Nanoparticle carrying a single probe for target DNA detection and single nucleotide discrimination

2009 ◽  
Vol 25 (2) ◽  
pp. 313-319 ◽  
Author(s):  
Wei Jie Qin ◽  
Lin Yue Lanry Yung
Keyword(s):  
Dna Detection ◽  
Single Nucleotide ◽  
Single Probe ◽  
Target Dna

scholarly journals Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jiao Fan ◽  
Yige Ding ◽  
Chao Ren ◽  
Ziguo Song ◽  
Jie Yuan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Double Strand Breaks ◽  
Great Promise ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Dna Base ◽  
Target Dna ◽  
Single Nucleotide Variations ◽  
Adenine Deaminase ◽  
Target Rna

AbstractCytosine or adenine base editors (CBEs or ABEs) hold great promise in therapeutic applications because they enable the precise conversion of targeted base changes without generating of double-strand breaks. However, both CBEs and ABEs induce substantial off-target DNA editing, and extensive off-target RNA single nucleotide variations in transfected cells. Therefore, the potential effects of deaminases induced by DNA base editors are of great importance for their clinical applicability. Here, the transcriptome-wide deaminase effects on gene expression and splicing is examined. Differentially expressed genes (DEGs) and differential alternative splicing (DAS) events, induced by base editors, are identified. Both CBEs and ABEs generated thousands of DEGs and hundreds of DAS events. For engineered CBEs or ABEs, base editor-induced variants had little effect on the elimination of DEGs and DAS events. Interestingly, more DEGs and DAS events are observed as a result of over expressions of cytosine and adenine deaminases. This study reveals a previously overlooked aspect of deaminase effects in transcriptome-wide gene expression and splicing, and underscores the need to fully characterize such effects of deaminase enzymes in base editor platforms.

The Fabrication of 2D Cu-Based MOF Nanosheets for DNA Detection

2019 ◽  
Vol 72 (12) ◽  
pp. 939
Author(s):  
Xuan Qi ◽  
Lingyu Xia ◽  
Yunong Li ◽  
Tieqiang Wang ◽  
Xuemin Zhang ◽  
...  
Keyword(s):  
Detection Limit ◽  
Dna Detection ◽  
Metal Organic Framework ◽  
Linear Range ◽  
Spray Method ◽  
Target Dna ◽  
Metal Organic ◽  
Dna Mixture ◽  
2D Structure ◽  
Application Scope

The Cu-based metal–organic framework (MOF) analogues, copper 1,4-benzenedicarboxylate (CuBDC), copper 2,6-naphthalenedicarboxylate (Cu(2,6-NDC)), and copper 1,4-naphthalenedicarboxylate (Cu(1,4-NDC)) MOF nanosheets, are prepared as biosensor nanoplatforms for DNA detection by a spray method. With the ultrathin 2D structure, the fabricated MOF nanosheets exhibited better detection of target DNA, in particular when compared with the corresponding 3D MOF bulky crystals, when used as a DNA biosensor platform. The Cu(1,4-NDC) nanosheets display a distinct sensitivity with a detection limit of 0.3nM and linear range of 0–20nM, and selectivity for the target DNA or target DNA mixture. The feasible biosensor nanoplatform composed of 2D MOF nanosheets broadens the application scope of MOF nanosheets.

A dual-cycling biosensor for target DNA detection based on the toehold-mediated strand displacement reaction and exonuclease III assisted amplification

2018 ◽  
Vol 42 (6) ◽  
pp. 4714-4718 ◽  
Author(s):  
Yu Ling ◽  
Xiao Fang Zhang ◽  
Xiao Hui Chen ◽  
Li Liu ◽  
Xiao Hu Wang ◽  
...  
Keyword(s):  
Dna Detection ◽  
Dna Biosensor ◽  
Displacement Reaction ◽  
Strand Displacement ◽  
Exonuclease Iii ◽  
Target Dna ◽  
Strand Displacement Reaction

