IP Library › Granted Patent US 12,644,149
Granted Patent B2
US 12,644,149 · App. 16/959,949 · Granted Jun 2, 2026

Primers and uses thereof

Inventors: Bernhard Zimmermann (Manteca, CA); Ryan Swenerton (Millbrae, CA); Scott Dashner (Sunnyvale, CA); Fei Lu (Fremont, CA); Himanshu Sethi (Sunnyvale, CA)
Assignee: Natera, Inc.
C12Q1/6853C12Q1/6858C12Q2525/155C12Q2525/161C12Q2525/191C12Q2525/301C12Q2537/143C12Q2563/179
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Quick Facts
Patent No.
US 12,644,149
App. No.
16/959,949
Granted
Jun 2, 2026
Kind
B2
Abstract

Disclosed here is a composition comprising a primer that is (a) a loopable primer comprising a target-specific section, an adaptor section, and a stem-forming section, wherein the stem-forming section is hybridizable to a portion of the target-specific section to form a stem structure, or (b) a split primer comprising a first target-specific section, a second target-specific section, and an adaptor section positioned between the first target-specific section and the second target-specific section, or (c) a split-loopable primer comprising a first target-specific section, a second target-specific section, a stem-forming section positioned between the first target-specific section and the second target-specific section, and an adaptor section, or comprising a first adaptor section, a second adaptor section, a stem-forming section positioned between the first adaptor section and the second adaptor section, and a target-specific section.

Claims (12)

1 . A composition comprising a loopable primer comprising a target-specific section, an adaptor section, and a stem-forming section, wherein the stem-forming section is hybridizable to a portion of the target-specific section to form a stem structure; wherein the target-specific section comprises a 5′-portion and a 3′-portion, wherein the stem-forming section is hybridizable to the 3′-portion of the target-specific section, wherein hybridization between the stem-forming section and the 3′-portion of the target-specific section forms a loop that comprises the adaptor section and the 5′-portion of the target-specific section, and wherein the loopable primer further comprises one or more mismatched nucleotides at the 3′-terminus of the target-specific section that are not hybridizable to the nucleotides at the 5′-terminus of the stem-forming section and one or more mismatched nucleotides at the 5′-terminus of the stem-forming section that are not hybridizable to the nucleotides at the 3′-terminus of the target-specific section.

2 . The composition of claim 1 , wherein the loopable primer further comprises a molecular indexing section positioned between the target-specific section and the adaptor section.

3 . The composition of claim 2 , wherein the molecular indexing section is positioned at the 5′ side of the target-specific section and the 3′ side of the adaptor section, wherein hybridization between the stem-forming section and the portion of the target-specific section forms a loop that comprises the adaptor section and the molecular indexing section.

4 . The composition of claim 3 , comprising at least 2,500 different loopable primers each comprising a different combination of the stem-forming section and the molecular indexing section.

5 . The composition of claim 1 , wherein the composition comprises at least a forward loopable primer and a reverse loopable primer that target the same locus of interest for amplification.

6 . The composition of claim 5 , wherein the adaptor section comprises a universal adaptor sequence for PCR amplification and/or sequencing.

7 . The composition of claim 5 , comprising at least 50 different loopable primers each comprising a different stem-forming section and/or a different molecular indexing section.

8 . A method comprising performing at least two pre-amplification cycles using a primer that is:

a loopable primer comprising a target-specific section, an adaptor section, and a stem-forming section, wherein the stem-forming section is hybridizable to a portion of the target-specific section to form a stem structure, wherein the target-specific section comprises a 5′-portion and a 3′-portion, wherein the stem-forming section is hybridizable to the 3′-portion of the target-specific section, wherein hybridization between the stem-forming section and the 3′-portion of the target-specific section forms a loop that comprises the adaptor section and the 5′-portion of the target-specific section, and wherein the loopable primer further comprises one or more mismatched nucleotides at the 3′-terminus of the target-specific section that are not hybridizable to the nucleotides at the 5′-terminus of the stem-forming section and one or more mismatched nucleotides at the 5′-terminus of the stem-forming section that are not hybridizable to the nucleotides at the 3′-terminus of the target-specific section,

wherein each pre-amplification cycle comprises annealing the loopable primer to a template DNA or pre-amplification product thereof and elongating the annealed loopable primer.

9 . A kit for amplifying a target locus of interest, comprising a primer that is:

a loopable primer comprising a target-specific section, an adaptor section, and a stem-forming section, wherein the stem-forming section is hybridizable to a portion of the target-specific section to form a stem structure, wherein the target-specific section comprises a 5′-portion and a 3′-portion, wherein the stem-forming section is hybridizable to the 3′-portion of the target-specific section, wherein hybridization between the stem-forming section and the 3′-portion of the target-specific section forms a loop that comprises the adaptor section and the 5′-portion of the target-specific section, and wherein the loopable primer further comprises one or more mismatched nucleotides at the 3′-terminus of the target-specific section that are not hybridizable to the nucleotides at the 5′-terminus of the stem-forming section and one or more mismatched nucleotides at the 5′-terminus of the stem-forming section that are not hybridizable to the nucleotides at the 3′-terminus of the target-specific section.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 7, 2020
From: ZIMMERMANN, BERNHARD; SWENERTON, RYAN; DASHNER, SCOTT; LU, FEI; SETHI, HIMANSHU
To: NATERA, INC.
Reel/Frame 053995/0775 →
Continuity (2)
Provisional Application 62617066 · Jan 12, 2018
Related Publication 20210071246A1 · Mar 11, 2021
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