Endonuclease-rolling circle amplification-based method for sensitive analysis of DNA-binding protein

A sensitive approach for the qualitative detection of DNA-binding protein on the microarray was developed. DNA complexes in which a partial duplex region is formed from a biotin-primer and a circle single strand DNA （ssDNA） were spotted on a microarray. The endonuclease recognition site （ERS） and the DNA-binding sites （DBS） were arranged side by side within the duplex region. The working principle of the detection system is described as follows： when the DNA-binding protein capture the DBS, the endonuclease could not attach to the ERS, and the immobilized primer in the DNA complex could be extended along the circle ssDNA by rolling circle amplification （RCA）. When no protein protects the DBS, the ERS could be attacked by the endonuclease and subsequently no rolling circle amplification occurs. Thereby we can detect the sequence specific DNA-binding activity with high-sensitivity due to the signal amplification of RCA.

Rolling Circle Amplification on Biotin-Streptavidin Complexes Immobilized to Activated Cyclic Polyolefin Surfaces

Cyclic polyolefin (COP) is an inexpensive hydrophobic material with low auto-fluorescence, high light transmittance and thermal stability, broad chemical resistance and no non-specific protein binding. Here, the hydrophobic alkane COP was modified to have carbonyl functionalities through oxygen plasma and chemical etching treatments to increase usefulness for chemical and biochemical applications. Then, biotin-hydrazide was used to create biotinylated surfaces that bound streptavidin. A biotinylated target oligonucleotide was subsequently bound to the immobilized biotin-streptavidin and ligation mediated rolling circle amplification-based (L-RCA) SNP detection was demonstrated.

Research progress and prospects of nucleic acid isothermal amplification technology

Nucleic acid(DNA and RNA)detection and quantification methods play vital roles in molecular biology.With the development of molecular biology,isothermal amplification of DNA/RNA,as a new molecular biology technology,can be amplified under isothermal condition,it has the advantages of high sensitivity,high specificity,and high efficiency,and has been applied in various fields of biotechnology,including disease diagnosis,pathogen detection,food hygiene and safety detection and so on.This paper introduces the progress of isothermal amplification technology,including rolling circle amplification(RCA),nucleic acid sequence-dependent amplification(NASBA),strand displacement amplification(SDA),loop-mediated isothermal amplification(LAMP),helicase-dependent amplification(HDA),recombinase polymerase amplification(RPA),cross-priming amplification(CPA),and its principle,advantages and disadvantages,and application development are briefly summarized.

RNA SNP Detection Method With Improved Specificity Based on Dual-competitive-padlock-probe

Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.

High-throughput quantitative detection of triple-negative breast cancer-associated expressed miRNAs by rolling circle amplification on fluorescence-encoded microspheres

Compared with other types of breast cancer,triple-negative breast cancer(TNBC)has the characteristics of a high degree of malignancy and poor prognosis.Early diagnosis of TNBC through biological markers and timely development of effective treatment methods can reduce its mortality.Many Research experiments have confirmed that some specific mi RNA expression profiles in TNBC can used as markers for early diagnosis.However,detecting the expression profiles of multiple groups of miRNAs according to traditional detection methods is complicated and consumes many samples.To address this issue,we developed a method for high-throughput,high-sensitivity quantitative detection of multiple sets of miRNAs(including mi R-16,mi R-21,mi R-92,mi R-199,and mi R-342)specifically expressed in TNBC by rolling circle amplification(RCA)on fluorescence-encoded microspheres.Through the optimization of reaction system conditions,the developed method showed an extensive linear dynamic range and high sensitivity for all five miRNAs with the lowest limit of detection of 2 fmol/L.Meanwhile,this high-throughput detection method also appeared reasonable specificity.Only in the presence of a specific target miRNA,the fluorescence signal on the correspondingly encoded microspheres is significantly increased,while the fluorescence signal on other non-correspondingly encoded microspheres is almost negligible.Furthermore,this process exhibited good recovery and reproducibility in serum.The advantages of this method allow us to more conveniently obtain the expression profiles of multiple groups of TNBC-associated mi RNAs,which is beneficial for the early detection of TNBC.

Dual Rolling Circle Amplification- Assisted Single-Particle Fluorescence Profiling of Exosome Heterogeneity for Discriminating Lung Adenocarcinoma from Pulmonary Nodules

Exosomes secreted by tumor cells carry abundant molecular biomarkers that reflect the status of their originating cells.These tumor-derived exosomes(TDEs)have emerged as attractive diagnostic targets.However,the identification and characterization of highly heterogeneous TDEs remain practically challenging.Here,we report a dual rolling circle amplification(DRCA)-assisted approach for the selective encapsulation of single TDEs for fluorescence microscopic and flow cytometric analysis.TDEs have been targeted by aptamers that recognized their surface tumor marker and exosomal marker CD63,following DRCA that produced entangling polymeric DNA chains,resulting in facile particle enlargement that allows single-particle fluorescence profiling of exosome heterogeneity.We have demonstrated the use of a dual-marker positive ratio for exosome differentiation and applied division and multiplication operations for normalized andmagnified marker heterogeneity analysis.We further applied this assay to distinguish lung adenocarcinoma and pulmonary nodule patients and found an accuracy of 90%.We anticipate promising transformations of this straightforward assay into clinically implantable diagnostic methods.

