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. As featured in:  Research Highlights – Nat. Methods, 2023, 20, 1621.  News and Views – Nat. Biotechnol., 2023, https://doi.org/10.1038/s41587-023-02054-6 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. As featured in:  Research Highlights – Nat. Chem. Biol., 2023, 19, 1291.  Research Highlights – Nat. Methods, 2023, 20, 1621.  News and Views – Nat. Biotechnol., 2023, https://doi.org/10.1038/s41587-023-02054-6 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. As featured in: KRISHNAN, Y - p. 5  News and Views – Nat. Nanotechnol, 2021, 16, 1306-7. 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. As featured in:  Research Highlights – Nature, 2020, 587, 178.  Collection: Nature Portfolio: “Sensing at the Limit”, 2021 https://www.nature.com/collections/ggheegdfab  Scientific American, https://www.scientificamerican.com/custom-media/a-nanoscale-voltmeter-reveals- biology-hidden-in-plain-sight/ 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, https://doi.org/10.1016/j.tibs.2019.12.006.  Featured as Technology of the Month. 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, https://doi.org/10.1021/jacs.9b08959. KRISHNAN, Y - p. 6 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. As featured in:  Research Highlights –Nature, 2019 https://www.nature.com/articles/d41586-019-00533-y 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. As featured in:  Research Highlights – Nature Reviews Materials, 2019, 4, 2.  Editorial - Nature Nanotechnology, 2019, 14, 99. 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. As featured in:  The Author File – Nature Methods, 2019, 16, 3. 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, https://doi.org/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. KRISHNAN, Y - p. 7 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. As featured in:  Perspective – Science, 2017, 356, 701-702.  Spotlight – ACS Chem. Biol. 2017, 12, 1452-53  Biological Chemistry – C&E News, 2017, 95, 7  Journal Club PNAS – Proc. Natl. Acad. Sci. U.S.A 2017, http://blog.pnas.org/2017/05/journal-club-atp- could-help-proteins-dissolve-in-cells-prompting-a-rethink-about-its-function-and-evolution/  F1000 Prime, F1000 score 7. 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. As featured in:  News and Views – Nature Nanotechnology, 2017, 12, 1117–1119. 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. As featured in:  News and Views – Nature Biotechnology, 2016, 34, 1036. 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.  Featured as ACS Editor’s choice. KRISHNAN, Y - p. 8 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. As featured in:  News and Views – Nature Nanotechnology 2015, 10, 569-70.  A DNA-based sensor for intracellular chloride. Nat Methods, 2015, 12, 708. 