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The left-handed DNA structure, Z-DNA, is believed to play important roles in gene expression and regulation. Z-DNA forms sequence-specifically with a preference for sequences rich in pyrimidine/purine dinucleotide steps. In vivo, Z-DNA is generated in the presence of negative supercoiling or upon binding proteins that absorb the high energetic cost of the B-to-Z transition, including the creation of distorted junctions between B-DNA and Z-DNA. To date, the sequence preferences for the B-to-Z transition have primarily been studied in the context of sequence repeats lacking B–Z junctions. Here, we develop a method for characterizing sequence-specific preferences for Z-DNA formation and B–Z junction localization within heterogeneous DNA duplexes that is based on combining 2-aminopurine fluorescence measurements with a new quantitative application of circular dichroism spectroscopy for determining the fraction of B- versus Z-DNA. Using this approach, we show that at least three consecutive CC dinucleotide ste...
| Authors: | Jameson R. Bothe; Ky Lowenhaupt; Hashim M. Al-Hashimi | |
| Journal: | Biochemistry | |
| Year: | 2012 | |
| DOI: | 10.1021/bi300785b | |
| Publication date: | 17-08-2012 |
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