Multiplexed single molecule RNA visualization with a two-probe proximity ligation system
SNAIL provides cost-efficient detection of specific nucleic acids in single cells, and may be combined with flow cytometry to simultaneously analyze large numbers of cells for a plurality of nucleic acids, e.g. at least one, to up to 5, up to 10, up to 15, up to 20 or more transcripts can be simultaneously analyzed, at a rate of up to about 50, 100, 250, 500 or more cells/second. The methods require only two primers for amplification, and may further include a detection primer.
1. A method for determining the level of a target nucleic acid in a fixed and permeabilized single cell, the method comprising:
contacting a fixed and permeabilized single cell with a pair of SNAIL oligonucleotide primers under conditions permissive for a specific hybridizations of the pair of SNAIL oligonucleotide primers to the target nucleic acid, wherein the pair of SNAIL oligonucleotide primers comprises a Splint Primer Oligonucleotide (SPO) and a Padlock Oligonucleotide (PO), wherein each of SPO and PO comprise a first complementarity region and the first complementarity region of the SPO and the first complementarity region of the PO are complementary to two adjacent sequences on the target nucleic acid, wherein the first complementarity region of the SPO is CR1 and the first complementarity region of the PO is CR1′ and each of the SPO and the PO further comprises a second complementarity region, wherein the second complementarity region of the SPO is CR2 located adjacent to the CR1 and the second complementarity region of the PO is CR2′ located adjacent to the CR1′; wherein the CR2′ is a split region of the PO such that the 5′ and the 3′ ends of the PO hybridize to the CR2 and are positioned directly adjacent to one another after said contacting a fixed and permeabilized single cell with a pair of SNAIL oligonucleotide primers;
washing the cell to remove the pair of SNAIL oligonucleotide primers unbound to the target nucleic acid;
after the washing step, contacting the cell with a ligase such that the 5′ and the 3′ ends of the PO hybridized to the CR2 are ligated to each other and generating a closed circle;
performing in situ rolling circle amplification using the closed circle as a template and the SPO as a primer and generating an amplification product in situ;
contacting the amplification product in situ with a nucleic acid detection probe labeled with one or more of a fluorophore, an isotope, or a mass tag under conditions permissive for a specific hybridization of the detection probe to the amplification product and generating a labeled cell; and
determining the level of the target nucleic acid in the fixed and permeabilized single cell by detecting the level of the detection probe bound to the amplification product in the labeled cell and subjecting the labeled cell to an analysis performed by mass cytometry or fluorescence-activated flow cytometry.
2. The method of claim 1 , wherein the SNAIL oligonucleotide primer pairs are denatured by heating before said contacting a fixed and permeabilized single cell with a pair of SNAIL oligonucleotide primers.
3. The method of claim 1 , wherein the cell is present in a population of cells.
4. The method of claim 3 , wherein the cell population comprises a plurality of cell types.
5. The method of claim 1 , wherein the target nucleic acid is RNA.
6. The method of claim 5 , wherein the RNA is mRNA.
7. The method of claim 1 , wherein the target nucleic acid is DNA.
8. The method of claim 1 , further comprising: contacting the labeled cell with one or more marker detection reagents that specifically bind to one or more non-nucleic acid markers, determining the levels of the one or more marker detection reagents bound to the labeled cell, and profiling the levels of the one or more non-nucleic acid markers in the fixed and permeabilized single cell.
9. The method of claim 8 , wherein the one or more non-nucleic acid markers are protein markers.
10. The method of claim 1 , wherein the sequences of the pair of SNAIL oligonucleotide primers further comprises a detection barcode sequence for identification of the target nucleic acid.
11. The method of claim 1 , wherein the detection probe is removed from the amplification product after the detecting and subjecting step.
12. A method for determining the level of a target nucleic acid from different nucleic acids in a fixed and permeabilized single cell, the method comprising:
contacting a fixed and permeabilized single cell with a plurality of pairs of SNAIL oligonucleotide primers having specificity for different target nucleic acids under conditions permissive for a specific hybridization of the plurality of pairs of SNAIL oligonucleotide primers to the different target nucleic acids, wherein each pair of the plurality of pairs of SNAIL oligonucleotide primers comprises a Splint Primer Oligonucleotide (SPO) and a Padlock Oligonucleotide (PO), wherein each of the SPO and the PO of each pair of the plurality of pairs of SNAIL oligonucleotide primers comprises a first complementarity region and the first complementarity region of the SPO and the first complementarity region of the PO of each pair of the plurality of pairs of SNAIL oligonucleotide are complementary to two adjacent sequences on one of the different target nucleic acids, wherein the first complementarity region of the SPO of each pair of the plurality of pairs of SNAIL oligonucleotide is CR1 and the first complementarity region of the PO of each pair of the plurality of pairs of SNAIL oligonucleotide is CR1′; and each of the SPO and the PO of each pair of the plurality of pairs of SNAIL oligonucleotide further comprises a second complementarity region, wherein the second complementarity region of the SPO of each pair of the plurality of pairs of SNAIL oligonucleotide is CR2 and the CR1 and the CR2 of the SPO of each pair of the plurality of pairs of SNAIL oligonucleotide are located adjacent to one another and the second complementarity region of the PO of each pair of the plurality of pairs of SNAIL oligonucleotide is CR2′ and the CR1′ and the CR2′ of the PO of each pair of the plurality of pairs of SNAIL oligonucleotide are located adjacent to one another; wherein the CR2′ is a split region of the PO of each pair of the plurality of pairs of SNAIL oligonucleotide such that the 5′ and the 3′ ends of the PO of one pair of the plurality of pairs of SNAIL oligonucleotide hybridize to the CR2 of the SPO of the one pair of the plurality of pairs of SNAIL oligonucleotide and are positioned directly adjacent to one another after said contacting a fixed and permeabilized single cell with a plurality of SNAIL oligonucleotide primers;
washing the cell to remove the plurality of pairs of SNAIL oligonucleotide primers unbound to the different target nucleic acids;
after the washing step, contacting the cell with a ligase such that the 5′ and the 3′ ends of the PO of the one pair of the plurality of pairs of SNAIL oligonucleotide hybridized to the CR2 of the SPO of the one pair of the plurality of pairs of SNAIL oligonucleotide are ligated to each other and generating a closed circle;
performing rolling circle amplifications in situ using the closed circle as a template and the SPO of the one pair of the plurality of pairs of SNAIL oligonucleotide as a primer and generating an amplification product in situ;
contacting the amplification product in situ with a nucleic acid detection probe labeled with one or more of a fluorophore, an isotope, or a mass tag under conditions permissive for a specific hybridization of the detection probe to the amplification product and generating a labeled cell; and
determining the level of the target nucleic acid from the different nucleic acids in the fixed and permeabilized single cell by determining the level of the detection probe bound to the amplification product in the labeled cell and subjecting the labeled cell to an analysis performed by mass cytometry or fluorescence-activated flow cytometry.
13. The method of claim 12 , wherein the plurality of pairs of SNAIL oligonucleotide primers are specific for at least 5 of the different target nucleic acids.
14. The method of claim 12 , wherein the different target nucleic acids are RNAs.