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. KRISHNAN, Y - p. 9 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. As featured in:  Research Highlights – Nature Nanotechnology, 2011, doi:10.1038/nnano.2011.91  Science News – The Financial Express, New Delhi, 2011  Science News – Nature India, 29th June, 2011 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. As featured in:  Research Highlights – Nature Methods, 2009, 6, 404  Research Highlights – Nature, 2009, 458, 810  News – Nature, doi:10.1038/news.2009.340  Faculty of 1000 Biology  Research Highlights – Nature Asia-Pacific 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. KRISHNAN, Y - p. 10 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. KRISHNAN, Y - p. 11 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
  • Click here to view complete list of publications
    1. Rodriguez, R.*, Krishnan, Y.*(2023) The chemistry of Next Generation Sequencing. Nat. Biotechnol.
    2. Zou, J., Mitra, K., Anees, P., Oettinger, D., Ramirez, J., Veetil, A.T., Rao, R., Smith, J.A., Kratsios, P., Krishnan, Y.*(2023) A DNA nanodevice maps sodium at single organelle resolution. Nat. Biotechnol.
    3. Anees, P., Saminathan, A., Rozmus, E. R., Di, A., Malik, A. B., Delisle, B. P.*, Krishnan, Y.*(2023) Detectings organelle-specific activity of potassium channels with a DNA nanodevice. Nat. Biotechnol. 
    4. Huang, L. S., Zhou, B., Toth, P. T., Krishnan, Y., Di, A., Malik, A.B.*(2023) Endosomal Trafficking of Two Pore K+ Efflux Channel TWIK2 to Plasmalemma Mediates NLRP3 Inflammasome Activation and Inflammatory Injury. eLife12
    5. Zhang, S. J., Anees, P., Krishnan, Y., Fai, T.G.*, Szostak, J. W.*, Wang, A.*(2023) Passive endocytosis in protocells. Proc. Natl. Acad. Sci. e2221064120.
    6. Serulla, M., Anees, P., Trofimenko, E., Kalia, T., Krishnan, Y., Widmann, C.*(2023) Plasma membrane depolarization reveals endosomal escape incapacity of cell-penetrating peptides. Eur. J. Pharm. Biopharm. 116-124.
    7. Zajac, M., Modi, S., Krishnan, Y.*(2022) The evolution of organellar calcium mapping technologies.  Cell Calcium. 108, 102658.,  DOI: 10.1016/j.ceca.2022.102658
    8. C. Cui, K. Chakraborty, X. A. Tang, K. Q. Schoenfelt, A. Hoffman, A. Blank, B. Mcbeth, N. Pulliam, C. A. Reardon, S. Kulkarni, T. Vaisar, A. Ballabio, Y. Krishnan*, L. Becker*. (2021) A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumors Nat. Nanotechnol. 16, 1394-1402 (2021), DOI:10.1038/s41565-021-00988-z  
    9. B. Suresh, A. Saminathan†, K. Chakraborty†, C. Cui, M. Zajac, L. Becker*, Y. Krishnan*.(2021) Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis.  Proc. Natl. Acad. Sci. USA. Oct 2021, 118 (41) e2113174118, DOI: 10.1073/pnas.2113174118
    10. K. Chakraborty, P. Anees, S. Surana, S. Martin, J. Aburas, S. Moutel, F. Perez, S. P. Koushika, P. Kratsios* , Y. Krishnan*(2021) Tissue-specific targeting of DNA nanodevices in a multicellular living organism.  eLife 2021;10:e67830, DOI: 10.7554/eLife.67830  
    11. Nachtergaele, S. and Krishnan, Y.(2021) Cell surface GlycoRNAs open up new vistas. N Engl J Med 2021; 385:658-660, DOI: 10.1056/NEJMcibr2108679 
    12. Saminathan, A.†, Zajac, M.†, Anees, P., Krishnan, Y.*(2022) Achieving Organelle-level Precision with Next-Generation Targeting Technologies. Nature Reviews Materials, 7. 355-371.,DOI:10.1038/s41578-021-00396-8
    13. Osei-Owusu, J., Yang, J., Leung, K., Ruan, Z., Lü,W. Krishnan, Y., Qiu, Z.*(2021) Proton-activated chloride channel PAC regulates endosomal acidification and transferrin receptor-mediated endocytosis. Cell Reports,Vol. 34, No. 4, 2021, 108683, 2211-1247 
    14. Saminathan, A., Devany, J., Veetil, A.T., Suresh, B., Kavya, S. P., Schwake, M., Krishnan, Y.*(2021) A DNA-based voltmeter for organelles. Nature Nanotechnology, 16, 96–103.
    15. Krishnan, Y.* Jani, M. S., Zou, J.(2020) Quantitative Imaging of Biochemistry in Situ and at the Nanoscale.  ACS Cent. Sci. 2020, 6, 11, 1938–1954
    16. Veetil, A.T., Zou, J., Henderson, K. W., Jani, M. S., Metab, S., Sisodia, S. S., Hale, M. E., Krishnan, Y.*(2020) DNA-based probes of NOS-2 activity in live brains. Proceedings of the National Academy of Sciences Jun 2020, 117 (26) 14694-147020 
    17. Jani, M. S., Zou, J., Veetil A.T., Krishnan, Y.*(2020) A DNA-based fluorescent probe maps NOS3 activity levels with sub-cellular spatial resolution. Nature Chem. Biol., 16, 660–666, 2020
    18. Zajac, M., Chakraborty, K., Saha, S., Mahadevan, V., Infield, D., Accardi, A., Qiu, Z., Krishnan, Y.*(2020) What biologists want from their chloride reporters: a conversation between chemists and biologists. J. Cell Sci., 133, jcs240390
    19. Palapuravan, A., Zajac, M., Krishnan, Y.* (2020) Quantifying phagosomal HOCl at single immune-cell resolution. Meth. Cell Biol., in press.
    20. Jani, M. S., Veetil, A. T., Krishnan, Y.*(2020) Controlled release of bioactive signaling molecules.  Methods in enzymology, 638, 129–138.
    21. Sayresmith, N., Saminathan, A., Sailer, J., Patberg, S., Sandor, K., Krishnan, Y., Walter, M.*(2019) Photostable Voltage-Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles. J. Am. Chem. Soc., 141, 18780–18790
    22. Krishnan, Y.*and Seeman, N. C. (2019) Introduction: Nucleic Acid Nanotechnology. Chem. Rev. 119, 6271–6272
    23. Jani, M. S., Veetil, A.T. and Krishnan, Y.* (2019) Precision immunomodulation with synthetic nucleic acid technologies. Nature Review Materials 4, 451–485
    24. Prakash, V., Tsekouras, K., Venkatachalapathy, M., Heineke, H., Presse, S., Walter, N. and Krishnan, Y.* (2019) Quantitative maps of endosomal DNA processing by single molecule counting. Angew. Chem. Int. Ed.  58, 3073–3076
    25. Dan, K., Veetil, A.T., Chakraborty, K. and Krishnan, Y.*(2019) DNA nanodevices map enzymatic activity in organelles. Nature Nanotechnology 14, 252–259
    26. Thekkan, S., Jani, M. S., Cui, C., Dan, K., Zhou, G., Becker, L.* and Krishnan, Y.*(2019) A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome. Nature Chemical Biology 15, 1165–1172
    27. Narayanaswamy, N.,† Chakraborty, K.,†* Saminathan, A., Zeichner, E., Leung, K., Devany, J. and Krishnan, Y.*(2019) A pH-correctable, DNA-based fluorescent reporter for organellar Calcium. Nature Methods 16, 95–102(† both authors have contributed equally)
    28. Leung, K.,† Chakraborty, K.,† Saminathan, A. and Krishnan, Y.*(2019) A DNA Nanomachine chemically resolves lysosomes in live cells. Nature Nanotechnology 14, 176–183 († both authors have contributed equally)

