6 research outputs found
Supplementary_material - Identification of Significant Gene Signatures and Prognostic Biomarkers for Patients With Cervical Cancer by Integrated Bioinformatic Methods
<p>Supplementary_material for Identification of Significant Gene Signatures and Prognostic Biomarkers for Patients With Cervical Cancer by Integrated Bioinformatic Methods by Xiaofang Li, Run Tian, Hugh Gao, Feng Yan, Le Ying, Yongkang Yang, Pei Yang and Yan’e Gao in Technology in Cancer Research & Treatment</p
Powerful Amplification Cascades of FRET-Based Two-Layer Nonenzymatic Nucleic Acid Circuits
Nucleic
acid circuits have played important roles in biological
engineering and have increasingly attracted researchers’ attention.
They are primarily based on nucleic acid hybridizations and strand
displacement reactions between nucleic acid probes of different lengths.
Signal amplification schemes that do not rely on protein enzyme show
great potential in analytical applications. While the single amplification
circuit often achieves linear amplification that may not meet the
need for detection of target in a very small amount, it is very necessary
to construct cascade circuits that allow for larger amplification
of inputs. Herein, we have successfully engineered powerful amplification
cascades of FRET-based two-layer nonenzymatic nucleic acid circuits,
in which the outputs of catalyzed hairpin assembly (CHA) activate
hybridization chain reactions (HCR) circuits to induce repeated hybridization,
allowing real-time monitoring of self-assembly process by FRET signal.
The cascades can yield 50000-fold signal amplification with the help
of the well-designed and high-quality nucleic acid circuit amplifiers.
Subsequently, with coupling of structure-switching aptamer, as low
as 200 pM adenosine is detected in buffer, as well as in human serum.
To our knowledge, we have for the first time realized real-time monitoring
adaptation of HCR to CHA circuits and achieved amplified detection
of nucleic acids and small molecules with relatively high sensitivity
FRET Nanoflares for Intracellular mRNA Detection: Avoiding False Positive Signals and Minimizing Effects of System Fluctuations
A new
class of intracellular nanoprobe, termed fluorescence resonance
energy transfer (FRET) nanoflares, was developed to sense mRNA in
living cells. It consists of a gold nanoparticle (AuNP), recognition
sequences, and flares. Briefly, the AuNP functionalized with recognition
sequences hybridized to flares, which are designed as hairpin structures
and fluorescently labeled donors and acceptors at two ends, respectively.
In the absence of targets, the flares are captured by binding with
the recognition sequences, separating of the donor and acceptor, and
inducing low FRET efficiency. However, in the presence of targets,
the flares are gradually displaced from the recognition sequences
by the targets, subsequently forming hairpin structures that bring
the donor and acceptor into close proximity and result in high FRET
efficiency. Compared to the conventional single-dye nanoflares, the
upgraded FRET nanoflares can avoid false positive signals by chemical
interferences (such as nuclease and GSH) and thermodynamic fluctuations.
Moreover, the signal generation in FRET nanoflares can be easily made
with ratiometric measurement, minimizing the effect of system fluctuations
Aptazyme–Gold Nanoparticle Sensor for Amplified Molecular Probing in Living Cells
To
date, a few of DNAzyme-based sensors have been successfully
developed in living cells; however, the intracellular aptazyme sensor
has remained underdeveloped. Here, the first aptazyme sensor for amplified
molecular probing in living cells is developed. A gold nanoparticle
(AuNP) is modified with substrate strands hybridized to aptazyme strands.
Only the target molecule can activate the aptazyme and then cleave
and release the fluorophore-labeled substrate strands from the AuNP,
resulting in fluorescence enhancement. The process is repeated so
that each copy of target can cleave multiplex fluorophore-labeled
substrate strands, amplifying the fluorescence signal. Results show
that the detection limit is about 200 nM, which is 2 or 3 orders of
magnitude lower than that of the reported aptamer-based adenosine
triphosphate (ATP) sensors used in living cells. Furthermore, it is
demonstrated that the aptazyme sensor can readily enter living cells
and realize intracellular target detection
Ratiometric Fluorescent Sensing of pH Values in Living Cells by Dual-Fluorophore-Labeled i‑Motif Nanoprobes
We
designed a new ratiometric fluorescent nanoprobe for sensing
pH values in living cells. Briefly, the nanoprobe consists of a gold
nanoparticle (AuNP), short single-stranded oligonucleotides, and dual-fluorophore-labeled
i-motif sequences. The short oligonucleotides are designed to bind
with the i-motif sequences and immobilized on the AuNP surface via
Au–S bond. At neutral pH, the dual fluorophores are separated,
resulting in very low fluorescence resonance energy transfer (FRET)
efficiency. At acidic pH, the i-motif strands
fold into a quadruplex structure and leave the AuNP, bringing the
dual fluorophores into close proximity, resulting in high FRET efficiency,
which could be used as a signal for pH sensing. The nanoprobe possesses
abilities of cellular transfection, enzymatic protection, fast response
and quantitative pH detection. The <i>in vitro</i> and intracellular
applications of the nanoprobe were demonstrated, which showed excellent
response in the physiological pH range. Furthermore, our experimental
results suggested that the nanoprobe showed excellent spatial and
temporal resolution in living cells. We think that the ratiometric
sensing strategy could potentially be applied to create a variety
of new multicolor sensors for intracellular detection
MOESM1 of Understanding immune phenotypes in human gastric disease tissues by multiplexed immunohistochemistry
Additional file 1. Supplemental methods, supplementary tables for patients. Figure S1. H&E staining of the two TMAs. Figure S2. Comparison of the results of ImageJ software and the score by pathologists