Template Switching RT Basic Q

[aryehhirt]

What exactly happens at the end of template switching RT, and why is it advantageous? Lets assume we are using a MMLV reverse transcriptase to add the ccc at the end of the fragment. What happens next? I could not find a clear explanation online.

[luc]

An DNA oligo with a rGrGrG 3'-end ((the template switching oligo) will anneal to the CCC overhang and the RT will continue to work on this newly added template. This allows you to add a defined (PCR-amplify-able) sequence to the 5'-end of your cDNA.

[ashishbansal]

The reverse transcriptase encoded by the non-long terminal repeat retrotransposon R2 has been shown to be able to jump from the 5′-end of one RNA template (the donor) to the 3′-end of a second RNA template (the acceptor) in the absence of preexisting sequence identity between the two templates. These jumps between RNA templates have similarity to the end-to-end template jumps described for the RNA-directed RNA polymerases encoded by certain RNA viruses. Here we describe for the first time the mechanism by which such end-to-end template jumps can occur. Most template jumps by the R2 reverse transcriptase are brought about by the enzyme's ability to add nontemplated (overhanging) nucleotides to the cDNA when it reaches the end of the donor RNA. The enzyme then anneals these overhanging nucleotides to sequences at the 3′-end of the acceptor RNA. The annealing is most efficient if it involves the terminal nucleotide(s) of the acceptor RNA but can occur to sites at least 5 nucleotides from the 3′-end. These end-to-end jumps are similar to steps proposed to be part of the integration reaction of non-long terminal repeat retrotransposons and can explain chimeric integration products derived from multiple RNA templates.