        29. Complete list of Publications

        1. Nucleic acid nano-devices in live imaging
        2. Nucleic acid structure and dynamics
        3. Naturally occurring nucleic acid nano-devices
        4. Reviews and commentaries
        5. Patents

          6. Nucleic acid nano-devices in live imaging

          1. Zou, J., Mitra, K., Anees, P., Oettinger, D., Ramirez, J., Veetil, A.T., Rao, R., Smith, J.A., Kratsios, P., Krishnan, Y.*(2023) A DNA nanodevice maps sodium at single organelle resolution.   Nat. Biotechnol.
          2. Anees, P., Saminathan, A., Rozmus, E. R., Di, A., Malik, A. B., Delisle, B. P.*, Krishnan, Y.*(2023) Detectings organelle-specific activity of potassium channels with a DNA nanodevice.  Nat. Biotechnol. 
          3. Saminathan, A., Devany, J., Veetil, A.T., Suresh, B., Kavya, S. P., Schwake, M., Krishnan, Y.*(2020) A DNA-based voltmeter for organelles. Nature Nanotechnology, in press.
          4. Veetil, A.T., Zou, J., Henderson, K. W., Jani, M. S., Metab, S., Sisodia, S. S., Hale, M. E., Krishnan, Y.*(2020) DNA-based probes of NOS-2 activity in live brains. Proc. Natl. Acad. Sci. U.S.A., 117, 14694–15702
          5. Jana, S., Veetil, A.T., Krishnan, Y., Pike, V.*(2020) Synthesis and Labeling of Potential PET Radioligands for Receptor Interacting Protein Kinase 1. J. Nucl. Med., 61, 1106
          6. Jani, M. S., Zou, J., Veetil A.T., Krishnan, Y.*(2020) A DNA-based fluorescent probe maps NOS3 activity levels with sub-cellular spatial resolution. Nature Chem. Biol.,  16, 660–666
          7. Sayresmith, N., Saminathan, A., Sailer, J., Patberg, S., Sandor, K., Krishnan, Y., Walter, M.*(2020) Photostable Voltage-Sensitive Dyes Based on Simple, Solvatofluorochromic, Asymmetric Thiazolothiazoles. J. Am. Chem. Soc., 141, 18780–18790
          8. Prakash, V., Tsekouras, K., Venkatachalapathy, M., Heineke, H., Presse, S., Walter, N. and Krishnan, Y.* (2019) Quantitative maps of endosomal DNA processing by single molecule counting. Angew. Chem. Int. Ed.  58, 3073–3076
          9. Dan, K., Veetil, A.T., Chakraborty, K. and Krishnan, Y.*(2019) DNA nanodevices map enzymatic activity in organelles. Nature Nanotechnology  14, 252–259
          10. Thekkan, S., Jani, M. S., Cui, C., Dan, K., Zhou, G., Becker, L.* and Krishnan, Y.*(2019) A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome. Nature Chemical Biology 15, 1165–1172
          11. Narayanaswamy, N.,† Chakraborty, K.,†* Saminathan, A., Zeichner, E., Leung, K., Devany, J. and Krishnan, Y.*(2019) A pH-correctable, DNA-based fluorescent reporter for organellar Calcium. Nature Methods 16, 95–102(† both authors have contributed equally)
          12. Leung, K.,† Chakraborty, K.,† Saminathan, A. and Krishnan, Y.*(2019) A DNA Nanomachine chemically resolves lysosomes in live cells. Nature Nanotechnology 14, 176–183 († both authors have contributed equally)
          13. Salgado, E., Rodriguez, B.G., Narayanaswamy, N., Krishnan, Y. and Harrison S.C.*(2018) Visualization of Ca2+ loss from rotavirus during cell entry. J. Virol.,  92, e01327-18
          14. Veetil, A.T., Jani, M. S., and Krishnan, Y.* (2018) Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule. Proc. Natl. Acad. Sci. U.S.A., 115, 9432–9437
