Weak-cooperative binding of a long single-stranded DNA chain on a surface

Area of Science:

• Molecular Biology
• Biophysics
• Biosensor Technology

Background:

• Binding long, single-stranded nucleic acids to surface probes is crucial for biophysics and diagnostics.
• Conformational dynamics of nucleic acid chains hinder accessibility and hybridization efficiency.
• Developing effective methods for capturing genomic material on biosensors remains a challenge.

Purpose of the Study:

• To investigate the binding of bacteriophage M13mp18 genome to surface-immobilized probes.
• To identify factors governing the capturing performance of oligonucleotide probes for genomic DNA.
• To elucidate the mechanism of nucleic acid hybridization on biosensor surfaces.

Main Methods:

• Utilized a multi-spot, label-free biosensor to study M13mp18 genome binding.
• Employed various 20-mer probes immobilized on the biosensor surface.
• Combined experimental binding data with computational analysis of genomic strand structure.

Main Results:

• Identified specific probes exhibiting strong binding capability with dissociation constants as low as 10 pM.
• Found probe capturing performance correlates with the multiplicity of binding sites on the genomic strand.
• Observed that secondary and tertiary structures have minimal impact on probe capturing efficiency.

Conclusions:

• A model of weak cooperativity of transient bonds explains enhanced probe capturing.
• The presence of over 20 partial pairings with favorable binding energy significantly improves capture.
• Optimized probe selection based on binding site multiplicity can enhance genomic strand detection.