Oligonucleotides form a duplex with non-helical properties on a positively charged surface

Area of Science:

• Biotechnology
• Molecular Biology
• Surface Chemistry

Background:

• The double helix structure of DNA forms via hybridization of complementary strands in aqueous solutions.
• Cation-coated surfaces are utilized in biotechnology for immobilizing nucleic acids on microarrays.
• These surfaces bind nucleic acids electrostatically via their negatively charged phosphate groups.

Purpose of the Study:

• To present a straightforward method for creating DNA microarrays.
• To investigate the structure and hybridization properties of adsorbed oligonucleotides on a positively charged surface.
• To explore the potential for non-helical DNA duplex formation on charged surfaces.

Main Methods:

• Fabrication of DNA microarrays using adsorptive attachment of oligonucleotides to a positively charged surface.
• Characterization of the adsorbed oligonucleotide layer, including density and hybridization capacity.
• Analysis of strand dissociation kinetics and DNase digestion rates of the formed DNA duplexes.

Main Results:

• Adsorbed oligonucleotide probes form a densely packed monolayer on the charged surface.
• The adsorbed probes retain the capacity for base pair-specific hybridization with target DNA strands.
• Kinetic and digestion data suggest the formation of a highly asymmetrical and unwound DNA duplex, deviating from the standard helical structure.
• A non-helical DNA duplex appears to be the preferred structural isomer under these conditions.

Conclusions:

• A simple adsorptive method for DNA microarray fabrication is demonstrated.
• DNA hybridization on charged surfaces can lead to non-helical duplex formation.
• This finding challenges the universal assumption of the double helix structure under all conditions, particularly on charged surfaces.