Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.

Numerous riboswitches have been discovered that specifically recognize metabolites and modulate gene expression. Each riboswitch class is defined either by the consensus sequence and structural features of its metabolite-binding aptamer domain, or by the distinct metabolite that the aptamer recognizes. Several distinct classes of riboswitches that respond to S-adenosylmethionine (SAM or AdoMet) have been discovered.

Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling.

We have identified a highly conserved RNA motif that occurs upstream of genes involved in S-adenosyl-L-methionine (SAM) recycling in many Gram-positive and Gram-negative species of bacteria. The phylogenetic distribution and the conserved structural features of representatives of this motif are indicative of riboswitch function. Riboswitches are widespread metabolite-sensing gene control elements that are typically found in the 5' untranslated regions (UTRs) of bacterial mRNAs.

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.

We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches.

Antibacterial lysine analogs that target lysine riboswitches.

Lysine riboswitches are bacterial RNA structures that sense the concentration of lysine and regulate the expression of lysine biosynthesis and transport genes. Members of this riboswitch class are found in the 5' untranslated region of messenger RNAs, where they form highly selective receptors for lysine. Lysine binding to the receptor stabilizes an mRNA tertiary structure that, in most cases, causes transcription termination before the adjacent open reading frame can be expressed.

The effect of a single boranophosphate substitution with defined configuration on the thermal stability and conformation of a DNA duplex.

Substitution of one non-bridging oxygen in a natural phosphodiester internucleotide linkage with a borano (-BH3) group results in a chiral phosphorus center in boranophosphate. UV thermal melting profiles were recorded for DNA duplexes formed between a DNA 9-mer with either an Sp or a Rp boranophosphate linkage in the middle and the complementary DNA 9-mer, as well as for their unmodified parent duplex. The thermal stability of the DNA duplexes was in the order of normal > Sp borano > Rp borano.

Synthesis of 5-(1-propynyl)-2'-deoxyuridine 5'-(alpha-P-borano)triphosphate and kinetic characterization as a substrate for mmlv reverse transcriptase.

In order to introduce pyrimidine C5-propynyl modification into boranophosphate oligodeoxyribonucleotides (BP- ODNs), 5-(1-propynyl)-2'-deoxyuridine 5'-(alpha-P-borano) triphosphate (d5PUTPalphaB) was synthesized. The two diastereomers were separated by reverse-phase HPLC. Kinetic studies showed that the Rp isomer was a slightly better substrate for MMLV reverse transcriptase than thymidine triphosphate or Rp-thymidine 5'-(alpha-P-borano)triphosphate.