          15. Devany J., Chakraborty, K. and Krishnan, Y.* (2018) Sub-cellular nanorheology reveals lysosomal viscosity as a reporter for lysosomal storage diseases. Nano Lett., 18, 1351–1359
          16. Chakraborty, K., Leung, K., and Krishnan, Y.* (2017) High lumenal chloride in the lysosome is critical for lysosome function. eLife, 6, e28862.
          17. Veetil, A.T., Chakraborty, K.,† Xiao, K.,† Minter, R. M.,† Sisodia, S. S., and Krishnan, Y.* (2017) Cell targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nature Nanotechnology, 12, 1183–1189 († equal contributions)
          18. 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.* and Krishnan, Y.* (2016) Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nature Nanotechnology, 11, 1112–1119
          19. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349–373
          20. Prakash, V.,† Saha, S.,† Chakraborty, K. and Krishnan, Y.* (2016) Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chemical Science, 7, 1946–1953. († both authors have contributed equally)
          21. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
          22. Saha, S., Prakash, V., Halder, S., Chakraborty, K. and Krishnan, Y.* (2015) A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells Nature Nanotechnology, 10, 645–651
          23. Banerjee, A., Grazon, C., Nadal, B., Pons, T., Krishnan, Y. and Dubertret, B. * (2015) Fast, efficient and stable conjugation of multiple DNA strands on colloidal quantum dots Bioconjugate Chem., 26, 1582–1589
          24. Modi, S., Halder, S., Nizak, C. and Krishnan, Y.* (2014) Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale, 6, 1144–1152
          25. Ganesh, K.N. and Krishnan Y. (2013) Nucleic Acids - Chemistry and Applications. J. Org. Chem. 78, 12283–12287.
          26. Modi, S., Nizak, C., Surana, S., Halder, S. and Krishnan, Y*. (2013)Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nature Nanotechnology, 8, 459–467
          27. Surana, S., Bhatia, D. and Krishnan, Y.* (2013) A method to study in vivo stability of DNA nanostructures. Methods, 64, 94–100.
          28. Surana, S. and Krishnan, Y.* (2013) A method to map spatiotemporal pH changes in a multicellular living organism using a DNA nanosensor. Methods Mol. Biol. 991, 9–23
          29. Krishnan, Y.*, Bathe, M.* (2012) Designer nucleic acids to probe and program the cell.Trends in Cell Biology, 22, 624–633
          30. Modi, S. and Krishnan, Y.* (2011) A method to map spatiotemporal pH changes insde living cells using a pH triggered DNA nanoswitch. Methods Mol. Biol. 749, 61–77.
          31. Surana, S., Bhat, J.M., Koushika, S.P. and Krishnan, Y.* (2011) An autonomous DNA nanomachine maps spatiotemporal pH changes in a molticellolar living organism.Nature Communications, 2, 340
          32. Bhatia, D., Surana, S., Chakraborty, S., Koushika, S.P. and Krishnan, Y.* (2011) A synthetic, icosahedral DNA-based host-cargo complex for functional in vivo imaging.Nature Communications, 2, 339
          33. Modi, S., Swetha, M. G., Goswami, D., Gupta, G. D., Mayor, S., Krishnan, Y.* (2009) A DNA nanomachine maps spatiotemporal pH changes in living cells. Nature Nanotechnology, 4, 325–330

