Abstract: Methods and apparatuses rapidly and cyclically heating and cooling a fluid sample during PCT testing to reduce the duration for full amplification of target DNA using most PCR procedures. Instead of heating and cooling static target solution in a reaction tube, the target solution reciprocates (alternately flows) back and forth within an elongate, thick-walled, small-bore tube. Sections of the tube are maintained at different temperatures so that an ascending/descending temperature gradient is maintained along the length of the tube. As the target solution flows within and along the tube from section to section, it rapidly achieves thermal equilibrium with the tube at each section, thereby rapidly thermally cycling the target solution.

Abstract: Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Abstract: A sensor chip that includes: a fluorescence quenching surface; a nucleic acid probe that contains first and second ends with the first end bound to the fluorescence quenching surface, a first region, and a second region complementary to the first region, the nucleic acid probe having, under appropriate conditions, either a hairpin conformation with the first and second regions hybridized together or a non-haipin conformation; and a first fluorophore bound to the second end of the first nucleic acid molecule. When the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface substantially quenches fluorescent emissions by the first fluorophore; and when the first nucleic acid molecule is in the non-hairpin conformation, fluorescent emissions by the fluorophore are substantially free of quenching by the fluorescence quenching surface.