FfAME:org :: Nilesh Karalkar's 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."

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 43-56 (2008)

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.