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
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) 879-895 (2010)
<Abstract>
Nucleoside triphosphates having a 3'-ONH(2) blocking group have been prepared with and without fluorescent tags on their nucleobases. DNA polymerases were identified that accepted these, adding a single nucleotide to the 3'-end of a primer in a template-directed extension reaction that then stops. Nitrite chemistry was developed to cleave the 3'-ONH(2) group under mild conditions to allow continued primer extension. Extension-cleavage-extension cycles in solution were demonstrated with untagged nucleotides and mixtures of tagged and untagged nucleotides. Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3'-ONH(2) blocking group in "next generation sequencing."
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)
<Abstract>
Enzymatic ligation methods are useful in diagnostic detection of DNA sequences. Here we describe the investigation of nonenzymatic phosphorothioate-iodide DNA autoligation chemistry as a method for detection and identification of both RNA and DNA sequences. Combining ligation specificity with the hybridization specificity of the ligated product is shown to yield discrimination of a point mutation as high as >10(4)-fold. Unlike enzymatic ligations, this reaction is found to be equally efficient on RNA or DNA templates. The reaction is also shown to exhibit a significant level of self-amplification, with the template acting in catalytic fashion to ligate multiple pairs of probes. A strategy for fluorescence labeling of three autoligating energy transfer (ALET) probes and directly competing them for autoligation on a target sequence is described. The method is tested in several formats, including solution phase, gel, and blot assays. the ALET probe design offers direct RNA detection, combining high sequence specificity with an easily detectable color change by fluorescence resonance energy transfer (FRET).
A mild and efficient method for the preparation of 5 '-dimethoxytrityl-2 '-deoxynucleoside using poly(4-vinylpyridine)-costyrene
Karalkar, NB; Akerkar, VG; Salunkhe, MM
Indian J. Chem., Sect B
38 (3) 370-371 (1999)
<Abstract>
5'-O-4,4'-Dimethoxytrityl-2'-deoxynucleosides have been synthesized in high yield by the reaction of 2'-deoxynucleosides with 4, 4'-dimethoxytrityl chloride in acetonitrile using poly (4-vinylpyridine)-costyrene (styrene 10%).
Synthesis of sulfoxides by the oxidation of sulfides with polymer supported periodate ion
Karalkar, NB; Salunkhe, MM; Talekar, KP; Maldar, NN
Indian J. Chem., Sect B
37 (11) 1184-1185 (1998)
<Abstract>
Aromatic and aliphatic sulfides have been oxidized by polymer-supported periodate ion to give sulfoxides in high yield and purity without undesirable side reaction.
Synthesis and properties of new chelating resin with a spacer containing alpha-nitroso-beta-naphthol as the functional group
Akerkar, VG; Karalkar, NB; Sharma, RK; Salunkhe, MM
Talanta
46 (6) 1461-1467 (1998)
<Abstract>
A new chelating ion-exchange resin with a spacer CH2-NH-C6H4- based on a microreticular chloromethylated styrene-divinylbenzene copolymer containing alpha-nitroso-beta-naphthol as a functional group has been synthesized. The sorption characteristics for manganese(II), iron(III), cobalt(II), nickel(II), copper(II), and zinc(II) have been investigated over the pH range 1.0-7.0. The resin is highly stable in acidic and alkaline medium. Iron(III) and cobalt(II); copper(II) and iron(III) are separated very effectively in a column operation by stepwise elution. (C) 1998 Elsevier Science B.V. All rights reserved.
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