Thermal and pH Stabilities of i-DNA: Confronting in vitro Experiments with Models and In-Cell NMR Data

Area of Science:

• Biochemistry
• Molecular Biology
• Genetics

Background:

• Recent research suggests the DNA i-motif (i-DNA), a four-stranded structure, forms in vivo.
• Systematic studies on sequence-dependent stability of i-DNA are lacking.

Purpose of the Study:

• To systematically investigate sequence effects on DNA i-motif stability.
• To identify key determinants of i-DNA formation and stability in cellular contexts.

Main Methods:

• Tested 271 different DNA sequences with varying cytosine tract lengths (3-6 bases) and spacer lengths.
• Analyzed i-DNA stability under different pH conditions.

Main Results:

• i-DNA stability is largely independent of total spacer length but significantly influenced by the central spacer.
• Cytosine tract length critically affects i-DNA stability at both acidic and neutral pH.
• Determinants of i-DNA stability differ from those of G-quadruplexes.

Conclusions:

• Provides a comprehensive understanding of i-DNA stability based on sequence.
• Highlights the structural roles of loops and C-tracts in i-DNA formation.
• Establishes rules for predicting i-DNA stability and confirms its in vivo relevance.