Detection of DNA or RNA using single molecule arrays and other techniques
Inventors
Duffy, David C. • Song, Linan • Shan, Dandan • Zhao, Mingwei
Assignees
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Publication Number
US-10640814-B2
Publication Date
2020-05-05
Expiration Date
Abstract
Described herein are methods and systems for detecting DNA or RNA using single molecules array or other techniques. DNA or RNA from the sample may be fragmented and exposed to a first type of binding ligand and a second type of binding ligand that comprise nucleic acid sequences complimentary at least a portion of a sequence contained in the target DNA or RNA. At least a portion of the fragmented DNA or RNA associates with at least one of the first type of binding ligand and/or the second type of binding ligand, wherein the first type of binding ligand and second type of binding ligand comprises nucleic acid sequences complimentary to a different portions of a sequence contained in the DNA or RNA. A portion of the sample exposed to the binding ligands is analyzed to determine the number of fragmented DNA or RNA sequences.
Core Innovation
The method determines, detects, or measures the concentration of DNA or RNA molecules and fragments derived from molecules in a sample. Fragments are exposed to first and second capture objects, each comprising a capture probe complementary to a different portion of the target sequence, wherein both capture-object populations produce substantially similar signals. A portion of the sample is analyzed to determine the number of fragments associated with at least one of the capture-object types.
The disclosure indicates that multiple probe sites improve target capture and detection despite target fragmentation or steric hindrance. Reported single-molecule DNA and RNA detection results demonstrate concentration-dependent signal measurement, target-specific responses in multiplex assays, and detection of bacterial DNA across blood and river water samples. The background problem being solved is not explicitly described due to omitted introductory patent sections.
Claims Coverage
The claims identify one independent claim comprising two inventive features covering target binding to multiple capture objects and subsequent quantitative analysis.
Capture objects with probes for different sequence portions
First capture objects comprise a first capture probe complementary to a first portion of the DNA or RNA sequence, and second capture objects comprise a second capture probe complementary to a different portion, wherein the first and second capture objects produce substantially similar signals.
Determination of the number of associated fragments
A portion of the sample from the exposing step is analyzed to determine the number of DNA or RNA fragments associated with at least one of the first and second capture objects.
The independent claim combines fragment capture using two capture-object types directed to distinct sequence portions while generating substantially similar signals with quantitative analysis of associated fragments.
Stated Advantages
The reported assay optimizations improve RNA signals.
NaOH-denatured DNA produces signals comparable to or better than heat-denatured DNA.
The reported assays detect Sendai virus RNA and Staphylococcus aureus DNA, and the multiplex DNA assay shows target-specific responses.
Multiple probe sites can improve capture and detection despite target fragmentation or steric hindrance.
Documented Applications
Direct detection and concentration measurement of DNA or RNA fragments in a sample.
Detection of Sendai virus RNA.
Multiplex DNA detection using a 10-plex bead-encoded assay and multiplex detection of bacterial targets.
Detection of bacterial DNA in blood samples and river water, including genomic DNA from E. coli, S. aureus, and C. perfringens.
Interested in licensing this patent?