A thermodynamic and kinetic study of the binding of PNA probes to DNA and RNA hairpin structures

An introduction to polynucleotides and their applications outlines the functional importance of polynucleotide structures, contemporary oligonucleotides analogs, and a number of diagnostic and medicinal applications of oligonucleotides (Chapter I).; The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using Absorbance Hypochromicity (ABS), Circular Dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands (Chapter II).; Further thermodynamic and kinetic study illustrates the binding of PNA and DNA probes to a 16-mer RNA hairpin with the same sequence as the P9 loop of the DiGIR-1 group I-like intron. An 11-mer PNA probe is shown to hybridize to the RNA hairpin with high affinity, and high rates of hybridization (5 × 105 M−1 min−1 ; Chapter III).; Finally, a thermodynamic and kinetic study of the binding of PNA and DNA probes to two DNA hairpins with 6 and 16 base loops is performed. A molecular beacon of the hairpin containing a 16-mer loop indicates that the stem of the hairpin is not opened upon hybridization of DNA or PNA probes (Chapter IV).