A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• Standard DNA detection relies on nondenaturing conditions for Watson-Crick base pairing.
• This method is effective for short DNA sequences (15-25 nucleotides) but limited for longer sequences.
• Single-nucleotide polymorphism (SNP) detection in longer DNA segments remains a challenge.

Purpose of the Study:

• To develop a new DNA detection method for SNP identification in longer DNA sequences (35-90 nucleotides).
• To overcome the limitations of traditional nondenaturing methods for SNP detection in extended DNA fragments.

Main Methods:

• Incorporation of a DNA molecule forming a stable G-quadruplex structure.
• Utilizing denaturing conditions (7 molar urea) to stabilize the G-quadruplex.
• Developing systems that generate colorimetric and fluorescent signals upon target binding.

Main Results:

• Successfully detected single-nucleotide polymorphisms (SNPs) in DNA sequences ranging from 35 to 90 nucleotides.
• Demonstrated the efficacy of G-quadruplex formation under denaturing conditions for SNP detection.
• Achieved both colorimetric and fluorescent readouts for target binding.

Conclusions:

• The novel G-quadruplex-based method enables accurate SNP detection in longer DNA sequences.
• This approach offers a viable alternative to traditional methods, particularly for complex genetic analyses.
• The dual signaling system enhances the versatility and applicability of the DNA detection technique.