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The Krishnamurthy Lab

Publications

 

  1. Surveying the sequence diversity of model prebiotic peptides by mass spectrometry. Forsythe, J.G., Petrov, A. S.; Sheng-Sheng, Y., Krishnamurthy, R., Grover, M., Hud, N. V., Facundo, M. F. Proc. Natl. Acad. Soc. 2017, 114, E7652-E7659.
  2. Nitrogenous Derivatives of Phosphorus and the Origins of Life: Plausible Prebiotic Phosphorylating Agents in Water. Karki, M.; Gibard, C.; Bhowmik, S.; Krishnamurthy, R. Life, 2017, 7, 32.  TOC graphic       Abstract
  3. Orotidine Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence ) of RNA. Kim, E.-K.; Martin, V.; Krishnamurthy, R.Chem. Eur. J. 2017, 23, 12668-12675TOC graphic     Abstract
  4. Investigations towards the synthesis of 5-amino-L-lyxofuranosides and 4-amino-lyxopyranosides and NMR analysis. Alba Diez-Martinez, A.; Krishnamurthy, R. SynOpen, 2017, 1, 29-40 Abstract Figure
  5. Anchimeric-assisted Spontaneous Hydrolysis of Cyanohydrins Under Ambient Conditions: Implications for Cyanide Initiated Selective Transformations. Yerabolu, J. R.; Liotta, C.L.; Krishnamurthy, R. Chem. Eur. J. 2017, 23, 8756-8765. Cyanide initiated chemistry abstract     
  6. Reaction of Glycine with Glyoxylate: Competing Transaminations, Aldol Reactions, and Decarboxylations. Conley, M.; Mojica, M.; Mohammed, F.;  Chen, K.;  Napoline , J. W.; Pollet, P.; Krishnamurthy, R.; Liotta, C. L. J. Phys. Org. Chem. 2017, Accepted.Glycine Glyoxyate   
  7. Giving Rise to Life: Transition from Prebiotic Chemistry to Protobiology. Krishnamurthy, R. Acc. Chem Res. 2017, 50, 455–459.Abstract
  8. Prebiotic Organic Chemistry and Chemical pre-Biology: Speaking to the Synthetic Organic Chemists. Krishnamurthy, R.; Snieckus, V. Synlett, 2017, 28, 27-29.ClusterSynlett 2017 Cover
  9. Nucleobase Modification by an RNA Enzyme. Poudyal, R. R.; Ngyuyen, P. D. M.; Lokugamage, M. P.; Callaway, M. K.; Gavette, J. V.; Krishnamurthy, R.; Burke, D. H. Nucleic Acids Res. 2017, 45, 1345-1354.                                        Abstract              
  10. A Plausible Prebiotic Origin of Glyoxylate: Nonenzymatic Transamination Reactions of Glycine with Formaldehyde. Mohammed, F. S.; Chen, K.; Mojica, M.; Conley, M.; Napoline, J. W.; Butch, C. J.; Pollet, P.; Krishnamurthy, R.; Liotta, C. L. Synlett, 2017, 28, 93-97.Liotta         

    Mineral-Induced Enantioenrichment of Tartaric Acid, Gherase, D.; Hazen, R. M.; Krishnamurthy, R.; Blackmond, D. Synlett, 2017, 28, 88-92.Blackmond paper   

