Real-Time Investigation of Intracellular Polynucleotide Kinase Using a Cascaded Amplification Circuit

Polynucleotide kinase (PNK) shows an in-depth correlationship with DNA repair and metabolism processes. The in situ visualization of intracellular PNK revealed an extremely biological significance in supplementing reliable and quantitative information on its spatiotemporal distribution in live cells. Herein, we developed a versatile cascaded DNA amplification circuit through the integration of catalytic DNA assembly and hybridization chain reaction circuits and realized the accurate evaluation of intracellular PNK activity via the Förster resonance energy transfer (FRET) principle. Initially, without PNK, trigger T was firmly caged in the PNK-recognizing hairpin H_T, resulting in no disturbance of the concatenated circuit. However, with the introduction of PNK, the 5'-OH terminal of PNK-addressing H_T was phosphorylated, then the phosphorylated H_T could be subsequently digested by λ exonuclease (λ Exo) to produce trigger T of the cascaded DNA circuit. As a result, the integrated circuit was stimulated to produce an amplified FRET signal for quantitatively monitoring the activity of PNK. Due to the λ Exo-specific digestion of 5'-phosphate DNA and the high signal gain of the cascade circuit, our proposed strategy enables the sensitive analysis of PNK activity in vitro and in complex biological samples. Furthermore, our PNK-sensing platform was extensively explored in HeLa cells for realizing reliable intracellular PNK imaging and thus showed high potential in the future diagnosis and treatment of kinase-related diseases.

Zirconium ion-mediated assembly of a single quantum dot-based nanosensor for kinase assay

We demonstrate the zirconium ion-mediated assembly of a single quantum dot (QD)-based nanosensor for accurate detection of protein kinases (PKA) and polynucleotide kinases (PNK). This nanosensor is very sensitive with a detection limit of 8.82 × 10-4 U mL-1 for PKA and 1.40 × 10-5 U mL-1 for PNK. Moreover, it can be used to analyze the enzyme kinetic parameters and screen the inhibitors of PKA and PNK, with potential applications in drug discovery and clinical diagnosis.

A ligation-driven CRISPR-Cas biosensing platform for non-nucleic acid target detections

Herein, we describe a CRISPR-Cas12a sensing platform activated by a DNA ligation reaction for the sensitive detection of non-nucleic acid targets, including NAD⁺, ATP and polynucleotide kinase (PNK). In this design, the DNA ligation reaction triggered by these biomolecules generates DNA duplexes, which can activate the nuclease activity of Cas12a to produce amplified fluorescence signals. As a result, this work provides an alternative strategy to expand the applicability of the CRISPR-Cas system into the detection of non-nucleic acid biomolecules.

Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase

A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.

Terminal Deoxynucleotidyl Transferase-Catalyzed Preparation of pH-Responsive DNA Nanocarriers for Tumor-Targeted Drug Delivery and Therapy

Developing a highly efficient carrier for tumor-targeted delivery and site-specific release of anticancer drugs is a good way to overcome the side effects of traditional cancer chemotherapy. Benefiting from the nontoxic and biocompatible characteristics, DNA-based drug carriers have attracted increasing attention. Herein, we reported a novel and readily manipulated strategy to construct spherical DNA nanocarriers. In this strategy, terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA extension reaction is used to prepare a thick DNA layer on a gold nanoparticle (AuNP) surface by extending long poly(C) sequences from DNA primers immobilized on AuNPs. The poly(C) extension products can then hybridize with G-rich oligonucleotides to give CG-rich DNA duplexes (for loading anticancer drug doxorubicin, Dox) and multiple AS1411 aptamers. Via synergic recognition of multiple aptamer units to nucleolin proteins, biomarker of malignant tumors, Dox-loaded DNA carrier can be efficiently internalized in cancer cells and achieve burst release of drugs in acidic organelles because of i-motif formation-induced DNA duplex destruction. An as-prepared pH-responsive drug carrier was demonstrated to be promising for highly efficient delivery of Dox and selective killing of cancer cells in both in vitro and in vivo experiments, thus showing a huge potential in anticancer therapy.

A novel fluorescence method for the highly sensitive detection of T4 polynucleotide kinase based on polydopamine nanotubes

A novel fluorescence method has been developed for the detection of T4 PNK using FRET between dye-labeled ssDNA and PDANTs.

Trifunctional integrated DNA-based universal sensing platform for detection of diverse biomolecules in one-pot isothermal exponential amplification mode

Template constructed with only a short single-stranded DNA is necessary; it is first recognized by the target enzyme, then multiple amplification cycles are initiated, achieving ultra-high sensitivity by a one-pot isothermal reaction.

A modified exponential amplification reaction (EXPAR) with an improved signal-to-noise ratio for ultrasensitive detection of polynucleotide kinase

We reported a modified exponential amplification reaction strategy and applied it to design an ultrasensitive biosensor for the detection of endogenous polynucleotide kinase activity at single-cell level.