Papers by Vineetha Jayasena
Complement-stabilized D-loop
Journal of Molecular Biology, Apr 1, 1993
ABSTRACT
Proceedings of the National Academy of Sciences of the United States of America, Sep 30, 1997
RNAs that undergo a rapid site-specific cleavage at low pH have been selected by in vitro selecti... more RNAs that undergo a rapid site-specific cleavage at low pH have been selected by in vitro selection (the SELEX process). The cleavage does not require the addition of any divalent metal ions, and is in fact inhibited by divalent metal ions, spermine, or high concentrations of monovalent metal ions. This low pH catalyzed cleavage results in a 2,3-cyclic phosphate at the 3 end and a free hydroxyl at the 5 end. The reaction proceeds with a calculated rate of 1.1 min ؊1 at room temperature in cacodylate buffer at pH 5.0. The rate of cleavage is dependent on the pH and shows an optimum around pH 4.0. The rate constant is independent of RNA concentration, indicating to an intramolecular reaction. Autocatalytic cleavage at low pH, in the absence of a metal ion requirement, adds to the reaction possibilities that may have existed on the prebiotic earth.
Biochemistry, 1996
T4 RegB endonuclease specifically cleaves at-GGAG-sites in several early T4 messages, rendering t... more T4 RegB endonuclease specifically cleaves at-GGAG-sites in several early T4 messages, rendering them nonfunctional. Not all-GGAG-sites are processed equally by RegB; those found at the Shine-Dalgarno sequences and in intercistronic regions are processed with higher efficiency than the-GGAG-sites located in coding regions. The low activity of RegB observed in Vitro is enhanced by 1-2 orders of magnitude by the Escherichia coli ribosomal protein S1. We have used SELEX (systematic evolution of ligands by exponential enrichment) on a combinatorial RNA library to obtain molecules that are specifically cleaved by T4 RegB endonuclease in the presence of S1. The sequences obtained contain the required-GGAG-tetranucleotide and were unusually enriched in adenosine and cytosine nucleotides. No consensus structure or sequence motif other than-GGAG-was conserved among the selected molecules. The majority of the RNAs are entirely dependent on S1 for RegB-catalyzed cleavage; however, a few RNAs are found to be S1 independent but are cleaved by RegB with much lower rates.
Nucleic Acids Research, 1989
In order to examine sequence-dependent structural effects in DNA, the ability of alternating puri... more In order to examine sequence-dependent structural effects in DNA, the ability of alternating purinepyrimidine fragments to undergo a B-Z transition when cloned in a supercoiled plasmid was determined solely as a function of sequence, with base and nearest-neighbor composition held constant. Sequences of 22 GC and 2 AT base pairs were synthesized such that the AT base pairs varied between contiguous placement and separation by eight GC base pairs. Results show, surprisingly, that the ease of the B-Z transition varies with the position of the two AT base pairs, occurring at lower superhelical densities when AT base pairs are contiguous, and at higher torsional strain when the AT base pairs are moved further apart.
Proceedings of The National Academy of Sciences, 1997
RNAs that undergo a rapid site-specific cleavage at low pH have been selected by in vitro selecti... more RNAs that undergo a rapid site-specific cleavage at low pH have been selected by in vitro selection (the SELEX process). The cleavage does not require the addition of any divalent metal ions, and is in fact inhibited by divalent metal ions, spermine, or high concentrations of monovalent metal ions. This low pH catalyzed cleavage results in a 2',3'-cyclic phosphate at
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Papers by Vineetha Jayasena