R-loops are structures where an RNA strand is base paired with one DNA strand of 
a DNA duplex, leaving the displaced DNA strand single-stranded. Stable R-loops 
exist in vivo at prokaryotic origins of replication, the mitochondrial origin of 
replication, and mammalian immunoglobulin (Ig) class switch regions in activated 
B lymphocytes. All of these R-loops arise upon generation of a G-rich RNA strand 
by an RNA polymerase upon transcription of a C-rich DNA template strand. These 
R-loops are of significant length. For example, the R-loop at the col E1 origin 
of replication appears to be about 140 bp. Our own lab has focused on class 
switch regions, where the R-loops can extend well over a kilobase in length. 
Here, methods are described for detection and analysis of R-loops in vitro and 
in vivo.