Nicole M. Nichols

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T4 RNA ligase 1 catalyzes the ATP-dependent covalent joining of single-stranded 5'-phosphoryl termini of DNA or RNA to single-stranded 3'-hydroxyl termini of DNA or RNA. T4 RNA ligase 2 also catalyzes the joining of a 3'-hydroxyl terminus of RNA to a 5'-phosphorylated RNA or DNA; unlike T4 RNA ligase 1, this enzyme prefers double-stranded substrates. A(More)
Use of the naturally split, self-splicing Synechocystis sp. PCC6803 DnaE intein permits separate purification of the N- and C-terminal intein domains. Otherwise spontaneous intein-mediated reactions can therefore be controlled in vitro, allowing detailed study of intein kinetics. Incubation of the Ssp DnaE intein with ZnCl(2) inhibited trans splicing,(More)
Full-length human p53 protein was examined using tryptophan fluorescence and circular dichroism spectroscopy (CD) to monitor unfolding. No significant alteration in tryptophan fluorescence for the tetrameric protein was detectable over a wide range of either urea or guanidine hydrochloride concentrations, in contrast to results with the isolated DNA binding(More)
DNA binding is crucial to the protective role of the tumor suppressor protein p53, a nuclear phosphoprotein and transcription factor. The mutant human p53 protein S392E is a phosphorylation mimic that has been previously demonstrated to represent an "activated" form of p53 in both in vivo and in vitro assays [Hupp and Lane (1995) J. Biol. Chem. 270, 18165;(More)
16,16-Dimethyl PGE2 (dmPGE2) has previously been shown to protect the in vivo rat liver against CCl4-induced damage. These studies were undertaken to determine if this protection could be demonstrated in vitro where factors of absorption, secretion, and blood flow are not present. Primary hepatocyte cultures were established by perfusing rat liver with(More)
This unit describes a simple and efficient DNA engineering method that combines nucleotide sequence alteration, multiple PCR fragment assembly, and directional cloning. PCR primers contain a single deoxyuracil residue (dU), and can be designed to accommodate nucleotide substitutions, insertions, and/or deletions. The primers are then used to amplify DNA in(More)
The ability to separately purify the naturally split Synechocystis sp. PCC6803 (Ssp) DnaE intein domains has allowed detailed examination of both universal and Ssp DnaE intein-specific steps in the protein splicing pathway. By engineering substitutions at both the +1 and penultimate intein positions, we have further characterized intein reaction kinetics in(More)
Full-length p53 protein purified from Escherichia coli in the unmodified, "latent" form was examined by several methods to correlate thermal stability of structure with functional DNA binding. Structure prediction algorithms indicate that the majority of beta-sheet structure occurs in the p53 core DNA binding domain. Circular dichroism spectra demonstrate(More)
Polbase ( is a freely accessible database of DNA polymerases and related references. It has been developed in a collaborative model with experts whose contributions reflect their varied backgrounds in genetics, structural biology and biochemistry. Polbase is designed to compile detailed results of polymerase experimentation,(More)
DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. In order to achieve a high sensitivity and(More)