Methods and compositions for nucleic acid detection

A method for detecting presence in a sample of a minority allele that is a sequence variant differing from a more abundant corresponding allele at a single base position, the method comprising:

• subjecting portions of the sample to nucleic acid amplification reactions in reaction mixtures under conditions to amplify a region of the minority allele and the more abundant allele comprising the sequence variant using a pair of loop primers;
• wherein a first reaction mixture comprises a first loop primer and a polymerase, a second reaction mixture comprises a second loop primer and a polymerase, and further wherein:
• (a) the first loop primer comprises sequence A1, a linker sequence D1, and sequence B1, oriented from 5′ to 3′ on a single strand;
• wherein the first loop primer specifically hybridizes to the minority allele via (i) sequence complementarity between sequence A1 of the loop primer and sequence A1′ on the minority allele, and (ii) sequence complementarity between sequence B1 of the loop primer and sequence B1′ on the minority allele, wherein sequence A1′ and sequence B1′ are oriented 5′ to 3′ on the minority allele;
• (b) the second loop primer comprises sequence A2, a linker sequence D2, and sequence B2, oriented from 5′ to 3′ on a single strand;
• wherein the second loop primer specifically hybridizes to the more abundant allele via (i) sequence complementarity between sequence A2 of the loop primer and sequence A2′ on the more abundant allele, and (ii) sequence complementarity between sequence B2 of the loop primer and sequence B2′ on the more abundant allele, wherein sequence A2′ and sequence B2′ are oriented 5′ to 3′ on the more abundant allele;
• and
• (c) a polymerase extends sequence B1 or sequence B2 of the first or second loop primer from 5′ to 3′ along the respective allele that serves as template for template-directed primer extension to produce complementary sequence of the respective alleles, the complementary sequence of the minority allele having, from 5′ to 3′, sequence A1, sequence D1 sequence B1, sequence A1 and a sequence C1, the sequence C1 complementary to a sequence C1′ of the minority allele, the sequence C1′ located 5′ of the sequence A1′.

A method for detecting presence in a sample of a minority allele that is a sequence variant differing from a more abundant corresponding allele, the method comprising:

• subjecting the sample to a nucleic acid amplification reaction in a reaction mixture under conditions to amplify a region of the minority allele and the more abundant allele using a pair of loop primers, wherein the reaction mixture comprises:
• (a) a first loop primer that comprises sequence A1, a linker sequence D1, and sequence B1, oriented from 5′ to 3′ on a single strand;
• wherein the first loop primer specifically hybridizes to the minority allele via (i) sequence complementarity between sequence A1 of the loop primer and sequence A1′ on the minority allele, and (ii) sequence complementarity between sequence B1 of the loop primer and sequence B1′ on the minority allele, wherein sequence A1′ and sequence B1′ are oriented 5′ to 3′ on the minority allele;
• (b) a second loop primer that comprises sequence A2, a linker sequence D2, and sequence B2, oriented from 5′ to 3′ on a single strand;
• wherein the second loop primer specifically hybridizes to the more abundant allele via (i) sequence complementarity between sequence A2 of the loop primer and sequence A2′ on the more abundant allele, and (ii) sequence complementarity between sequence B2 of the loop primer and sequence B2′ on the more abundant allele, wherein sequence A2′ and sequence B2′ are oriented 5′ to 3′ on the more abundant allele;
• and
• (c) a polymerase that extends sequence B1 and sequence B2 of the first and second loop primers from 5′ to 3′ along the respective allele that serves as template for template-directed primer extension to produce complementary sequence of the respective alleles, the complementary sequence of the minority allele having, from 5′ to 3′, sequence A1, sequence D1 sequence B1, sequence A1 and a sequence C1, the sequence C1 complementary to a sequence C1′ of the minority allele, the sequence C1′ located 5′ of the sequence A1′.