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Figure 12 | BMC Biotechnology

Figure 12

From: Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: Comparison of single base mismatches and base bulges

Figure 12

Stability orders of MM-types X · Y for hybridization in solution ( a ) and on microarrays ( b, d, e ). In the microarray experiments (b, d and e) MM binding affinities have been normalized with the corresponding PM binding affinity, whereas the orders a) and c) reflect the absolute impact of the MM pairs on duplex binding affinity. For the microarray MM-pairs (in b, d and e) the probe base X (DNA) is on the left and the target base Y (DNA or RNA) is on the right. The efficiency of RNA interference (c) (from [2]) is assumed to be determined by the stability of A-form RNA duplexes between the RISC-bound guide strand and the complementary mRNA. The left base X is part of the guide strand (at position 10) and the right base Y is part of the mRNA. Apart from the the base pair X·Y the mRNA and siRNA sequences remained fixed. In (a) to (c) purine bases are highlighted in blue. In (d) and (e) mismatches with respect to a perfect matching C·G base pair are highlighted in red. Details on the individual stability orders are provided in the text.

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