  11. The Abiotic Oxidation of Organic Acids to Malonate.Rice, G. B.; Yerabolu, J. R.; Krishnamurthy, R.; Springsteen, G. Synlett, 2017, 28, 98-102. Greg Synlett Cluster   
  12. Kinetics of prebiotic depsipeptide formation from the ester–amide exchange reaction. Yu, S-S.; Krishnamurthy, R.; Fernandez, F.; Hud, N. V.; Schork, F. J.; Grover, M. A.Phys. Chem. Chem. Phys. 2016, 18, 28441-28450.                                             Martha Collaboration
  13. RNA-DNA Chimeras in the Context of an RNA-world Transition to an RNA/DNA-world. Gavette, J. V.; Stoop. M.; Hud, N. V.; Krishnamurthy, R. Angew. Chemie, Int, Ed. 2016, 55, 13204-13209.  Abstract
  14. Spontaneous Formation and Base Pairing of Plausible Prebiotic Nucleotides in Water. Cafferty, B. J.;  Fialho, D.;  Khanam, J.;  Krishnamurthy, R.; Hud, N.Nature Communications 2016, 7, Article number: 11328Abstract
  15. Small molecule-mediated duplex formation of nucleic acids with ‘incompatible’ backbones. Cafferty, B. J.; Musetti, C.; Kim, K.; Horowitz, E.D.; Krishnamurthy, R.; Hud, N. V. ChemComm. 2016, 52, 5436-543.  Abstract              Figure 1

  16. pH Controlled Reaction Divergence of Decarboxylation versus Fragmentation in Reactions of Dihydroxyfumarate with Glyoxylate and Formaldehyde: Parallels to Biological Pathways. Butch, C.J.; Wang, J.; Gu, J.; Vindas, R.; Crowe, J.; Pollet, P.; Gelbaum, L.; Leszczynski, J.; Krishnamurthy, R.; L. Liotta, C. L. J. Phys. Org. Chem. 2016, 29, 352-360.                                                                                                                                                                                                                                                                AbstractAbstractCover page
  17. Hydrogen-Bonding Complexes of 5-Azauracil and Uracil Derivatives in Organic Medium.  Diez-Martinez, A.; Kim, E-K.; Krishnamurthy, R. J. Org. Chem. 2015, 80, 7066-7075.Abstract JOC 2015
  18. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on Prebiotic Earth. Forsythe, J.G.; Yu, S-S.; Mamajanov, I.; Grover, M.A.; Krishnamurthy, R.; Fernandez, F.M.; Hud, N.H. Angew. Chem. Int . Ed. 2015, 54, 9871-9875, DOI: 10.1002/ange.201503792AbstrMechanism
  19. Synthesis of Orotidine by Intramolecular Nucleosidation. Kim, E-K.; Krishnamurthy, R. ChemComm. 2015, 51, 5618-5621.

    Abstract

  20. The Emergence of RNA. Krishnamurthy, R. Israel J. Chemistry, 2015, 55, 837-850; Cover page

    ACRCover Page

  21. Microwave-Assisted Phosphitylations of DNA and RNA Nucleosides and Their Analogs. Efthymiou, T.; Krishnamurthy, R. Curr. Protoc. Nucleic Acid Chem. 60:2.19.1-2.19.20, 2015,DOI:10.1002/0471142700.nc0219s60.

    AbstractMW

  22. Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid. Kim, K.; Punna, V.; Karri, P.; Krishnamurthy, R.Beil. J. Org. Chem. 2014, 10, 2131-2138. Abstract Beilstein
  23. A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth. Parker, E. T.; Zhou, M.; Burton, A. S.; Glavin, D. P.; Dworkin, J. P.; Krishnamurthy, R.; Fernandez, F. M.; Bada, J. L. Angew. Chem. Int. Ed. 2014, 53, 8132-8136.Illustrated Back CoverAbstract
  24. Microwave-Assisted Preparation of Nucleoside-Phosphoramidites. Meher, G.; Efthymiou, T.; Stoop, M.; Krishnamurthy, R. ChemComm, 2014, 50, 7463-7465.   AbstractMW phosphitylation
  25. RNA as an Emergent Entity: An Understanding Gained Through Studying its Non-Functional Alternatives. Krishnamurthy, R. Synlett, 2014, 25, 1511-1518.           AbstractAbstract
  26. Spontaneous Prebiotic Formation of a β-Ribofuranoside That Self-Assembles with a Complementary Heterocycle. Chen, M.C.; Cafferty, B.J.; Mamajanov, I.; Gallego, I.; Khanam, J.; Krishnamurthy, R.; Hud, N. V. J. Am. Chem. Soc. 2014, 136, 5640-5646.

