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Yamuna Krishnan

TitleProfessor
InstitutionUniversity of Chicago
DepartmentChemistry
AddressChicago IL 60637
Email
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Osei-Owusu J, Yang J, Leung KH, Ruan Z, Lü W, Krishnan Y, Qiu Z. Proton-activated chloride channel PAC regulates endosomal acidification and transferrin receptor-mediated endocytosis. Cell Rep. 2021 Jan 26; 34(4):108683. PMID: 33503418.
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    2. Saminathan A, Devany J, Veetil AT, Suresh B, Pillai KS, Schwake M, Krishnan Y. A DNA-based voltmeter for organelles. Nat Nanotechnol. 2021 01; 16(1):96-103. PMID: 33139937.
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    3. Krishnan Y, Zou J, Jani MS. Quantitative Imaging of Biochemistry in Situ and at the Nanoscale. ACS Cent Sci. 2020 Nov 25; 6(11):1938-1954. PMID: 33274271.
      View in: PubMed
    4. 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 06 30; 117(26):14694-14702. PMID: 32554491.
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    5. Jani MS, Veetil AT, Krishnan Y. Controlled release of bioactive signaling molecules. Methods Enzymol. 2020; 638:129-138. PMID: 32416910.
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    6. Jani MS, Zou J, Veetil AT, Krishnan Y. A DNA-based fluorescent probe maps NOS3 activity with subcellular spatial resolution. Nat Chem Biol. 2020 06; 16(6):660-666. PMID: 32152543.
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    7. Saminathan A, Noyola VS, Krishnan Y. Chemically Resolving Lysosome Populations in Live Cells. Trends Biochem Sci. 2020 04; 45(4):365-366. PMID: 32169175.
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    8. 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). PMID: 31974277.
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    9. 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. PMID: 31939296.
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    10. 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. PMID: 31660737.
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    11. 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. PMID: 31099939.
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    12. Leung K, Krishnan Y. Dynamic RNA Nanotechnology Enters the CRISPR Toolbox. ACS Cent Sci. 2019 Jul 24; 5(7):1111-1113. PMID: 31404241.
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    13. Krishnan Y, Seeman NC. Introduction: Nucleic Acid Nanotechnology. Chem Rev. 2019 05 22; 119(10):6271-6272. PMID: 31117417.
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    14. Dan K, Veetil AT, Chakraborty K, Krishnan Y. DNA nanodevices map enzymatic activity in organelles. Nat Nanotechnol. 2019 03; 14(3):252-259. PMID: 30742135.
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    15. 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. PMID: 30667589.
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    16. 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. PMID: 30643216.
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    17. 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. PMID: 30532082.
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    18. 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. PMID: 30531966.
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    19. 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. PMID: 30510277.
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    20. 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). PMID: 30258012.
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    21. 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. PMID: 29531078.
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    22. Devany J, Chakraborty K, Krishnan Y. Subcellular Nanorheology Reveals Lysosomal Viscosity as a Reporter for Lysosomal Storage Diseases. . 2018 02 14; 18(2):1351-1359. PMID: 29313356.
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    23. 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. PMID: 28976518.
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    24. Chakraborty S, Krishnan Y. A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Res. 2017 Sep 19; 45(16):9694-9705. PMID: 28934477.
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    25. 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. PMID: 28825714.
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    26. Chakraborty K, Leung K, Krishnan Y. High lumenal chloride in the lysosome is critical for lysosome function. Elife. 2017 07 25; 6. PMID: 28742019.
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    27. 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. PMID: 28522535.
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    28. 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. PMID: 28304019.
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    29. 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. PMID: 27548358.
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    30. Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem. 2016 Jun 02; 85:349-73. PMID: 27294440.
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    31. 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. PMID: 26963549.
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    32. 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. PMID: 30050672.
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    33. 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. PMID: 26329110.
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    34. 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. PMID: 25992903.
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    35. 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. PMID: 26032298.
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    36. 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. PMID: 26098226.
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    37. Halder S, Krishnan Y. Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. Nanoscale. 2015 Jun 14; 7(22):10008-12. PMID: 25990365.
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    38. 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. PMID: 25044725.
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    39. Ghosh A, Krishnan Y. At a long-awaited turning point. Nat Nanotechnol. 2014 Jul; 9(7):491-4. PMID: 24990209.
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    40. 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. PMID: 24712860.
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    41. 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. PMID: 24297098.
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    42. Ganesh KN, Krishnan Y. Nucleic acids--chemistry and applications. Org Lett. 2013 Dec 20; 15(24):6115. PMID: 24354722.
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    43. Ganesh KN, Krishnan Y. Nucleic acids--chemistry and applications. J Org Chem. 2013 Dec 20; 78(24):12283-7. PMID: 24354734.
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    44. 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. PMID: 23716499.
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    45. 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. PMID: 23708428.
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    46. Surana S, Bhatia D, Krishnan Y. A method to study in vivo stability of DNA nanostructures. Methods. 2013 Nov; 64(1):94-100. PMID: 23623822.
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    47. 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. PMID: 23546654.
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    48. Bhatia D, Chakraborty S, Mehtab S, Krishnan Y. A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol Biol. 2013; 991:65-80. PMID: 23546660.
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    49. Krishnan Y, Bathe M. Designer nucleic acids to probe and program the cell. Trends Cell Biol. 2012 Dec; 22(12):624-33. PMID: 23140833.
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    50. Bhatia D, Chakraborty S, Krishnan Y. Gene delivery: Designer DNA give RNAi more spine. Nat Nanotechnol. 2012 Jun 03; 7(6):344-6. PMID: 22659610.
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    51. 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. PMID: 22450760.
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    52. 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. PMID: 22278189.
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    53. Bhatia D, Sharma S, Krishnan Y. Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol. 2011 Aug; 22(4):475-84. PMID: 21652202.
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    54. 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. PMID: 21654639.
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    55. 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. PMID: 21654640.
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    56. Krishnan Y, Simmel FC. Nucleic acid based molecular devices. Angew Chem Int Ed Engl. 2011 Mar 28; 50(14):3124-56. PMID: 21432950.
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    57. 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. PMID: 21674365.
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    58. 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. PMID: 20486230.
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    59. 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. PMID: 19421220.
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    60. 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. PMID: 19279188.
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    61. 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. PMID: 19222079.
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    62. 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. PMID: 18358847.
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    63. 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. PMID: 18401893.
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    64. 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. PMID: 18668497.
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    65. 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. PMID: 17330917.
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    66. Pitchiaya S, Krishnan Y. First blueprint, now bricks: DNA as construction material on the nanoscale. Chem Soc Rev. 2006 Nov; 35(11):1111-21. PMID: 17057840.
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    67. 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. PMID: 16936319.
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