6 research outputs found
Collapse of DNA Tetrahedron Nanostructure for “Off–On” Fluorescence Detection of DNA Methyltransferase Activity
As a potential detection
technique, highly rigid and versatile functionality of DNA tetrahedron
nanostructures is often used in biosensing systems. In this work,
a novel multifunctional nanostructure has been developed as an “off–on”
fluorescent probe for detection of target methyltransferase by integrating
the elements of DNA tetrahedron, target recognition, and dual-labeled
reporter. This sensing system is initially in an “OFF”
state owing to the close proximity of fluorophores and quenchers.
After the substrate is recognized by target methyltransferase, the
DNA tetrahedron can be methylated to produce methylated DNA sites.
These sites can be recognized and cut by the restriction endonuclease <i>Dpn</i>I to bring about the collapse of the DNA tetrahedron,
which leads to the separation of the dual-labeled reporters from the
quenchers, and thus the recovery of fluorescence signal to produce
an “ON” state. The proposed DNA tetrahedron-based sensing
method can detect Dam methyltransferase in the range of 0.1–90
U mL<sup>–1</sup> with a detection limit of 0.045 U mL<sup>–1</sup> and shows good specificity and reproducibility for
detection of Dam methyltransferase in a real sample. It has been successfully
applied for screening various methylation inhibitors. Thus, this work
possesses a promising prospect for detection of DNA methyltransfrase
in the field of clinical diagnostics
Quantitative Proteomic Analysis To Identify Differentially Expressed Proteins in Myocardium of Epilepsy Using iTRAQ Coupled with Nano-LC–MS/MS
Epilepsy is a difficult-to-manage
neurological disease that can
result in organ damage, such as cardiac injury, that contributes to
sudden unexpected death in epilepsy (SUDEP). Although recurrent seizure-induced
cardiac dysregulation has been reported, the underlying molecular
mechanisms are unclear. We established an epileptic model with Sprague–Dawley
rats by applying isobaric tags for a relative and absolute quantification
(iTRAQ)-based proteomics approach to identify differentially expressed
proteins in myocardial tissue. A total of seven proteins in the acute
epilepsy group and 60 proteins in the chronic epilepsy group were
identified as differentially expressed. Bioinformatics analysis suggested
that the pathogenesis of cardiac injury in acute and chronic epilepsy
may be due to different molecular mechanisms. Three proteins, a receptor
for activated protein kinase C1 (RACK1), aldehyde dehydrogenase 6
family member A1 (ALDH6A1), and glycerol uptake/transporter 1 (Hhatl),
were identified as playing crucial roles in cardiac injury during
epilepsy and were successfully confirmed by Western blot and immunohistochemistry
analysis. Our study not only provides a deeper understanding of the
pathophysiological mechanisms of myocardial damage in epilepsy, but
also suggests some potential novel therapeutic targets for preventing
cardiac injury and reducing the incidence of sudden death due to heart
failure
Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs
A target-switched DNA nanotweezer
is designed for AND logic gate operation and enzyme-free detection
of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent
DNAzyme formation. The double crossover motif-based nanotweezer consists
of an arched structure as the set strand for target inputs and two
split G-rich DNAs at the termini of two arms for signal output. Upon
a CHA, a small amount of binary target inputs can switch numerous
open nanotweezers to a closed state, which leads to the formation
of proximity-dependent DNAzyme in the presence of hemin to produce
a highly sensitive biosensing system. The binary target inputs can
be used for successful building of AND logic gate, which is validated
by polyacrylamide gel electrophoresis, surface plasmon resonance and
the biosensing signal. The developed biosensing system shows a linear
response of the output chemiluminescence signal to input binary miRNAs
with a detection limit of 30 fM. It can be used for miRNAs analysis
in complex sample matrix. This system provides a simple and reusable
platform for logic gate operation and enzyme-free, highly sensitive,
and specific multianalysis of miRNAs
Pre-Folded G‑Quadruplex as a Tunable Reporter to Facilitate CRISPR/Cas12a-Based Visual Nucleic Acid Diagnosis
Clustered regularly interspaced short palindromic repeats
(CRISPR)/Cas12a-based
detection strategies with a fluorophore quencher-labeled ssDNA reporter
or gold nanoparticle ssDNA reporter have been widely used in point-of-care
(POC) molecular diagnostics. However, the potential of these CRISPR/Cas12a
strategies for POC molecular diagnostics is often compromised due
to the complex labeling, high cost, and low signal-to-noise ratio.