    Abstract


     

  27. Production of Tartrates by Cyanide Mediated Dimerization of Glyoxylate: A Potential Abiotic Pathway to the Citric Acid Cycle. Butch, C.; Cope, E.D.; Pollet, P.L.; Gelbaum, L.; Krishnamurthy, R.; Liotta, C. J. Am. Chem. Soc. 2013, 135, 13440-1344.Tartrate JACS 2013 abstract
  28. Chemical Etiology of Nucleic Acid Structure. The Pentulofuranosyl Oligonucleotide Systems: (1'→3')-β-L-Ribulo, (4'→3')-α-L-Xylulo, and (1'3')-α-L-Xylulo Nucleic Acids. Stoop, M.; Meher, G.; Karri, P.; Krishnamurthy, R. Chem. Eur. J. 2013, 19, 15336-15345.Pentulose-NA

  29. Base-Pairing Properties of a Structural Isomer of Glycerol Nucleic Acid. Karri, P.; Punna, V.; Kim, K.; Krishnamurthy, R. Angew. Chem. Int. Ed. 2013, 52, 5840-5844.isoGNA
  30. The Origin of RNA and ‘‘My Grandfather’s Axe’’. Hud, N.; Cafferty, B.J.; Krishnamurthy, R.; Williams, L.D. Chemistry & Biology, 2013, 20, 466-474.
  31. Role of pKa of Nucleobases in the Origins of Chemical Evolution. Krishnamurthy, R. Acc. Chem. Res. 2012, 45, 2035-2044. Correction.pKa of nucleobases
  32. A Unified Mechanism for Abiotic Adenine and Purine Synthesis in Formamide. Hudson, J. S.; Eberle, J. F.; Vachhani, R. H.; Rogers, L. C.; Wade, J. H.; Krishnamurthy, R.; Springsteen, G. Angew. Chemie. Int. Ed. 2012, 51, 5134-5137.                                                          Unified Mechanism
  33. Exploratory Experiments on the Chemistry of the "Glyoxylate Scenario": Formation of Ketosugars from Dihydroxyfumarate. Sagi, V.N.; Punna, V.; Hu, F.; Meher, G.; Krishnamurthy, R. J. Am. Chem. Soc. 2012, 134, 3577-3589. PMCID# PMC3284196DHF-glyoxylate
  34. Diastereoselective Self-Condensation of Dihydroxyfumaric Acid in Water: Potential Route to Sugars. Sagi, V.N.; Karri, P.; Hu, F., Krishnamurthy, R. Angew. Chem. Int. Ed. 2011, 50, 8127-8130.                                                                                             DHF self condensation
  35. An expedient synthesis of L-ribulose and derivatives. Meher, G.; Krishnamurthy, R. Carbohydr. Res. 2011, 346, 703-707.ribulose
  36. Mapping the Landscape of Potentially Primordial Informational Oligomers: (3’→2’)-D-Phosphoglyceric Acid Linked Acyclic Oligonucleotides Tagged with 2,4-Disubstituted 5-Aminopyrimidines as Recognition Elements. Hernández-Rodríguez M.; Xie, J.; Osornio, Y. M.; Krishnamurthy, R. Chemistry An Asian Journal, 2011, 6, 1251-1262.     glyceric acid NAGlyceric acid NA2

