Browsing by Author "Wu, Ruojia"

Now showing 1 - 4 of 4
  • Thumbnail Image
    Item
    Fine-tuned ultraspecific nucleic acid hybridization probes
    (2021-01-26) Zhang, David Yu; Wang, Juexiao; Wu, Ruojia; Rice University; United States Patent and Trademark Office
    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 (ΔG°rxn=ΔG°t-TC−ΔG°nh-PC+(ΔG°v-TC−ΔG°h-PC)) is from about −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 (−Rτ ln(([P]0−[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 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.
  • Thumbnail Image
    Item
    Method, apparatus, and computer-readable medium for predicting a hybridization rate constant of a first sequence
    (2022-10-18) Zhang, Xuemeng; Fang, Zheng; Wu, Ruojia; Duan, Wei; Zhang, David; Rice University; William Marsh Rice University; United States Patent and Trademark Office
    Embodiments of methods, systems, and tangible non-transitory computer readable medium having instructions are presented. A method includes calculating a plurality of feature values for a number of bioinformatic features of the desired hybridization reaction; and calculating distances between the plurality of feature values and corresponding database rate constant values stored in a database, the database comprising a plurality of hybridization reactions having known rate constants. The method additionally includes calculating a weighted average of a logarithm of the database rate constant values, with larger weights assigned to value instances having values lower in distance to the plurality of feature values of the desired hybridization reaction; and providing the weighted average as a predicted logarithm of the rate constant of the desired hybridization reaction.
  • Thumbnail Image
    Item
    Simple, Multiplexed, and Ultraspecific Nucleic Acid-based Diagnostic Technologies
    (2017-06-15) Wu, Ruojia; Zhang, David Y
    The economical and high-throughput detection and quantitation of disease-relevant nucleic acid sequences is a key goal in the road to widespread adoption of precision medicine, wherein optimal individualized treatment is provided to each patient based on his or her unique genetic and disease profile. Current widely used technology platforms such as microarray, NGS, and PCR are either expensive and time-consuming, or difficult to scale up to multiplexed assays. Additionally, highly specific and sensitive detection of small nucleotide variants is still challenging using conventional methods. During my PhD, I have developed several novel molecular approaches to improve the specificity and / or multiplexibility of existing technology platforms, and further validated them using biological and clinical samples. The philosophy behind these works is to pursue reliable in silico assay design and thus less empirical optimization, to develop methods that are generalizable to any target sequence in the genome, and to make the experimental procedures simple, cheap, and fast.
  • Thumbnail Image
    Item
    Stoichiometric tuning of nucleic acid hybridization probes by auxiliary oligonucleotide species
    (2024-01-23) Zhang, David Yu; Wu, Ruojia; Wang, Juexiao; William Marsh Rice University; United States Patent and Trademark Office
    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.