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 carryover 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.