US 12,297,499 B2
Multicomponent nucleic acid probes for sample analysis
Evan Daugharthy, Cambridge, MA (US); Richard Terry, Carlisle, MA (US); Soo Hee Lee, Somerville, MA (US); Michele A. Busby, Needham, MA (US); Shoshoni Droz, Boston, MA (US); and Ryan Gilmore, Somerville, MA (US)
Assigned to 10X GENOMICS, INC., Pleasanton, CA (US)
Filed by 10x Genomics, Inc., Pleasanton, CA (US)
Filed on Aug. 16, 2021, as Appl. No. 17/403,169.
Claims priority of provisional application 63/066,707, filed on Aug. 17, 2020.
Prior Publication US 2022/0049302 A1, Feb. 17, 2022
Int. Cl. C12Q 1/6876 (2018.01); C12Q 1/6832 (2018.01)
CPC C12Q 1/6876 (2013.01) [C12Q 1/6832 (2013.01)] 20 Claims
OG exemplary drawing
 
1. A method for analyzing a sample, comprising:
(a) forming a hybridization complex comprising a first probe, a second probe, a splint, and a target nucleic acid molecule in the sample, wherein:
the target nucleic acid molecule comprises a first target sequence and a second target sequence,
the splint comprises a first splint sequence and second splint sequence,
the first probe comprises, from one end to another: (i) a first splint-hybridizing region forming a first duplex with the first splint sequence and (ii) a first target-hybridizing region hybridized to the first target sequence,
the second probe comprises, from one end to another: (i) a second target-hybridizing region hybridized to the second target sequence, (ii) a barcode region corresponding to the target nucleic acid molecule or a sequence thereof, and (iii) a second splint-hybridizing region forming a second duplex with the second splint sequence, and
the first duplex and the second duplex differ in stability;
(b) generating a circular probe by (i) ligating the first target-hybridizing region and the second target-hybridizing region and (ii) ligating the first splint-hybridizing region and the second splint-hybridizing region; and
(c) determining a sequence of the barcode region or complement thereof in the circular probe or an amplification product thereof,
thereby detecting the target nucleic acid molecule in the sample.