Recent publications
# - co-first authors; * - corresponding author(s)
- 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.
- 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.
- 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.
- Rodriguez, R.*, Krishnan, Y.* “The chemistry of Next Generation Sequencing.” Nat. Biotechnol. 2023, 41,
1709-1715.
- Mitra, K., Krishnan, Y.* “Lightly counting membrane proteins in native nanodiscs.” Nat. Nanotechnol.
2024, 19, 5-6.
- 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.
- 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.
- 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.
- Zajac, M., Modi, S., Krishnan, Y.* “The evolution of organellar calcium mapping technologies” Cell
Calcium, 2022, 108, 102658.
- Saminathan, A., Zajac, M., Palapuravan, A., Krishnan, Y.* “Achieving Organelle-level Precision with Next-
Generation Targeting Technologies.” Nature Reviews Materials, 2022, 7. 355-371.
- 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.
- 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.
- Nachtergaele, S. and Krishnan, Y. ” Cell Surface GlycoRNAs Open New Vistas.” New Engl. J. Med. 2021
385, 658-660.
- 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.
- 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.
- 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.
- 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.
- 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.
- Krishnan, Y.*, Zou, J., Jani, M.S. “Quantitative imaging of biochemistry in situ and at the nanoscale.” ACS
Cent. Sci., 2020, 6, 1938–1954.
- 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.
- Jani, M. S., Veetil A. T., Krishnan, Y.* “Controlled release of bioactive signaling molecules.” Meth.
Enzymol. 2020, 638, 129-138.
- 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.
- 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.
- 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.
- 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.
- 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.
- Jani, M. S., Veetil, A.T., Krishnan, Y.* “Precision immunomodulation with synthetic nucleic acid
technologies.” Nature Reviews Materials, 2019, 4, 451-485.
- Dan, K., Veetil, A. T., Chakraborty, K., Krishnan, Y.* “DNA nanodevices map enzymatic activity in
organelles.” Nature Nanotechnology, 2019, 14, 252-257.
- Leung, K.H. # , Chakraborty, K. # , Saminathan, A., Krishnan, Y.* "A DNA nanomachine chemically resolves
lysosomes in live cells." Nature Nanotechnology, 2019, 14, 176-183.
- 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.
- 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).
- Sharma, S., Zajac, M., Krishnan, Y.* “A DNA aptamer for cyclic adenosine monophosphate that shows
adaptive recognition.” ChemBioChem, 2019, 10.1002/cbic.201900259. (invited)
- 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)
- Leung, K.H., Krishnan, Y.,* “Dynamic RNA nanotechnology enters the CRISPR toolbox.” ACS Cent. Sci..
2019, 5, 1111. (News & Views)
- 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)
- 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.
- 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.
- 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.
- Chakraborty, S., Krishnan, Y.* "A structural map of oncomiR-1 at single-nucleotide resolution." Nucleic
Acids Res. 2017, 45, 9694–9705.
- Chakraborty, K., Leung, K., Krishnan, Y.* "High lumenal chloride in the lysosome is critical for lysosome
function." eLife, 2017, 6, e28862.
- 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.
- 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.
- 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.
- Krishnan, Y. "Nano on Reflection." 10th anniversary issue. Nature Nanotechnology, 2016, 11, 831-832.
(invited)
- 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)
- 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.
- 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.
- Chakraborty, K., Veetil, A. T., Jaffrey, S. R.,* Krishnan, Y.* Nucleic acid-based nanodevices in biological
imaging. Ann. Rev. Biochem., 2016, 85, 349-73.
- 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.
- Krishnan, Y.* Crack the cliques, enable visionaries. Nature, 2015, 521, 152.
- 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.
- Halder, S., Krishnan, Y.* Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices
Nanoscale 2015, 7, 10008-10012.
- Lannes, L., Halder, S., Krishnan, Y., Schwalbe, H.* Tuning the pH-response of i-motif DNA
oligonucleotides. ChemBioChem, 2015, 16, 1647-1656.
- 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.
- Ghosh, A., Krishnan, Y. At a long awaited turning point. Nature Nanotechnology, 2014, 9, 491-4.
- 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.
- 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.
- 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.
- Ganesh, K. N.*, Krishnan, Y. Nucleic Acids – Chemistry and Applications. J. Org. Chem. 2013, 78, 12283-
12287.
- 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.
- Surana, S., Bhatia, D., Krishnan, Y.* A method to study in vivo stability of DNA nanostructures. Methods,
2013, 64, 94-100.
- 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.
- Bhatia, D., Chakraborty, S., Mehtab, S., Krishnan, Y.* A method to encapsulate molecular cargo within
DNA icosahedra. Methods Mol. Biol. 2013, 991, 65-80.
- 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.
- Krishnan, Y., Bathe, M. Designer Nucleic Acids to probe and program the Cell. Trends in Cell Biol. 2012,
22, 624-633.
- Bhatia, D., Chakraborty, S., Krishnan, Y.* Designer DNA gives RNAi more spine. Nature Nanotechnology,
2012, 7, 344-346.
- 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.
- Tunable, colorimetric DNA based pH sensors mediated by A-motif formation. Saha, S., Chakraborty, K.,
Krishnan, Y.* Chem. Commun. 2012, 48, 2513-2515.
- 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.
- Synthetic, biofunctional nucleic acid based molecular devices. Bhatia, D., Sharma, S., Krishnan, Y.* Curr.
Opin. Biotechnol. 2011, 22, 475-484.
- 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.
- 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.
- Nucleic Acid Based Molecular Devices. Krishnan, Y., Simmel. F. C. Angew. Chem. Int. Ed., 2011, 50, 3124
– 3156.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- First Blueprint, Now Bricks: DNA as construction material on the nanoscale. Pitchiaya, S.; Krishnan, Y.*;
Chem. Soc. Rev., 2006, 35, 1111-1121.
- 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.
- PNA forms an I-motif. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* Chem. Commun. 2005,
5278-5280.
- 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.
- A PNA 4 quadruplex. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* J. Am. Chem. Soc. 2004, 126,
5944-5945.
- Formation of an interlocked quadruplex dimer by d(GGGT). Krishnan-Ghosh, Y.; Liu, D.;
Balasubramanian, S.* J. Am. Chem. Soc. 2004, 126, 11009-11016.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- Membrane formation from oxyethylene bearing cationic cholesterol derivatives. Krishnan-Ghosh, Y.,
Bhattacharya, S.* Ind. J. Chem. B 2001, 40, 891-894.
- 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.
- 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.
- 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.
- 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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