RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.

Using a graph representation of RNA structures, we have studied the ensembles of secondary and tertiary graphs of two sets of RNA with Monte Carlo simulations. The first consisted of 91 target ribozyme and riboswitch sequences of moderate lengths (<150 nt) having a variety of secondary, H-type pseudoknots and kissing loop interactions. The second set consisted of 71 more diverse sequences across many RNA families.

Diagrammatic approaches to RNA structures with trinucleotide repeats.

Trinucleotide repeat expansion disorders are associated with the overexpansion of (CNG) repeats on the genome. Messenger RNA transcripts of sequences with greater than 60-100 (CNG) tandem units have been implicated in trinucleotide repeat expansion disorder pathogenesis. In this work, we develop a diagrammatic theory to study the structural diversity of these (CNG) RNA sequences.

Topological Constraints and Their Conformational Entropic Penalties on RNA Folds.

Functional RNAs can fold into intricate structures using a number of different secondary and tertiary structural motifs. Many factors contribute to the overall free energy of the target fold. This study aims at quantifying the entropic costs coming from the loss of conformational freedom when the sugar-phosphate backbone is subjected to constraints imposed by secondary and tertiary contacts.

H2O2 Detection at Carbon Nanotubes and Nitrogen-Doped Carbon Nanotubes: Oxidation, Reduction, or Disproportionation?

The electrochemical behavior of hydrogen peroxide (H2O2) at carbon nanotubes (CNTs) and nitrogen-doped carbon nanotubes (N-CNTs) was investigated over a wide potential window. At CNTs, H2O2 will be oxidized or reduced at large overpotentials, with a large potential region between these two processes where electrochemical activity is negligible. At N-CNTs, the overpotential for both H2O2 oxidation and reduction is significantly reduced; however, the reduction current from H2O2, especially at low overpotentials, is attributed to increased oxygen reduction rather than the direct reduction of H2O2, due to a fast chemical disproportionation of H2O2 at the N-CNT surface.