US 12,258,631 B2
RNA and DNA analysis using engineered surfaces
Gudrun Stengel, San Diego, CA (US); Hua Yu, San Diego, CA (US); Andrew Price, San Diego, CA (US); Jerome Santos, San Diego, CA (US); Yu-Hsien Hwang-Fu, San Diego, CA (US); and Byron Purse, San Diego, CA (US)
Assigned to ALIDA BIOSCIENCES INC., San Diego, CA (US)
Filed by ALIDA BIOSCIENCES, INC., San Diego, CA (US)
Filed on Jun. 28, 2023, as Appl. No. 18/343,028.
Application 18/343,028 is a continuation of application No. PCT/US2022/080452, filed on Nov. 23, 2022.
Claims priority of provisional application 63/388,036, filed on Jul. 11, 2022.
Claims priority of provisional application 63/282,808, filed on Nov. 24, 2021.
Prior Publication US 2023/0416828 A1, Dec. 28, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6883 (2018.01); C12N 9/22 (2006.01); C12N 15/10 (2006.01); C12Q 1/48 (2006.01); C12Q 1/6806 (2018.01); C12Q 1/6853 (2018.01); C12Q 1/6874 (2018.01)
CPC C12Q 1/6883 (2013.01) [C12N 9/22 (2013.01); C12N 15/1065 (2013.01); C12Q 1/485 (2013.01); C12Q 1/6806 (2013.01); C12Q 1/6853 (2013.01); C12Q 1/6874 (2013.01)] 30 Claims
 
1. A method for detecting a plurality of non-canonical features in a plurality of target nucleic acids, the method comprising:
(i) providing a plurality of target nucleic acids by reverse transcribing target RNA molecules to form DNA-RNA heteroduplex molecules or providing target double-stranded DNA molecules;
(ii) contacting a solution comprising the plurality of target nucleic acids with a composition comprising:
a substrate,
a binding domain coupled to the substrate via a first linker or a secondary recognition element,
mosaic end (ME) adapters coupled to the substrate via a second linker or recognition element, and
a transposase,
wherein the transposase is loaded to the immobilized ME adapters,
wherein the binding domain binds specifically to a non-canonical feature of a DNA or an RNA,
wherein at least one of the ME adapters comprises a nucleic acid barcode sequence unique to the non-canonical feature; or
the substrate,
the binding domain coupled to the substrate via a linker or secondary recognition element, and
the transposase coupled to the binding domain,
wherein the transposase is loaded with ME adapters,
wherein the binding domain binds specifically to a non-canonical feature of a DNA or an RNA,
wherein at least one of the ME adapters comprises a nucleic acid barcode sequence unique to the non-canonical feature;
(iii) transferring, using transposase, two adapters, at least one of them comprising the nucleic acid barcode, to a double-stranded target nucleic acid comprising the non-canonical feature to generate barcoded target nucleic acids,
(iv) amplifying the barcoded target nucleic acids; and
(v) sequencing the barcoded target nucleic acids,
wherein steps (ii) and (iii) are performed concurrently or sequentially.