William Marsh Rice University

Juexiao Wang

David Y Zhang

Ruojia Wu

David Yu Zhang

Yan Yan

This invention describes a method of controlling the hybridization yield of nucleic acid probes by adjusting the relative concentrations of auxiliary oligonucleotides to the probes and the targets. The auxiliary oligonucleotide is partially or fully complementary to either the probe or the target, and is released upon hybridization of the probe to the target.

Stoichiometric tuning of nucleic acid hybridization probes by auxiliary oligonucleotide species

This present disclosure describes hybridization probes modularly constructed from several oligonucleotides with a pattern of designed complementary interactions, allowing the probes to sequence-specifically capture or analyze nucleic acid target sequences that are long and/or complex.

Molecular hybridization probes for complex sequence capture and analysis

The present disclosure describes the thermodynamic design and concentrations necessary to design probe compositions with desired optimal specificity that enable enrichment, detection, quantitation, purification, imaging, and amplification of rare-allele-bearing species of nucleic acids (prevalence &#x3c;1%) in a large stoichiometric excess of a dominant-allele-bearing species (wildtype). Being an enzyme-free and homogeneous nucleic acid enrichment composition, this technology is broadly compatible with nearly all nucleic acid-based biotechnology, including plate reader and fluorimeter readout of nucleic acids, microarrays, PCR and other enzymatic amplification reactions, fluorescence barcoding, nanoparticle-based purification and quantitation, and in situ hybridization imaging technologies.

Competitive compositions of nucleic acid molecules for enrichment of rare-allele-bearing species

Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (&#x394;G&#xb0;=&#x394;G&#xb0;&#x2212;&#x394;G&#xb0;+(&#x394;G&#xb0;&#x2212;&#x394;G&#xb0;)) is from about &#x2212;4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (&#x2212;R&#x3c4; ln(([P]&#x2212;[C])/[C])]), where the [P]term of Expression 2 equals the concentration of the protector strand and the [C]term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.

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Houston, TX, United States of America

Juexiao Wang