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Associate

Nilesh Karalkar

Education

  • PhD in Chemistry. Mumbai University, India (1999)
  • Postdoctoral Research Associate. Standford University, CA (2001)
  • Research Scientist, Medicinal Chemistry. Geron Corporation, Menlo Park, CA (2003)
  • Scientist, Speciality Nucleic Acid Chemistry. Transgenomic, Boulder, CO (2006)

Research summary

My current research involves chemically synthesized base pairs that will recognize each other through hydrogen bonds in a manner similar to natural bases (A,C,G,T) but with altered H-bonding directionality. This technology could be implemented in a wide variety of applications including mutation detection, mixed population genotyping, and multiplexed genetic analysis.

My past research has included the following topics:

Affinity purification of high value proteins. Since its discovery, affinity chromatography has evolved as one of the most powerful and effective fractionation techniques for the purification of proteins. The unique interaction between the target molecule and complementary ligand covalently attached to an insoluble matrix provides the specificity required for the isolation of biomolecules from complex mixtures, such as cell extracts. I have worked on developing a method/approach for the capture of molecules and/or assemblies that is mediated by interaction of a substrate with a capture phase.

Telomerase inhibitors. One of the enzymes found in 90 percent of cancer cells is a compound called telomerase; it replaces the bit of telomere clipped off after each cell division. If telomerase production can be turned on in normal cells, it seems reasonable that normal cells could become immortal. My past research has focused on inhibition of human telomerase (hTR). Towards this goal I have designed, synthesized, and evaluated novel lipid conjugated N3'-P5' oligonucleotide as telomerase inhibitors.

Recent Publications

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Electrochemical Reduction and Oxidation of Eight Unnatural 2'-Deoxynucleosides at a Pyrolytic Graphite Electrode
Spacek, J., Karalkar, N., Fojta, M., Wang, J., Benner, S. A
Electrochimica acta , International Society of Electrochemistry (2020) 362:137210, DOI:10.1016/j.electacta.2020.137210
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Hachimoji DNA and RNA: A genetic system with eight building blocks
Hoshika H, Leal N, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins Jr. NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr. J, Georgiadis MM, Benner SA
Science (2019) 22 Feb 2019: Vol. 363, Issue 6429, pp. 884-887. DOI: 10.1126/science.aat0971
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The Challenge of Synthetic Biology. Synthetic Darwinism and the Aperiodic Crystal Structure.
Karalkar, N.B. and Benner, S.A.
Curr. Op. Chem Biol. (2018) 46C:188-195, DOI:10.1016/j.cbpa.2018.07.008
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Tautomeric equilibria of iso-guanine and related purine analogs
Nilesh B. Karalkar, Kshitij Khare, Robert Molt, and Steven A. Benner
Nuc. Nuc. Nuc. acids , Taylor & Francis Group (2017) Apr 3;36(4):256-274. doi: 10.1080/15257770.2016.1268694
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Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase
Mariko F. Matsuura, Ryan W. Shaw, Jennifer D. Moses, Hyo-Joong Kim, Myong-Jung Kim, Myong-Sang Kim, Shuichi Hoshika, Nilesh Karalkar, and Steven A. Benner
ACS Synthetic Biology , American Chemical Society (2016) 5 (3), pp 234-240 DOI: 10.1021/acssynbio.5b00172
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Synthesis and Enzymology of 2'-Deoxy-7-deazaisoguanosine Triphosphate and Its Complement: A Second Generation Pair in an Artificially Expanded Genetic Information System
Karalkar NB, Leal NA, Kim MS, Bradley KM, Benner SA
ACS Synthetic Biology , American Chemical Society (2016) doi: 10.1021/acssynbio.5b00276
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Alternative Watson-Crick Synthetic Genetic Systems
Steven A. Benner, Nilesh B. Karalkar, Shuichi Hoshika, Roberto Laos, Ryan W. Shaw, Mariko Matsuura, Diego Fajardo, and Patricia Moussatche
Cold Spring Harb Perspect Biol , Cold Spring Harbor Laboratory Press (2016) doi: 10.1101/cshperspect.a023770
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Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups
Hutter, D; Kim, MJ; Karalkar, N; Leal, NA; Chen, F; Guggenheim, E; Visalakshi, V; Olejnik, J; Gordon, S; Benner, SA
Nuc. Nuc. Nuc. acids 29 (11) , Taylor & Francis Group 879-895 (2010)
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Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules
Kim, HJ; Kim, MJ; Karalkar, N; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 , Taylor & Francis Group 43-56 (2008)

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Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations
Xu, YZ; Karalkar, NB; Kool, ET
Nat. Biotechnol. 19 (2) 148-152 (2001)
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