  37. Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligo-Dipeptides Tagged with 6-Carboxy-pyrimidines as Recognition Elements. Zhang, X.; Krishnamurthy, R. Angew. Chem. Int. Ed. 2009, 48, 8124-8128.                        orotic acid tagged dipeptide
  38. A search for Structural Alternatives of RNA. Krishnamurthy, R. J. Mex. Chem. Soc. 2009, 53, 23-33.pKa of nucleobases correlation
  39. Structure of TNA-TNA complex in solution: NMR Study of the Octamer Duplex Derived from α-(L)-threofuranosyl-(3’–2’)-CGAATTCG. Ebert, M-O.; Mang, C.; Krishnamurthy, R.; Eschenmoser, A.; Jaun, B. J. Am. Chem. Soc. 2008, 130, 15105-15115.TNA NMR structure
  40. Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligo-Dipeptides Tagged with 2,4-Disubstituted 5-amino-pyrimidines as Recognition Elements. Mittapalli, G.K.; Osornio, Y.M.; Guerrero, M.A.; Ravinder, K.R.; Krishnamurthy, R.; Eschenmoser, A. Angew. Chem. Int. Ed. 2007, 46, 2478-2484.trazines
  41. Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligo-dipeptides and Oligo-dipeptoids Tagged with Triazines as Recognition Elements. Mittapalli, G.K.; Ravinder, K.R.; Xiong, H.; Munoz, O.; Han, B.; De Riccardis, De F.; Krishnamurthy, R.; Eschenmoser, A. Angew. Chem. Int. Ed. 2007, 46, 2470-2477.Triazines
  42. Tautomerism in 5,8-Diaza-7,9-dicarbaguanine (‘Alloguanine’). Wagner, T.; Han, B.; Krishnamurthy, R.; Eschenmoser, A. Helv. Chim. Acta. 2005, 88, 1960-1968.
  43. Mannich-Type C-nucleosidations with 7-Carba-purines and 4-Amino-pyrimidines. Han, B.; Rajwanshi, V.; Nandy, J.; Krishnamurthy, R.; Eschenmoser, A. Synlett. 2005, 744-750.
  44. Mannich-Type C-Nucleosidations in the 5,8-Diaza-7,9-dicarba-purine Family.  Han, B.; Jaun, B.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett. 2004, 6, 3691-3694.
  45. Base-Pairing Systems Related to TNA Containing Phosphoramidate Linkages: Synthesis of Building Blocks and Pairing Properties. Ferenic, M.; Reddy, G.; Wu, X.; Guntha, S.; Nandy, J.; Krishnamurthy, R.; Eschenmoser, A. Chemistry & Biodiversity, 2004, 1, 939-979.
  46. The β-D-Ribopyranosyl-(4’→2’)-oligonucleotide System (‘pyranosyl-RNA’): Synthesis and Resumé of Base-Pairing Properties. Pitsch, S.; Wendeborn, S.; Krishnamurthy, R.; Holzner, A.; Minton, M.; Bolli, M.; Miculca, C.; Windhab, N.; Micura, R.; Stanek, M.; Jaun, B.; Eschenmoser, A. Helv. Chim. Acta. 2003, 86, 4270-4363.
  47. Assignment of the 1H and 13C-NMR Spectra of N2,N6-dibenzoyl-N2,N9-bis(2’,3’-di-O-benzoyl-(a)-L-Threofuranosyl)-2,6-diaminopurine. Delgado, G.; Krishnamurthy, R. Revista de la Sociedad Quimica de Mexico, 2003, 47, 216-220.
  48. Why Does TNA Cross-Pair More Strongly with RNA Than with DNA? An Answer From X-ray Analysis. Pallan, P. S.; Wilds, C. J.; Wawrzak, Z.; Krishnamurthy, R.; Eschenmoser, A., Egli., M Angew. Chem. Int. Ed. 2003, 42, 5893-5895.
  49. C-Nucleosidations with 2,6-Diamino-5,8-diaza-7,9-dicarba-purine. Han, B.; Wang, Z.; Jaun, B.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett. 2003, 5, 2071-2074.
