Methods for localized in situ detection of mRNA
First Claim
1. A method for localized in situ detection of mRNA which codes for one or more mutations of the KRAS gene in a sample of cells that were formalin-fixed paraffin-embedded (FFPE) on a slide surface, comprising:
- (a) generating cDNA from mRNA in the sample using a primer;
(b) digesting the mRNA hybridized to said cDNA;
(c) contacting said sample with one or more padlock probes specific for mutations to the KRAS gene;
(d) joining, directly or indirectly, the ends of said padlock probe(s) to form circularized padlock probe(s);
(e) subjecting said circularized padlock probe(s) to rolling circle amplification (RCA) to generate rolling circle amplification products; and
,(f) detecting the rolling circle amplification product(s), wherein the padlock probe comprises;
(i) Y1-X1-Z1-A(ii) Y1-X1-Z1-T(iii) Y1-X1-Z1-C(iv) Y2-X1-Z2-A(v) Y2-X1-Z2-T(vi) Y2-X1-Z2-C(vii) Y3-X1-Z3-A;
(viii) Y1-X2-Z1-G(ix) Y2-X2-Z2-G, or(x) Y3-X2-Z3-Gwhere;
X1 or X2 is from 16-50 nucleotides;
Y1+Z1=20 to 29 nucleotides;
Y2+Z2=20 to 29 nucleotides;
Y3+Z3=20 to 29 nucleotides;
Y1 is GTGGCGTAGGCAAGA (SEQ ID NO;
1), GTGGCGTAGGCAAG (SEQ ID NO;
2), GTGGCGTAGGCAA (SEQ ID NO;
3), GTGGCGTAGGCA (SEQ ID NO;
4), GTGGCGTAGGC (SEQ ID NO;
5), GTGGCGTAGG (SEQ ID NO;
6), GTGGCGTAG, GTGGCGTA, GTGGCGT, or GTGGCG;
Y2 is TGGCGTAGGCAAGAG (SEQ ID NO;
7), TGGCGTAGGCAAGA (SEQ ID NO;
8), TGGCGTAGGCAAG (SEQ ID NO;
9), TGGCGTAGGCAA (SEQ ID NO;
10), TGGCGTAGGCA (SEQ ID NO;
11), TGGCGTAGGC (SEQ ID NO;
12), TGGCGTAGG, TGGCGTAG, TGGCGTA, or TGGCGT;
Y3 is CGTAGGCAAGAGTGC (SEQ ID NO;
13), CGTAGGCAAGAGTG (SEQ ID NO;
14), CGTAGGCAAGAGT (SEQ ID NO;
15), CGTAGGCAAGAG (SEQ ID NO;
113), CGTAGGCAAGA (SEQ ID NO;
114), CGTAGGCAAG (SEQ ID NO;
115), CGTAGGCAA, CGTAGGCA, CGTAGGC, or CGTAGG;
Z1 is TGGTAGTTGGAGCT (SEQ ID NO;
27), GGTAGTTGGAGCT (SEQ ID NO;
28), GTAGTTGGAGCT (SEQ ID NO;
29), TAGTTGGAGCT (SEQ ID NO;
30), AGTTGGAGCT (SEQ ID NO;
31), GTTGGAGCT, TTGGAGCT, TGGAGCT, GGAGCT, or GAGCT;
Z2 is GGTAGTTGGAGCTG (SEQ ID NO;
16), GTAGTTGGAGCTG (SEQ ID NO;
17), TAGTTGGAGCTG (SEQ ID NO;
18), AGTTGGAGCTG (SEQ ID NO;
19), GTTGGAGCTG (SEQ ID NO;
20), TTGGAGCTG, TGGAGCTG, GGAGCTG, GAGCTG, or AGCTG; and
Z3 is AGTTGGAGCTGGTG (SEQ ID NO;
21), GTTGGAGCTGGTG(SEQ ID NO;
22), TTGGAGCTGGTG(SEQ ID NO;
23), TGGAGCTGGTG(SEQ ID NO;
24), GGAGCTGGTG(SEQ ID NO;
25), GAGCTGGTG(SEQ ID NO;
26), AGCTGGTG, GCTGGTG, CTGGTG, or TGGTG.
