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Figure 2 | BMC Biotechnology

Figure 2

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 2

Mismatch defect profile (A) (hybridization signal vs. defect base position) obtained from the hybridization signals of the feature block shown in the right part of Additional file 9. Solution-background correction (see Methods section) was applied on raw hybridization signal intensities. The probe sequence motif 3'-TATTACTGGACCTGAC-5' is complementary to the target oligonucleotide COM. Markers depict the substituent base type (A red crosses; C green circles; G blue stars; T cyan triangles). The black line indicates the 'mean profile' (moving average of all mismatch hybridization signals over positions p - 2 to p + 2). PM probes, included as control to detect erroneous bias, have the largest hybridization signals (at a level of about 0.38 a.u.). The variation of the PM probe intensities also provides an estimate for the error of the measurement. Errors between distant microarray features, due to gradient effects, are expected to be larger than errors between the compactly arranged features corresponding to a particular defect position. (B) Deviation profile. The strong position dependent component of the hybridization signal is eliminated by subtraction of the mean profile. (C) Comparison of mean mismatch hybridization signals (average of the three mismatch hybridization signals at a particular defect position) at the sites of C·G base pairs to mean MM hybridization signals at the site of adjacent A·T base pairs. A marker (red star: A·T; blue circle C·G) is set in the upper row if the hybridization signal of the mismatches at the corresponding site is higher than at the adjacent site; otherwise a marker is set in the lower row. We noticed that mismatches substituting a C·G base pair usually have systematically lower hybridization signals than mismatches substituting a neighboring A·T base pair.

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