Recombinase polymerase amplification
This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes. Further described are novel properties and approaches for use of probes monitored by light in dynamic recombination environments.
1. A recombinase polymerase amplification process of DNA amplification of a double stranded target nucleic acid molecule comprising a first strand of DNA and second strand of DNA, the process comprising:
(a) contacting in a solution a uvsX recombinase agent with a first nucleic acid primer and a second nucleic acid primer to form a first nucleoprotein primer and a second nucleoprotein primer, wherein each of the first and second nucleic acid primers comprise a single stranded region at its 3′ end;
(b) contacting the first and the second nucleoprotein primers with the double stranded target nucleic acid molecule thereby forming:
(1) a first double-stranded structure at a first portion of the first strand and
(2) a second double stranded structure at a second portion of the second strand such that the 3′ end of each of the first nucleoprotein primer and the second nucleoprotein primer are oriented toward one another on the same double-stranded template nucleic acid molecule;
(c) extending the 3′ end of each of the first and second nucleoprotein primers with dNTPs and one or more DNA polymerases with strand-displacing properties to generate a first double-stranded nucleic acid product and a second double-stranded nucleic acid product and a first displaced strand of nucleic acid product and a second displaced strand of nucleic acid product; and
(d) repeating (b) and (c) to amplify the double stranded target nucleic acid molecule;
wherein the solution further comprises a gp32 single-stranded DNA binding protein;
wherein the solution further comprises a recombinase loading factor uvsY at a concentration of between 0.2 and 8 micromolar;
wherein the solution further comprises a crowding agent at a concentration of between 1% and 12%;
wherein the one or more DNA polymerase lack 5′ to 3′ exonuclease activity and lack FLAP endonuclease activity;
wherein the solution further comprises a hydrolysable nucleoside triphosphate; and
wherein the process is performed at a temperature of between 20° C. and 50° C.
2. A process of nested recombinase polymerase amplification, the process comprising:
(a) amplifying a region of DNA using the recombinase polymerase amplification process of claim 1 using a first primer and a second primer to produce a first amplified product;
(b) amplifying the first amplified product using a third primer and a fourth primer using the recombinase polymerase amplification process of claim 1 to produce a second amplified product, wherein the second amplified product is a smaller sequence contained within the first amplified product.
3. A process comprising:
providing an aqueous solution comprising
(1) at least one recombinase;
(2) at least one single stranded DNA binding protein;
(3) at least one DNA polymerase;
(4) dNTPs or a mixture of dNTPs and ddNTPs;
(5) a reducing agent;
(6) ATP or ATP analog;
(7) at least one recombinase loading protein; and
(8) a crowding agent; and
freeze-drying the aqueous solution.
4. The process of claim 3 , wherein the at least one recombinase comprises a uvsX recombinase.
5. The process of claim 3 , wherein the at least one single stranded DNA binding protein comprises a gp32 single stranded DNA binding protein.
6. The process of claim 3 , wherein the at least one DNA polymerase comprises a DNA polymerase I fragment.
7. The process of claim 3 , wherein the reducing agent comprises dithiothreitol (DTT).
8. The process of claim 3 , wherein the at least one recombinase loading protein comprises a uvsY recombinase loading protein.
9. The process of claim 3 , wherein the aqueous solution further comprises one or more of potassium acetate, magnesium acetate, phosphocreatine, and creatine kinase.
10. The process of claim 3 , wherein the crowding agent comprises polyethylene glycol.
11. The process of claim 3 , wherein the aqueous solution further comprises at least one nucleic acid primer.
12. The process of claim 3 , wherein:
the at least one recombinase comprises a uvsX recombinase;
the at least one single stranded DNA binding protein comprises a gp32 single stranded DNA binding protein;
the at least one DNA polymerase comprises a DNA polymerase I fragment;
the reducing agent comprises dithiothreitol (DTT); and
the at least one recombinase loading protein comprises a uvsY recombinase loading protein.
13. The process of claim 12 , wherein the aqueous solution further comprises one or more of potassium acetate, magnesium acetate, phosphocreatine, and creatine kinase.
14. The process of claim 12 , wherein the crowding agent comprises polyethylene glycol.
15. The process of claim 3 , wherein:
the at least one recombinase comprises a uvsX recombinase;
the at least one single stranded DNA binding protein comprises a gp32 single stranded DNA binding protein;
the at least one DNA polymerase comprises a DNA polymerase I fragment;
the reducing agent comprises dithiothreitol (DTT); and
the at least one recombinase loading protein comprises a uvsY recombinase loading protein;
the crowding agent comprises polyethylene glycol, and
wherein the aqueous solution further comprises potassium acetate, magnesium acetate, phosphocreatine, and creatine kinase.
16. The process of claim 15 , wherein the aqueous solution further comprises trehalose.
17. The process of claim 15 , wherein the aqueous solution further comprises at least one nucleic acid primer.
18. The process of claim 3 , wherein the aqueous solution is freeze-dried onto a solid support.
19. The process of claim 12 , wherein the aqueous solution is freeze-dried onto a solid support.
20. The process of claim 15 , wherein the aqueous solution is freeze-dried onto a solid support.