Open Access Research article

Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study

Christian Trapp*, Marc Schenkelberger and Albrecht Ott*

Author Affiliations

Experimentalphysik, Universität des Saarlandes, D-66041 Saarbrücken, Germany

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BMC Biophysics 2011, 4:20  doi:10.1186/2046-1682-4-20

Published: 13 December 2011

Additional files

Additional file 1:

Influence of the microarray surface on the hybridization signal. We test the influence of the microarray surface on the hybridization signal by synthesizing probes with reversed sequence (3'-CATTACAACAACCATTAATACTCATCATAACTT-5'). The 5'-end of the sequence employed throughout this work corresponds to the 3'-end of the reversed sequence. No significant influence of the surface can be detected.

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Additional file 2:

Duplex stability of DNA duplexes with bulged loops of different sequences as a function of loop length. Instead of the discussed poly-T loop sequences, we synthesize probes containing poly-C loop sequences and random loop sequences respectively at three different positions (the number of additional bases vary from one to thirteen; the random loop sequences are listed in table b) of this file). Upon hybridization with the target sequence listed in table 1, we note a monotonic decrease of the fluorescent signal as a function of loop length. After averaging over all loop positions, we compare the experimental signals as a function of loop length with the model predictions. We show that the experimental data is reproduced by our theory.

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Additional file 3:

Influence of the number of MMs on the fluorescent signal. In order to reproduce our experimental data, it is sufficient to consider up to 3 synthesis-related defects in the zipper model. We confirm this by measuring the fluorescent signals of probes with 1 to 4 MMs. MMs are incorporated into the PM probe motif at 8 given positions resulting in 162 different probe sequences. To generate the MMs, we replace the bases at these specific positions with a thymine base (or with an adenine base, if a thymine base is already present at the specific position). After categorizing the probes into groups according to their number of MMs, we calculate the average signal of each group and plot it against the number of MMs (PM signal is set to 1, background signal is set to 0). Based on this data, we can estimate the error caused by neglecting probes with more than 3 synthesis defects: the error ≪ 4%, smaller than the experimental error.

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Additional file 4:

Hybridization signals resulting from Zdouble zipper and comparison to Zextended,right + Zextended,left. We compare the calculated hybridization signals resulting from Zdouble zipper to the signals resulting from. Zextended,right + Zextended,left.The predicted hybridization signals are similar in shape but differ regarding absolute values. In the figure, the scaling factor C, which relates the predictions to the absolute signal intensities of the experiments, has been changed to 3 in case of Zdouble zipper, compared to C = 1.5 · 10-3 throughout this study.

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