Palindromic Molecule Beacon-Based Cascade Amplification for Colorimetric Detection of Cancer Genes

Abstract

A highly sensitive and selective colorimetric assay based on a multifunctional molecular beacon with palindromic tail (PMB) was proposed for the detection of target p53 gene. The PMB probe can serve as recognition element, primer, and polymerization template and contains a nicking site and a C-rich region complementary to a DNAzyme. In the presence of target DNA, the hairpin of PMB is opened, and the released palindromic tails intermolecularly hybridize with each other, triggering the autonomous polymerization/nicking/displacement cycles. Although only one type of probe is involved, the system can execute triple and continuous polymerization strand displacement amplifications, generating large amounts of G-quadruplex fragments. These G-rich fragments can bind to hemin and form the DNAzymes that possess the catalytic activity similar to horseradish peroxidase, catalyzing the oxidation of ABTS by HO and producing the colorimetric signal. Utilizing the newly proposed sensing system, target DNA can be detected down to 10 pM with a linear response range from 10 pM to 200 nM, and mutant target DNAs are able to be distinguished even by the naked eye. The desirable detection sensitivity, high specificity, and operation convenience without any separation step and chemical modification demonstrate that the palindromic molecular beacon holds the potential for detecting and monitoring a variety of nucleic acid-related biomarkers.

Tumor-targeting [2]catenane-based grid-patterned periodic DNA monolayer array forin vivotheranostic application

“…The vast sequence space and the powerful DNA assembly technique can be rationally utilized to design and construct DNA nanostructures with predefined topologies and geometries, thus bringing new opportunities for the development of 1D architectures with planned structural features and functionalities. Especially, since the complementary strand of a palindromic fragment reads the same sequence in the opposite direction, 77 palindrome-based assembly provides a simple strategy for the construction of DNA nanoobjects of different shapes 78–80 and has application-specific advantages in bioassays 81–83 and cargo loading/transportation. 40 Meanwhile, based on their outstanding serum stability 84,85 and potential applications in the topological labeling of nucleic acids, 86–88 catenane-based DNA materials have recently attracted increasing interest 89 and shown great promise in biotechnology 90–97 and biosensing.…”

“…40 Meanwhile, based on their outstanding serum stability 84,85 and potential applications in the topological labeling of nucleic acids, 86–88 catenane-based DNA materials have recently attracted increasing interest 89 and shown great promise in biotechnology 90–97 and biosensing. 81,82,98,99 These technical advances offer a promising method for the construction of DNA arrays capable of actively traveling through the bloodstream and reaching diseased sites following systemic administration.…”

Ultrasensitive Electrochemical DNA Biosensor Fabrication by Coupling an Integral Multifunctional Zirconia-Reduced Graphene Oxide-Thionine Nanocomposite and Exonuclease I-Assisted Cleavage

“…The P53 gene has been well-known as the guardian of the genome that can code and express p53 protein to suppress the malignant transformation of cells. The p53 gene has been associated with the occurrence of many human tumors such as liver, breast, bladder, and stomach cancers and so on (Hasanzadeh and Shadjou, 2017 ; Shen et al, 2018 ). Therefore, the current electrochemical nucleic acid biosensing strategy not only would pave a new avenue for biosensor fabrication by nanomaterials but also is anticipated to show potential for applications in bioanalysis and medical diagnosis.…”

Palindromic Fragment-Mediated Single-Chain Amplification: An Innovative Mode for Photoelectrochemical Bioassay

“…For instance, Li et al devised a newly palindromic fragment-incorporated molecular beacon-based fluorescence aptasensor for detection of tumor suppressor gene p53 . Shen et al established a sensing system for the convenient and sensitive colorimetric bioassay detection of cancer genes based on a multifunctional molecular beacon with a palindromic tail . However, the fascinating feature of this palindromic self-hybridization urgently needs to be extended for other non-nucleic acid target (NNAT) detection.…”