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Abstract
The present invention relates to the detection of RNA in a sample of cells. More particularly, the present invention relates to the localized detection of RNA in situ. The method relies on the conversion of RNA to complementary DNA prior to the targeting of the cDNA with a padlock probe(s). The hybridization of the padlock probe(s) relies on the nucleotide sequence of the cDNA which is derived from the corresponding nucleotide sequence of the target RNA. Rolling circle amplification of the subsequently circularized padlock probe produces a rolling circle product which may be detected. Advantageously, this allows the RNA to be detected in situ.
26 Citations
28 Claims
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1. A method for localized in situ detection of mRNA which codes for one or more mutations of the KRAS gene in a sample of cells that were formalin-fixed paraffin-embedded (FFPE) on a slide surface, comprising:
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(a) generating cDNA from mRNA in the sample using a primer; (b) digesting the mRNA hybridized to said cDNA; (c) contacting said sample with one or more padlock probes specific for mutations to the KRAS gene; (d) joining, directly or indirectly, the ends of said padlock probe(s) to form circularized padlock probe(s); (e) subjecting said circularized padlock probe(s) to rolling circle amplification (RCA) to generate rolling circle amplification products; and
,(f) detecting the rolling circle amplification product(s), wherein the padlock probe comprises; (i) Y1-X1-Z1-A (ii) Y1-X1-Z1-T (iii) Y1-X1-Z1-C (iv) Y2-X1-Z2-A (v) Y2-X1-Z2-T (vi) Y2-X1-Z2-C (vii) Y3-X1-Z3-A; (viii) Y1-X2-Z1-G (ix) Y2-X2-Z2-G, or (x) Y3-X2-Z3-G where; X1 or X2 is from 16-50 nucleotides; Y1+Z1=20 to 29 nucleotides; Y2+Z2=20 to 29 nucleotides; Y3+Z3=20 to 29 nucleotides; Y1 is GTGGCGTAGGCAAGA (SEQ ID NO;
1), GTGGCGTAGGCAAG (SEQ ID NO;
2), GTGGCGTAGGCAA (SEQ ID NO;
3), GTGGCGTAGGCA (SEQ ID NO;
4), GTGGCGTAGGC (SEQ ID NO;
5), GTGGCGTAGG (SEQ ID NO;
6), GTGGCGTAG, GTGGCGTA, GTGGCGT, or GTGGCG;Y2 is TGGCGTAGGCAAGAG (SEQ ID NO;
7), TGGCGTAGGCAAGA (SEQ ID NO;
8), TGGCGTAGGCAAG (SEQ ID NO;
9), TGGCGTAGGCAA (SEQ ID NO;
10), TGGCGTAGGCA (SEQ ID NO;
11), TGGCGTAGGC (SEQ ID NO;
12), TGGCGTAGG, TGGCGTAG, TGGCGTA, or TGGCGT;Y3 is CGTAGGCAAGAGTGC (SEQ ID NO;
13), CGTAGGCAAGAGTG (SEQ ID NO;
14), CGTAGGCAAGAGT (SEQ ID NO;
15), CGTAGGCAAGAG (SEQ ID NO;
113), CGTAGGCAAGA (SEQ ID NO;
114), CGTAGGCAAG (SEQ ID NO;
115), CGTAGGCAA, CGTAGGCA, CGTAGGC, or CGTAGG;Z1 is TGGTAGTTGGAGCT (SEQ ID NO;
27), GGTAGTTGGAGCT (SEQ ID NO;
28), GTAGTTGGAGCT (SEQ ID NO;
29), TAGTTGGAGCT (SEQ ID NO;
30), AGTTGGAGCT (SEQ ID NO;
31), GTTGGAGCT, TTGGAGCT, TGGAGCT, GGAGCT, or GAGCT;Z2 is GGTAGTTGGAGCTG (SEQ ID NO;
16), GTAGTTGGAGCTG (SEQ ID NO;
17), TAGTTGGAGCTG (SEQ ID NO;
18), AGTTGGAGCTG (SEQ ID NO;
19), GTTGGAGCTG (SEQ ID NO;
20), TTGGAGCTG, TGGAGCTG, GGAGCTG, GAGCTG, or AGCTG; andZ3 is AGTTGGAGCTGGTG (SEQ ID NO;
21), GTTGGAGCTGGTG(SEQ ID NO;
22), TTGGAGCTGGTG(SEQ ID NO;
23), TGGAGCTGGTG(SEQ ID NO;
24), GGAGCTGGTG(SEQ ID NO;
25), GAGCTGGTG(SEQ ID NO;
26), AGCTGGTG, GCTGGTG, CTGGTG, or TGGTG. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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Specification