        Nucleic acid structure and dynamics

        1. Sharma, S., Zajac, M. and Krishnan, Y.* (2019) A DNA aptamer for cyclic adenosine monophosphate that shows adaptive recognition. ChemBioChem  20, 1–7
        2. Patel, A., Malinovska, L., Saha, S., Wang, J., Alberti, S., Krishnan, Y.* and Hyman, A.A.* (2017) ATP as a biological hydrotrope. Science, 356, 753–756
        3. Joshi, H., Bhatia, D., Krishnan, Y. and Maiti, P.K.* (2017) Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations Nanoscale, 9, 4467–4477
        4. Halder, S. and Krishnan, Y.* (2015) Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. Nanoscale, 7, 10008–10012
        5. Lannes, L., Halder, S., Krishnan, Y. and Schwalbe, H.* (2015) Tuning the pH Response of i-Motif DNA Oligonucleotides ChemBioChem, 16, 1647–1656
        6. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710–1719
        7. Banerjee, A., Bhatia, D., Saminathan, A., Chakraborty, S., Kar, S. and Krishnan, Y.* (2013) Controlled release of encapsulated cargo from a DNA icosahedron using a chemical trigger. Angew. Chem. Int. Ed. 52, 6854–6857
        8. Bhatia, D., Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2013) A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol. Biol. 991, 65–80
        9. Bhatia, D. and Krishnan, Y. (2013) Designer nucleic acid-based devices in nanomedicine. In Erdmann, V.A., Barcisjewski, J. (eds), DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases. pp 1–10
        10. Saha, S. and Krishnan, Y. (2012) pH sensitive DNA devices. In Fox, K.R., Brown, T (ed), DNA Conjugates and Sensors. Royal Society of Chemistry publishing, Cambridge, pp166–183
        11. Saha, S., Chakraborty, K. and Krishnan, Y*. (2012) Tunable, colorimetric DNA based pH sensors mediated by A-motif formation. Chem. Commun. 48, 2513–2515
        12. Bhatia, D., Sharma, S. and Krishnan, Y*. (2011) Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol, 22, 475–484
        13. Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based Molecular Devices. Angew. Chem. Int. Ed. 50, 3124–3156
        14. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* (2010) Structural DNA Nanotechnology: From bases to bricks, from structure to function. J. Phys. Chem. Lett. 1, 1999–2005
        15. Saha, S., Bhatia, D., Krishnan, Y.* (2010) pH toggled DNA architectures: Reversible assembly of a 3WJ into extended 1D architectures through A-motif formation . Small, 6, 1288–1292
        16. Chakraborty, S., Sharma, S., Maiti, P. K., Krishnan, Y.* (2009) The poly dA helix: A new structural motif for high-performance DNA-based molecular switches . Nucleic Acids Res. 37, 2810-2817
        17. Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A., Krishnan, Y.*(2009)Icosahedral DNA nanocapsules via modular assembly. Angew. Chem. Int. Ed. 48, 4134–4137. (featured on journal frontispiece)
        18. Paol,  A.; Sengupta, P.;  Krishnan, Y.; Ladame, S.* (2008) Combining G-quadruplex targeting motifs on a single PNA scaffold: hybrid (3+1) PNA-DNA bimolecular quadruplex. Chem.Eur.J. 14, 8682-8689
        19. Chakraborty, S.; Krishnan, Y.* (2008) Kinetic Hybrid i-motifs: Intercepting DNA with RNA to form a DNA2-RNA2 i-motif. Biochimie, 90, 1088–1095
        20. Chakraborty, S.; Modi, S.; Krishnan, Y.* (2008) The RNA2-PNA2 Hybrid I-motif - A novel RNA-based building block. Chem. Commun., 70–72
