Skip to main content
Figure 4 | BMC Biotechnology

Figure 4

From: Design and cloning strategies for constructing shRNA expression vectors

Figure 4

Internal base pairing can cause intended loop configurations to collapse. (a) Structural predictions reveal that an 8 base loop containing a 6 base restriction site (ACUCGAGA) will remain in an 'open' configuration by virtue of a mismatched nucleotide pair positioned adjacent to the end of the stem. (b) The equivalent 6 base loop (CUCGAG), 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. (c) A commonly employed 9 base loop (UUCAAGAGA, 60 % of studies) is also predicted to collapse, forming a 5 base open loop with a similarly shifted stem-loop junction.

Back to article page