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We compared binding to OriP with a control region within the alternative replication initiation zone used in Raji cells, referred to as OriR [45].
To quantify the differences in affinities, we compared binding to three different epitopes that all form part of a high-mannose oligosaccharide.
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Furthermore, we compared the ability of cPPR-Telo1 and cPPR-Telo2 to bind ssDNA in G-quadruplex structures by comparing binding to two targets, where one could form a G-quadruplex structure and the other could not31.
These data indicated that sequences around BS1, BS2 and BS3 contribute to PTB binding (compare binding to 118 245 and 1 163 with 1 202, Fig 3a and c).
To be able to directly compare binding to ICL-containing DNA with binding to hemimethylated DNA, we designed two DNA molecules that are identical except for the central two base pairs.
The number of spectra obtained for each protein was used as an approximate measure of abundance and used to compare binding to the GTP- and GDP-bound forms of Arl5 (Fig. 3A).
Next, we compared binding of Mena/VASP to general αII-Spectrin and the SH3 i isoform.
When we compared binding of CTCF(L) to that of histone H3 we noted that CTCFL preferentially binds large H3-depleted areas.
To distinguish between these models, we directly compared binding of MW1 and 3B5H10 to normal and expanded polyQ repeats within huntingtin exon 1 fusion proteins.
The selectivity of interactions was even more significant when comparing binding to LRRTM2 vs NL1B or NL3A2.
To characterize the structural environment of NAD-/FAD-binding sites, we compared binding-site residues to whole-protein residues.
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