Decrease in RNA Folding Cooperativity by Deliberate Population of Intermediates in RNA G-Quadruplexes

Targeted Detection of G-Quadruplexes in Cellular RNAs

The G-quadruplex (G4) is a non-canonical nucleic acid structure which regulates important cellular processes. RNA G4s have recently been shown to exist in human cells and be biologically significant. Described herein is a new approach to detect and map RNA G4s in cellular transcripts. This method exploits the specific control of RNA G4-cation and RNA G4-ligand interactions during reverse transcription, by using a selective reverse transcriptase to monitor RNA G4-mediated reverse transcriptase stalling (RTS) events. Importantly, a ligation-amplification strategy is coupled with RTS, and enables detection and mapping of G4s in important, low-abundance cellular RNAs. Strong evidence is provided for G4 formation in full-length cellular human telomerase RNA, offering important insights into its cellular function.

Using the population-shift mechanism to rationally introduce "Hill-type" cooperativity into a normally non-cooperative receptor

Allosteric cooperativity, which nature uses to improve the sensitivity with which biomolecular receptors respond to small changes in ligand concentration, could likewise be of use in improving the responsiveness of artificial biosystems. Thus motivated, we demonstrate here the rational design of cooperative molecular beacons, a widely employed DNA sensor, using a generalizable population-shift approach in which we engineer receptors that equilibrate between a low-affinity state and a high-affinity state exposing two binding sites. Doing so we achieve cooperativity within error of ideal behavior, greatly steepening the beacon's binding curve relative to that of the parent receptor. The ability to rationally engineer cooperativity should prove useful in applications such as biosensors, synthetic biology and "smart" biomaterials, in which improved responsiveness is of value.

Optimizing the kinetics and thermodynamics of DNA i-motif folding

Under slightly acidic conditions, single cytidine-rich DNA strands can form four-stranded structures called i-motifs. The stability of the i-motif structure is based on the intercalation of hemiprotonated C-C(+) base pairs. In addition, the stability of these structures is influenced by pH, temperature, salt concentration, number of cytidines per C-rich stretch, and length of sequence; it also depends on the nucleotides in the connecting loop regions. Here, we investigated the influence of the loop nucleotides on i-motif stability, structure, and kinetics of folding, in five structures with the same loop-size but different adenosine and thymidine residues within the loop. The stabilities of the i-motif structures were determined by CD melting, and structure and kinetics of folding were studied by static and time-resolved NMR experiments.