Herein, we show a pre-folded G-quadruplex (G4) structure with tunable
tolerance to CRISPR/Cas12a trans-cleavage and explore its mechanism.
Two G4 structures (i.e., Tel22-10 and G16C) sensitive or tolerant
to CRISPR/Cas12a trans-cleavage are designed and used as signal elements
to fabricate a label-free visible fluorescent strategy or “signal-on”
colorimetric strategy, respectively. These two strategies facilitate
an ultrasensitive visual nucleic acid determination of Group B Streptococci with a naked-eye limit of detection
of 1 aM. The feasibility of the developed G4-assisted CRISPR/Cas12a
strategies for real-world applications is demonstrated in clinical
vaginal/anal specimens and further verified by a commercial qPCR assay.
This work suggests that the proposed G4 structures with tunable tolerance
can act as promising signal reporters in the CRISPR/Cas12a system
to enable ultrasensitive visible nucleic acid detection
Zipper-Confined DNA Nanoframe for High-Efficient and High-Contrast Imaging of Heterogeneous Tumor Cell
Current
study in the heterogeneity and physiological
behavior of
tumor cells is limited by the fluorescence in situ hybridization technology in terms of probe assembly efficiency,
background suppression capability, and target compatibility. In a
typically well-designed assay, hybridization probes are constructed
in a confined nanostructure to achieve a rapid assembly for efficient
signal response, while the excessively high local concentration between
different probes inevitably leads to nonspecific background leakage.
Inspired by the fabric zipper, we propose a novel confinement reaction
pattern in a zipper-confined DNA nanoframe (ZCDN), where two kinds
of hairpin probes are independently anchored respective tracks. The
metastable states of the dual tracks can well avoid signal leakage
caused by the nonspecific probe configuration change. Biomarker-mediated
proximity ligation reduces the local distance of dual tracks, kinetically
triggering an efficient allosteric chain reaction between the hairpin
probes. This method circumvents nonspecific background leakage while
maintaining a high efficiency in responding to targets. ZCDN is employed
to track different cancer biomarkers located in both the cytoplasm
and cytomembrane, of which the expression level and oligomerization
behavior can provide crucial information regarding intratumoral heterogeneity.
ZCDN exhibits high target response efficiency and strong background
suppression capabilities and is compatible with various types of biological
targets, thus providing a desirable tool for advanced molecular diagnostics
Visual Assay for Methicillin-Resistant <i>Staphylococcus aureus</i> Based on Rolling Circular Amplification Triggering G‑Quadruplex/Hemin DNAzyme Proximity Assembly
Nowadays, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have constituted a new
challenge for anti-infective treatment. Precise identification and
rapid clinical diagnostics of MRSA from other methicillin-sensitive
strains entail assays with robust diagnostic efficiency and simple
operation steps. Sensitive detection of MecA gene is promising to
indicate MRSA infection, but it is challenged by the lack of isothermal
and simple strategies. A visual assay based on isothermal rolling
circular amplification and G-quadruplex/hemin (G4/hemin) DNAzyme proximity
assembly was proposed for the immediate, efficient, and cost-effective
detection of MecA in simple operation steps and in a single tube.
The presence of MecA specifically drove the formation of circular
templates, which further triggered isothermal amplification. The amplified
product offered abundant binding sites for DNA-grafted hemin probes
to form a novel proximity-assembled G4/hemin DNAzyme structure for
colorimetric changing diagnosis. This tandem-repeated novel DNAzyme
possessed higher catalytic activity and a lower background signal
than traditional G4/hemin DNAzyme, ensuring sensitive discrimination
of MRSA (limit of detection: 9.6 pM). Assay stability and antimatrix
interference capability enable clinical application, which shows compared
diagnostic ability with classic methods (100% sensitivity and 100%
specificity) but possesses more simplified procedures and shorter
turnaround time (<6 h). This colorimetric strategy in a nonsite-specific
and hypersensitive manner holds foreseeable prospects in clinical
diagnostic and research applications