Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes

Area of Science:

• Molecular Biology
• Structural Biology
• Biochemistry

Background:

• Sequence-specific protein recognition of single-stranded DNA (ssDNA) is essential for numerous cellular processes, including DNA replication, repair, and telomere maintenance.
• Understanding these recognition mechanisms is crucial for deciphering fundamental biological pathways.

Purpose of the Study:

• To investigate the structural and thermodynamic basis of sequence-specific ssDNA recognition by the Oxytricha nova telomere end-binding protein (OnTEBP).
• To explore how OnTEBP accommodates non-cognate ssDNA sequences and identify potential novel recognition mechanisms.

Main Methods:

• Determined crystal structures of OnTEBP complexed with 10 different non-cognate ssDNAs.
• Evaluated binding affinities for these complexes.
• Analyzed structural rearrangements and thermodynamic effects of sequence variations.

Main Results:

• OnTEBP accommodates non-cognate ssDNA through subtle adjustments and significant structural rearrangements.
• Observed a phenomenon termed 'nucleotide shuffling' where ssDNA nucleotides are expelled and the sequence register shifts.
• Thermodynamic and structural effects of sequence changes were unpredictable from the cognate structure alone.

Conclusions:

• Nucleotide shuffling represents a potentially general mechanism for protein recognition of ssDNA.
• Protein recognition of ssDNA differs fundamentally from that of double-stranded DNA (dsDNA).
• This study provides critical insights into the flexibility and adaptability of ssDNA-protein interactions.