Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA...

Area of Science:

• Biochemistry
• Molecular Biology
• Analytical Chemistry

Background:

• Developing sensitive and specific DNA detection methods is crucial for diagnostics.
• Existing methods may lack specificity or require complex procedures.
• Colorimetric assays offer a simple and cost-effective detection approach.

Purpose of the Study:

• To develop a novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA).
• To utilize a Y-shaped DNA duplex combined with a G-quadruplex-hemin DNAzyme for enhanced detection.
• To achieve sensitive and selective detection of target DNA sequences.

Main Methods:

• A G-rich oligonucleotide (Oligo-1) with DNAzyme activity was designed.
• A Y-shaped DNA duplex was formed by the hybridization of Oligo-1, Oligo-2, and the target DNA.
• The formation of the Y-shaped duplex inactivated the DNAzyme, leading to a color change.

Main Results:

• The sensor demonstrated a turn-off colorimetric response upon target DNA binding.
• A linear relationship was observed between absorbance decrease and target DNA concentration (1.0–250 nM).
• A low detection limit of 0.95 nM was achieved, with successful discrimination of single- and double-base mismatched DNA.

Conclusions:

• The developed sensor provides a sensitive and sequence-specific method for ssDNA detection.
• The Y-shaped DNA duplex strategy effectively caging the DNAzyme enables a turn-off colorimetric assay.
• This approach holds promise for applications in molecular diagnostics and genetic analysis.