  50. 2,6-Diamino-5,8-diaza-7,9-dicarba-purine. Wang, Z.; Huynh, H. K.; Han, B.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett. 2003, 5, 2067-2070.
  51. Pentopyranosyl Oligonucleotide Systems. The α-L-Arabinopyranosyl-(4’→2’)-Oligonucleotide System: Synthesis and Pairing Properties. Jungmann, O.; Beier, M.; Luther, A.; Huynh, H. K.; Ebert, M. O.; Jaun, B.; Krishnamurthy, R.; Eschenmoser, A. Helv. Chim. Acta. 2003, 86, 1259-1308.
  52. The α-L-Threofuranosyl-(3’→2’)-Oligonucleotide System (‘TNA’): Synthesis and Pairing Properties. Schoning, K.-U.; Scholz, P.; Wu, X.; Guntha, S., Delgado, G.; Krishnamurthy, R.; Eschenmoser, A. Helv. Chim. Acta. 2002, 85, 4111-4153.
  53. Crystal Structure of a B-Form DNA Duplex Containing L-α-Threofuranosyl-(3’→2’)-Nucleosides: A Four-Carbon sugar is easily accommodated into the back bone of DNA. Wilds, C. J.; Wawrzak, Z.; Krishnamurthy, R.; Eschenmoser, A.; Egli, M. J. Am. Chem. Soc. 2002, 124, 13716-13721.
  54. NMR Solution Structure of Duplex Formed by Self-Pairing of α-(D)-Arabinopyranosyl-(4’→2’)-(CGAATTCG). Ebert, M-O.; Hoan, H. K.; Luther, A.; Krishnamurthy, R.; Eschenmoser, A., Jaun, B. Helv. Chim. Acta. 2002, 85, 4055-4073.
  55. 2,6-Diaminopurines in TNA: Effect on Duplex Stabilities and on the Efficiency of Template-Controlled Ligations. Wu, X.; Delgado, G.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett. 2002, 4, 1283-1286.
  56. Base-Pairing Systems Related to TNA: α-Threofuranosyl Oligonucleotides Containing Phosphoramidate Linkages. Wu, X.; Guntha, S.; Ferencic, M.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett. 2002, 4, 1279-1282.
  57. Pentopyranosyl Oligonucleotide Systems. β-(D)-Xylopyranosyl-(4’→2’)-oligonucleotide System. Wagner, T.; Hoan, H. K.; Krishnamurthy, R.; Eschenmoser, A. Helv. Chim. Acta. 2002, 85, 399-416.
  58. Pentopyranosyl Oligonucleotide Systems. Systems with Shortened Backbones: (D)-β-Ribopyranosyl-(4’→3’)- and (L)-α-Lyxopyranosyl-(4’→3’)-oligonucleotide System. Wippo, H.; Reck, F.; Kudick, R.; Ramasehsan, M.; Ceulemans, G., Bolli, M.; Krishnamurthy, R.; Eschenmoser, A. Bioorg. Med. Chem. 2001, 9, 2411-2428.
  59. Pentopyranosyl Oligonucleotide Systems. The α-L-Lyxopyranosyl-(4’→2’)-oligonucleotide System. Reck, F.; Wippo, H.; Kudick, R.; Krishnamurthy, R.; Eschenmoser, A. Helv. Chim. Acta. 2001, 84, 1778-1804.
  60. Chemical Etiology of Nucleic Acid Structure: The α-Threofuranosyl-(3’→2’) Oligonucleotide System. Schöning, K.-U.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy, R.; Eschenmoser, A. Science 2000, 290, 1347-1351.
  61. Concentration of Simple Aldehydes by Sulfite-Containing Double-Layer Hydroxide Minerals: Implications for Biopoesis. Pitsch, S.; Krishnamurthy, R.; Arrhenius. G. Helv. Chim. Acta. 2000, 83, 2398.
  62. Regioselective a-Phosphorylation of Aldoses in Aqueous Solution. Krishnamurthy, R.; Guntha, S.; Eschenmoser. A. Angewandte Chemie Int. Ed. 2000, 39, 2281.