        21. Ghodke, H. B.; Krishnan, R.; Vignesh, K.; Kumar, G.V.P.; Narayana, C.; Krishnan, Y.* (2007) The I-tetraplex building block: Rational Design and Controlled Fabrication of robust 1D DNA Scaffolds via non-Watson Crick self assembly. Angew. Chem. Int. Ed., 46, 2646–2649
        22. Gavory, G.; Symmons, M. F.; Krishnan-Ghosh, Y.;Klenerman, D.; Balasubramanian, S.* (2006) Structural Analysis of the Catalytic Core of Human Telomerase RNA by FRETand Molecolar Modeling. Biochemistry, 45, 13304–13311
        23. Modi, S., Wani, A. H., Krishnan, Y.* (2006) The PNA-DNA hybrid I-motif - Implications for sugar-sugar contacts in i-motif tetramerization. Nucleic Acids Research, 34, 4353–4363
        24. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.*(2005) PNA forms an I-motif. Chem. Commun. 5278–5280
        25. Krishnan-Ghosh, Y.; Whitney, A. M.; Balasubramanian, S.* (2005)  Dynamic covalent chemistry on self-templating PNA oligomers: Formation of a bimolecolar PNA quadruplex. Chem. Commun., 3068–3070
        26. Krishnan-Ghosh, Y.; Liu, D.; Balasubramanian, S.* (2004) Formation of an interlocked quadruplex dimer by d(GGGT). J. Am. Chem. Soc. 126, 11009–11016
        27. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* (2004)A PNA4 quadruplex.  J. Am. Chem. Soc.  126, 5944–5945
        28. Krishnan-Ghosh , Y.; Balasubramanian, S.* (2003) Dynamic covalent chemistry on self-templating peptides: Formation of a disolfide-linked beta-hairpin mimic. Angew. Chem. Int. Ed. 42, 2171–2173
        29. Ghosh Y. K.; Visweswariah, S. S.; Bhattacharya, S. * (2002) Advantage of the ether linkage between the positive charge and the cholesteryl skeleton in cholesterol-based amphiphiles as vectors for gene delivery. Bioconjugate Chem. 13, 378–384 
        30. Bhattacharya, S.*; Krishnan-Ghosh, Y. (2002) 2-Halooxyethylene ethers of cholesterol as novel single component, room temperature cholesteric LC materials.Mol. Cryst. Liq. Cryst. 381, 33-41 
        31. Wills, A. J.; Krishnan-Ghosh, Y.; Balasubramanian S.* (2002) Synthesis of a polymer-supported oxazolidine aldehyde for asymmetric chemistry. J. Org. Chem. 67, 6646-6652
        32. Horsey, I.; Krishnan-Ghosh, Y.; Balasubramanian, S. (2002) Enhanced cooperative binding of oligonucleotides to form DNA duplexes mediated by metal ion chelation Chem. Commun. 1950-1951 
        33. Bhattacharya, S.; Krishnan-Ghosh, Y. (2001) First report of phase selective gelation of oil from oil/water mixtures. Possible implications toward containing oil spills. Chem. Commun., 185–186
        34. Bhattacharya, S.; Krishnan-Ghosh, Y. (2001) Vesicle formation from oligo(oxyethylene)-bearing cholesteryl amphiphiles: Site-selective effects of oxyethylene units on the membrane order and thickness. Langmuir 17, 2067–2075
        35. Krishnan-Ghosh, Y.; Gopalan, R. S.; Kolkarni, G. U.; Bhattacharya, S. (2001) Structure of cholest-5-en-3 beta-oxy-5-bromopentane by single-crystal X-ray diffraction at 130 K. J. Mol. Structure 560, 345–355 
        36. Krishnan-Ghosh, Y.; Bhattacharya, S.* (2001) Membrane formation from oxyethylene bearing cationic cholesterol derivatives. Ind. J. Chem. B. 40, 891–894
        37. Krishnan-Ghosh, Y., Bhattacharya, S.* (2001) Thermal lipid order-disorder transitions in mixtures of cationic cholesteryl lipid analogues and dipalmitoyl phosphatidylcholine membranes. J. Phys. Chem. B. 105, 10257–10265
        38. Ghosh, Y.K., Visweswariah, S. S., Bhattacharya, S.* (2000) Nature of linkage between cationic headgroup and cholesteryl skeleton controls gene transfection efficiency .  FEBS Lett. 473, 341–344

