title: Efficient detection of secondary structure folded nucleic acids related to Alzheimer's disease based on junction probes.
abstract: Single stranded DNA often forms stable secondary structures under physiological conditions. These DNA secondary structures play important physiological roles. However, the analysis of such secondary structure folded DNA is often complicated because of its high thermodynamic stability and slow hybridization kinetics. In this article, we demonstrate that Y-shaped junction probes could be used for rapid and highly efficient detection of secondary structure folded DNA. Our approach contained a molecular beacon (MB) probe and an assistant probe. In the absence of target, the MB probe failed to hybridize with the assistant probe. Whereas, the MB probe and the assistant probe could cooperatively unwind the secondary structure folded DNA target to form a ternary Y-shaped junction structure. In this condition, the MB probe was also opened, resulting in separating the fluorophores from the quenching moiety and emitting the fluorescence signal. This approach allowed for the highly sensitive detection of secondary structure folded DNA target, such as a tau specific DNA fragment related to Alzheimer's disease in this case. Additionally, this approach showed strong SNPs identifying capability. Furthermore, it was noteworthy that this newly proposed approach was capable of detecting secondary structure folded DNA target in cell lysate samples.
authors.affiliation: The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry and Chemical Engineering, Fuzhou University, Fuzhou 350002, PR China.
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.forename: Xiu-Juan
authors.initials: XJ
authors.lastname: Qi
authors.forename: Yan-Yan
authors.initials: YY
authors.lastname: Du
authors.forename: Hua-E
authors.initials: HE
authors.lastname: Fu
authors.forename: Guo-Nan
authors.initials: GN
authors.lastname: Chen
authors.forename: Huang-Hao
authors.initials: HH
authors.lastname: Yang
mesh_terms: D000544:Alzheimer Disease / Q000175:diagnosis / Q000235:genetics; D015374:Biosensing Techniques; D004247:DNA / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry*; D005456:Fluorescent Dyes; D006367:HeLa Cells; D006801:Humans; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics; D016875:tau Proteins / Q000235:genetics*
chemical_list: D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; C054369:MAPT protein, human; D015345:Oligonucleotide Probes; D016875:tau Proteins; D004247:DNA