  63. Before RNA and After: Geophysical and Geochemical Constraints on Molecular Evolution. Mojzsis, S.; Krishnamurthy, R.; Arrhenius, G. in The RNA World’, second edition, pp 1-47, Eds. Gesteland, R. F.; Cech, T. R.; Atkins, J. F. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1999. DOI: 10.1101/087969589.37.1
  64. L-α-Lyxopyranosyl (4'→3') Oligonucleotides: A Base-Pairing System Containing a Shortened Backbone. Reck, F.; Wippo, H.; Kudick, R.; Krishnamurthy, R.; Eschenmoser, A. Organic Letters, 1999, 1, 1531-1534.
  65. Promiscuous Watson-Crick Cross-Pairing within the Family of Pentopyranosyl (4'→2') Oligonucleotides. Jungmann, O.; Wippo, H.; Stanek, M.; Huynh, H. K.; Krishnamurthy, R.; Eschenmoser, A. Organic Letters, 1999, 1, 1527-1530.
  66. Chemical Etiology of Nucleic Acid Structure: Comparing Pentopyranosyl-(2'→4') Oligonucleotides with RNA. Beier, M.; Reck, F.; Wagner, T.; Krishnamurthy, R.; Eschenmoser, A.  Science 1999, 283, 699-703.
  67. Formation of Glycolaldehyde Phosphate From Glycolaldehyde in Aqueous Solution. Krishnamurthy, R.; Arrhenius, G; Eschenmoser, A.  Origins Life Evol. Biosphere 1999, 29, 333-354.
  68. Mineral Induced Formation of Pentose-2,4-diphosphates. Krishnamurthy, R.; Pitsch, S.; Arrhenius, G.  Origins Life Evol. Biosphere 1999, 29, 139-152.
  69. Formation of sugar phosphates under potentially natural conditions. Krishnamurthy, R.; Pitsch, S.; Eschenmoser, A.; Arrhenius, G.  Mineral. Mag. 1998, 62A(Pt. 2), 815.
  70. Pyranosyl-RNA: Base-pairing beween Homochiral Oligonucelotide Strands of Opposite Sense of Chirality. Krishnamurthy, R.; Pitsch, S.; Minton, M.; Miculka, C.; Windhab, N.; Eschenmoser, A. Angewandte Chemie, Int. Ed. Engl. 1996, 35, 1537-1541.
  71. p-RNA, the pyranosyl isomer of RNA: Pairing properties and potential to replicate. Pitsch, S.; Krishnamurthy, R.; Wendeborn, S.; Holzner, A.; Minton, M.; Lesueur, C.; Schlönvogt, I.; Jaun, B.; Eschenmoser, A. Helevetica chimica Acta  1995, 78, 1621-1635.
  72. Bis(tri-n-butylstannyl)benzopinacolate: Preparation and Use as a Mediator of Intermolecular Free Radical Reactions. Hart, D. J.; Krishnamurthy, R.; PooK, L. M.; Seely, F. L. Tetrahedron Letters 1993, 34, 7819-7822.
  73. Synthesis of 6H-Dibenzo(b,d)pyran-6-ones via Dienone-Phenol Rearrangements of Spiro(2,5-Cyclohexadiene-1,1'(3'H)-isobenzofuran)-3'-ones. Hart, D. J.; Kim, A.; Krishnamurthy, R.; Merriman, G. H.; Waltos, A-M. Tetrahedron 1992, 48, 8179-8188.
  74. Investigation of a Model for 1,2-Asymmetric Induction in Reactions of a-Carbalkoxy Radicals: A Stereochemical Comparison of Reactions of α-Carbalkoxy Radicals and Ester Enolates. Hart, D. J.; Krishnamurthy, R. J. Org. Chem. 1992, 57, 4457-4470.
  75. Stereoselective Free Radical Reactions at C(20) of Steroid Chains. Hart, D. J.; Krishnamurthy, R., Synlett. 1991, 412-414.
  76. Free-Radical Cyclizations: Application to the Total Synthesis of dl-Pleuorotin and dl-Pleurotinic acid. Hart, D. J.; Huang, H.-C; Krishnamurthy, R.; Schwartz, T. J. Am. Chem. Soc. 1989, 111, 7507-7519.