The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.

CEITEC Central European Institute of Technology Masaryk University Kamenice 735 5 625 00 Brno Czech Republic

Institute of Biophysics of the Czech Academy of Sciences v v i Královopolská 135 612 65 Brno Czech Republic

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DNA i-motif formation at neutral pH is driven by kinetic partitioning

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip