Y.; Balasubramanian, S.* Angew. Chem. Int. Ed. 2003, 42, 2171-2173
  92. Enhanced cooperative binding of oligonucleotides to form DNA duplexes mediated by metal ion chelation. Horsey, I.; Krishnan-Ghosh, Y.; Balasubramanian, S.* Chem. Commun. 2002, 1950-1951.
  93. Synthesis of a polymer-supported oxazolidine aldehyde for asymmetric chemistry. Wills, A. J.; Krishnan- Ghosh, Y.; Balasubramanian S.* J. Org. Chem. 2002, 67, 6646-6652.
  94. 2-Halooxyethylene ethers of cholesterol as novel single component, room temperature cholesteric LC materials. Bhattacharya, S.*; Krishnan-Ghosh, Y. Mol. Cryst. Liq. Cryst. 2002, 381, 33-41.
  95. Advantage of the ether linkage between the positive charge and the cholesteryl skeleton in cholesterol-based amphiphiles as vectors for gene delivery Ghosh Y. K.; Visweswariah, S. S.; Bhattacharya, S.* Bioconjugate Chem. 2002, 13, 378-384.
  96. Thermal lipid order-disorder transitions in mixtures of cationic cholesteryl lipid analogues and dipalmitoyl phosphatidylcholine membranes. Krishnan-Ghosh, Y.; Indi, S. S.; Bhattacharya, S.* J. Phys. Chem. B 2001, 105, 10257-10265.
  97. Membrane formation from oxyethylene bearing cationic cholesterol derivatives. Krishnan-Ghosh, Y., Bhattacharya, S.* Ind. J. Chem. B 2001, 40, 891-894.
  98. Structure of cholest-5-en-3 beta-oxy-5-bromopentane by single-crystal X-ray diffraction at 130 K. Krishnan- Ghosh, Y.; Gopalan, R. S.; Kulkarni, G. U.; Bhattacharya, S.* J. Mol. Structure 2001, 560, 345-355.
  99. Vesicle formation from oligo(oxyethylene)-bearing cholesteryl amphiphiles: Site-selective effects of oxyethylene units on the membrane order and thickness. Bhattacharya, S.*; Krishnan-Ghosh, Y. Langmuir 2001, 17, 2067-2075.
  100. First report of phase selective gelation of oil from oil/water mixtures. Possible implications toward containing oil spills. Bhattacharya, S.*; Krishnan-Ghosh, Y. Chem Commun 2001, 185-186.
  101. Nature of linkage between the cationic headgroup and cholesteryl skeleton controls gene transfection efficiency. Ghosh Y. K.; Visweswariah S. S.; Bhattacharya, S.* FEBS Lett. 2000, 473, 341-344.


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