Single-molecule studies of the lysine riboswitch reveal effector-dependent conformational dynamics of the aptamer domain.

The lysine riboswitch is a cis-acting RNA genetic regulatory element found in the leader sequence of bacterial mRNAs coding for proteins related to biosynthesis or transport of lysine. Structural analysis of the lysine-binding aptamer domain of this RNA has revealed that it completely encapsulates the ligand and therefore must undergo a structural opening/closing upon interaction with lysine. In this work, single-molecule fluorescence resonance energy transfer (FRET) methods are used to monitor these ligand-induced structural transitions that are central to lysine riboswitch function.

The role of counterion valence and size in GAAA tetraloop-receptor docking/undocking kinetics.

For RNA to fold into compact, ordered structures, it must overcome electrostatic repulsion between negatively charged phosphate groups by counterion recruitment. A physical understanding of the counterion-assisted folding process requires addressing how cations kinetically and thermodynamically control the folding equilibrium for each tertiary interaction in a full-length RNA. In this work, single-molecule FRET (fluorescence resonance energy transfer) techniques are exploited to isolate and explore the cation-concentration-dependent kinetics for formation of a ubiquitous RNA tertiary interaction, that is, the docking/undocking of a GAAA tetraloop with its 11-nt receptor.

Thiolated dendrimers as multi-point binding headgroups for DNA immobilization on gold.

The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers.

Reactions of C=C-terminated self-assembled monolayers with gas-phase ozone.

Reactions of gas-phase ozone with alkene-terminated alkanethiol self-assembled monolayers on Au are explored using reflection-absorption infrared spectroscopy (RAIRS). The experiments are performed by using a directional doser to control the ozone flux onto the surface and in situ high vacuum techniques to eliminate reactions with atmospheric contaminants. We find that reactions between ozone and the C=C terminal group proceed through the formation of a carboxylic acid moiety that subsequently converts to an interchain carboxylic acid anhydride.