Self-assembly of DNA Origami Using Rolling Circle Amplification Based DNA Nanoribbons

During the development of structural DNA nanotechnology,the emerging of scaffolded DNA origami is marvelous.It utilizes DNA double helix inherent specificity of Watson-Crick base pairing and structural features to create self-assembling structures at the nanometer scale exhibiting the addressable character.However,the assembly of DNA origami is disorderly and unpredictable.Herein,we present a novel strategy to assemble the DNA origami using rolling circle amplification based DNA nanoribbons as the linkers.Firstly,long single-stranded DNA from Rolling Circle Amplification is annealed with several staples to form kinds of DNA nanoribbons with overhangs.Subsequently,the rectangle origami is formed with overhanged staple strands at any edge that would hybridize with the DNA nanoribbons.By mixing them up,we illustrate the one-dimensional even two-dimensional assembly of DNA origami with good orientation.

Ultrasensitive detection of DNA and protein markers in cancer cells

Cancer cells differ from normal cells in various parameters, and these differences are caused by genomic mutations and consequential altered gene expression. The genetic and functional heterogeneity of tumor cells is a major challenge in cancer research, detection, and effective treatment. As such, the use of diagnostic methods is important to reveal this heterogeneity at the single-cell level. Droplet microfluidic devices are effective tools that provide exceptional sensitivity for analyzing single cells and molecules. In this review, we highlight two novel methods that employ droplet microfluidics for ultrasensitive detection of nucleic acids and protein markers in cancer cells. We also discuss the future practical applications of these methods.

Signal Amplification for Highly Sensitive Immunosensing

To dissolve the bottleneck problem of life and biomedical science in detection of biomolecules with low abundance and acquisition of ultraweak biological signals,highly sensitive analytical methods coupling with the specificity of biological recognition events have been quickly developed by the exploring of signal amplification strategies.These strategies have extensively been introduced into the development of highly sensitive immunosensing methods by combining with highly specific immunological recognition.They can be divided into two groups.One group of strategies attempts to transfer the immunological recognition event into large number of reporter probes or signal probes for signal readout by employing nano/micro-materials as vehicles for multi-labeling and/or molecular biological amplification for increasing the abundance of the signal molecules.The other uses nanomaterials or enzyme mimics as catalytic tools/tags to obtain enhanced detection signal.This review focuses on the significant advances in design of signal amplification strategies for highly sensitive immunosensing.

Recent advancements in DNA nanotechnology-enabled extracellular vesicles detection and diagnosis:A mini review

Extracellular vesicles(EVs)are cell-derived nanosized vesicles widely recognized for their critical roles in various pathophysiological processes.Molecular analysis of EVs is currently being considered an emerging tool for diseases diagnosis.However,the small size and heterogeneity of EVs has staggered the EVs research for diseases diagnosis.DNA nanotechnology enables self-assembly of versatile DNA nanostructures and has shown enormous potential in assisting EVs biosensing.In this review,we briefly introduce the recent advances in DNA nanotechnology approaches for EVs detection.The approaches were categorized based on the dimension of DNA nanostructures.We provide critical evaluation of these approaches,and summarize the pros and cons of specific methods.Further,we discuss the challenges and future perspectives in this field.

Coating with flexible DNA network enhanced T-cell activation and tumor killing for adoptive cell therapy

Adoptive cell therapy(ACT)is an emerging powerful cancer immunotherapy,which includes a complex process of genetic modification,stimulation and expansion.During these in vitro or ex vivo manipulation,sensitive cells are inescapability subjected to harmful external stimuli.Although a variety of cytoprotection strategies have been developed,their application on ACT remains challenging.Herein,a DNA network is constructed on cell surface by rolling circle amplification(RCA),and T cell-targeted trivalent tetrahedral DNA nanostructure is used as a rigid scaffold to achieve high-efficient and selective coating for T cells.The cytoprotective DNA network on T-cell surface makes them aggregate over time to form cell clusters,which exhibit more resistance to external stimuli and enhanced activities in human peripheral blood mononuclear cells and liver cancer organoid killing model.Overall,this work provides a novel strategy for in vitro T cell-selective protection,which has a great potential for application in ACT.

A sensitive one-pot ROA assay for rapid miRNA detection

MicroRNAs(miRNAs)and short RNA fragments(18–25 nt)are crucial biomarkers in biological research and disease diagnostics.However,their accurate and rapid detection remains a challenge,largely due to their low abundance,short length,and sequence similarities.In this study,we report on a highly sensitive,one-step RNA O-circle amplification(ROA)assay for rapid and accurate miRNA detection.The ROA assay commences with the hybridization of a circular probe with the test RNA,followed by a linear rolling circle amplification(RCA)using dUTP.This amplification process is facilitated by U-nick reactions,which lead to an exponential amplification for readout.Under optimized conditions,assays can be completed within an hour,producing an amplification yield up to the microgram level,with a detection limit as low as 0.15 fmol(6 pM).Notably,the ROA assay requires only one step,and the results can be easily read visually,making it user-friendly.This ROA assay has proven effective in detecting various miRNAs and phage ssRNA.Overall,the ROA assay offers a user-friendly,rapid,and accurate solution for miRNA detection.