Design and cloning strategies for constructing shRNA expression vectors-3

<p><b>Copyright information:</b></p><p>Taken from "Design and cloning strategies for constructing shRNA expression vectors"</p><p>BMC Biotechnology 2006;6():1-1.</p><p>Published online 5 Jan 2006</p><p>PMCID:PMC1343552.</p><p></p> restriction site (CUCGAG) will remain in an 'open' configuration by virtue of a mismatched nucleotide pair positioned adjacent to the end of the stem. () The equivalent 6 base loop (UCGA), without a mismatched pair, is predicted to partially collapse, shortening the open loop to 4 bases and simultaneously extending the stem length (by 1 bp) thus altering the position of the stem-loop junction. () A commonly employed 9 base loop (CAAGA, 60 % of studies) is also predicted to collapse, forming a 5 base open loop with a similarly shifted stem-loop junction