Multiple four-stranded conformations of human telomere sequence d(CCCTAA) in solution

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• Human telomeres, composed of repeating d(TTAGGG) sequences, are crucial for chromosome stability.
• The d(CCCTAA) sequence is a human telomere repeating unit.
• DNA can form non-canonical structures, such as i-motifs, under specific conditions.

Purpose of the Study:

• To investigate the structural dynamics of the human telomere repeating unit d(CCCTAA) in a slightly acidic solution.
• To identify and characterize distinct tetrameric structures formed by d(CCCTAA).
• To determine the relative stability and thermodynamic properties of the identified DNA structures.

Main Methods:

• Detailed Nuclear Magnetic Resonance (NMR) analysis of the d(CCCTAA) sequence.
• NMR denaturation profiling to assess structural stability.
• Restrained molecular dynamics calculations to model DNA structures.

Main Results:

• Three distinct tetrameric structures (T:-form, R-form, S:-form) were identified, slowly exchanging in solution.
• A novel i-motif topology, the T:-form, was characterized, featuring T4 intercalation.
• The R-form, with C1 intercalated between C2 and C3, demonstrated the highest stability across 15-50°C.
• Thermodynamic analysis revealed the T:-form is enthalpically driven and entropically opposed, favoring lower temperatures.

Conclusions:

• The human telomere repeating unit d(CCCTAA) can adopt multiple tetrameric structures in solution.
• The relative stability of these structures is temperature-dependent.
• Inter-strand van der Waals contacts in narrow grooves likely contribute to the enthalpic stabilization of the T:-form.