        Naturally occurring nucleic acid nano-devices

        1. Sharma, S., Zaveri, A., Visweswariah, S.S and Krishnan, Y.* (2014) A fluorescent nucleic acid-based nanodevice quantitatively images elevated cAMP in membrane bound compartments. Small, 10, 4276–4280
        2. Chakraborty, S. and Krishnan, Y.* (2017) A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Research, 2017, 45, 9694–9705
        3. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710–1719
        4. Chakraborty, S., Mehtab, S., Patwardhan, A.R., Krishnan, Y.* (2012) Pri-miR-17-92a Transcript folds into a tertiary structure and autoregolates its processing. RNA 18, 1014–1028

        Reviews and commentaries:

        1. Rodriguez, R.*, Krishnan, Y.*(2023)  The chemistry of Next Generation Sequencing.   Nat. Biotechnol.
        2. Zajac, M., Modi, S., Krishnan, Y.*(2022) The evolution of organellar calcium mapping technologies.  Cell Calcium. 108, 102658.,  DOI: 10.1016/j.ceca.2022.102658
        3. Saminathan, A.†, Zajac, M.†, Anees, P., Krishnan, Y.*(2022) Achieving Organelle-level Precision with Next-Generation Targeting Technologies. Nature Reviews Materials, 7. 355-371.,DOI:10.1038/s41578-021-00396-8
        4. Krishnan, Y.* Jani, M. S., Zou, J.(2020) Quantitative Imaging of Biochemistry in Situ and at the Nanoscale.  ACS Cent. Sci.,  DOI: 10.1021/acscentsci.0c01076
        5. Palapuravan, A., Zajac, M., Krishnan, Y.* (2020) Quantifying phagosomal HOCl at single immune-cell resolution. Meth. Cell Biol., in press.
        6. Jani, M. S., Veetil, A. T., Krishnan, Y.*(2020) Controlled release of bioactive signaling molecules.  Methods in enzymology, 638, 129–138.
        7. Zajac, M., Chakraborty, K., Saha, S., Mahadevan, V., Infield, D., Accardi, A., Qiu, Z., Krishnan, Y.*(2020) What biologists want from their chloride reporters: a conversation between chemists and biologists. J. Cell Sci., 133, jcs240390.
        8. Saminathan, A., Noyola, V. S., Krishnan, Y.*(2020) Chemically Resolving Lysosome Populations in Live Cells. Trends in biochemical sciences, 45, 365–366.
        9. Krishnan, Y.*and Seeman, N. C. (2019) Introduction: Nucleic Acid Nanotechnology. Chem. Rev.  119, 6271-6272.
        10. Leung, K. and Krishnan, Y.* (2019) Dynamic RNA Nanotechnology enters the CRISPR toolbox. ACS Central Science  5, 1111–1113.
        11. Jani, M. S., Veetil, A.T. and Krishnan, Y.* (2019) Precision immunomodulation with synthetic nucleic acid technologies. Nature Review Materials, 4, 451–485.
        12. Voices of biotech   Nature Biotechnology, 34, (2016),  270–275.
        13. Nature nanotechnology 10 the anniversary issue opinion piece  Nature Nanotechnology (2016) 11,  828–834.
        14. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349–373.
        15. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747.
        16. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710–1719.
        17. Ghosh, A. and Krishnan, Y. (2014) At a long-awaited turning point. NatureNanotechnology, 9, 491–494.
        18. Krishnan, Y., Bathe, M. (2012) Designer nucleic acids to probe and program the cell.Trends in Cell Biology, 22, 624–633.
        19. Bhatia, D., Chakraborty, S. and Krishnan, Y.* (2012) Designer DNA give RNAi more spine. Nature Nanotechnology, 7, 344–346.
        20. Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based Molecolar Devices. Angew. Chem. Int. Ed. 50, 3124–3156.
        21. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* (2010) Structural DNA Nanotechnology: From bases to bricks, from structure to function. J.Phys. Chem. Lett. 1, 1999–2005.
        22. Pitchiaya, S., Krishnan, Y.* (2006) First Blueprint, Now Bricks: DNA as construction material on the nanoscale. Chem. Soc. Rev., 35, 1111–1121.

        Patents:

        1. Methods of multiplexing DNA sensors and localizing DNA sensor

          Y Krishnan, S Modi, S Surana

        2. Modular assembly of novel icosahedral DNA nanocapsules with encapsulating ability.

          Yamuna Krishnan. Under prosecution at USPTO.

        3. The A-motif: A pH trigger for hybridization of DNA strands

          Saikat Chakraborty and Yamuna Krishnan.
          US Patent granted July 10, 2012. USPTO no: 8216850.

        4. FRET based pH Sensor using nucleic acid assemblies.

          Yamuna Krishnan, Satyajit Mayor and Souvik Modi. Under prosecution at USPTO.

        5. An engineered nucleic acid assembly, vector, cell, methods and kit thereof

          Souvik Modi and Yamuna Krishnan. Complete IN and PCT filed.

        6. A process for encapsulating functional biomolecules and encapsulated product thereof.

          Dhiraj Bhatia and Yamuna Krishnan. Complete IN and PCT filed.
          Winner of the Amulya 2012 award from the Karnataka State Innovation Council.

        7. Nucleotide sequences, nucleic acid sensors and methods thereof.

          Suruchi Sharma and Yamuna Krishnan. Complete IN filed.

        8. Nucleic Acids based sensor and methods thereof.

          Sonali Saha and Yamuna Krishnan. Complete IN filed.

        9. A process for encapsulating functional biomolecules and encapsulated product thereof.

          Souvik Modi, Sunaina Surana and Yamuna Krishnan. PCT filed. PCT/IB/2014/059236