Based on the toehold-mediated strand displacement reaction and exonuclease III assisted amplification, a sensitive and simple target DNA biosensor was established.

scholarly journals CRISPR/Cas9 inhibits rather than induces non-targeted DNA cleavage more likely to cause off-target single-nucleotide variants

2021 ◽  
Author(s):  
Ze Zhang ◽  
Yuanyuan Guo ◽  
Rongjia Zhang ◽  
Wuchen Yang ◽  
Zhengqing Xie ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Free System ◽  
Cell Free System ◽  
Cell Extracts ◽  
Target Dna ◽  
Target Sequences

CRISPR/Cas9 gene targeting technology has become the most widely used gene editing technology in both plants and animals. However, substantial off-target effect remains as a major imperfection hindering its further application. Here, Nicotiana benthamiana leaf cell-free system was used to simulate in vivo environment. And the effects of different CRISPR/Cas9 components on DNA stability in cell-free system were studied to explore possible mechanisms causing CRISPR off-target. The results showed that overexpressing Cas9, nCas9 and dCas9 significantly inhibited DNA cleavage in the cell extracts. While overexpressing RNPs accelerated the target DNA cleavage but inhibited non-target DNA digestion in cell extracts, overexpressing nRNP and dRNP blocked the cleavage of either target or non-target sequences. Meanwhile, analysis of whole-genome sequencing data from mice and rice edited by different CRISPR tools revealed that the main off-target mutations were SNVs (single nucleotide variants), rather than Indels (insertions and deletions) that were readily induced by DNA double-strand breaks. The off-target sites did not match the conventionally predicted places but were PAM-rich sites preferred. Our study suggests that PAM-dependent binding without cleavage of CRISPR/Cas9 to non-target sequences may increase off-target mutation risks through impeding the necessary cleavage process for repairing spontaneous or environmentally induced non-targeted DNA mutations.

scholarly journals Optical Thickness-Encoded Suspension Array for High-Throughput Multiplexed Gene Detection

Sensors ◽  
2019 ◽  
Vol 19 (24) ◽  
pp. 5425
Author(s):  
Huiying Ma ◽  
Xuejing Chen ◽  
Bangrong Lu ◽  
Yanhong Ji
Keyword(s):  
Optical Thickness ◽  
Dna Detection ◽  
High Specificity ◽  
Analyte Concentration ◽  
Gene Detection ◽  
Suspension Array ◽  
Dna Molecule ◽  
Target Dna ◽  
Good Repeatability ◽  
Encoding Method

We proposed a coding and decoding method of suspension array (SA) based on micro-quartz pieces (MQPs) with different optical thicknesses. The capture probes (cDNA) were grafted onto the surfaces of MQPs and specifically recognized and combined with the partial sequence of the target DNA (tDNA) to form a MQP-cDNA-tDNA complex. Quantum dot-labeled signal probes were then used to specifically recognize and bind another portion of the tDNA in the complex to form a double-probe sandwich structure. This optical thickness-encoded SA can be decoded and detected by a dual-wavelength digital holographic phase fluorescence microscope system. We conducted a series of DNA molecule detection experiments by using this encoding method. Control experiments confirmed the specificity of optical thickness-encoded SA in DNA detection. The concentration gradient experiments then demonstrated the response of the MQPs based SA to analyte concentration. Finally, we used the encoding method to detect three types of DNA in a single sample and confirmed the feasibility of the proposed optical thickness-encoded SA in multiplexed DNA detection. The detection results are stable, and the detection exhibits high specificity and good repeatability.

Fabrication of fluorescence enhancement of quantum dots on a gold colloid formed film for oligonucleotide DNA detection

2017 ◽  
Vol 9 (3) ◽  
pp. 434-442 ◽  
Author(s):  
Jie Yang ◽  
Ji-Tao Song ◽  
Wei Hu ◽  
Yan Huang ◽  
Li-Juan Deng ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Quantum Dot ◽  
Fluorescence Enhancement ◽  
Dna Detection ◽  
Gold Colloid ◽  
Target Dna

This paper reported a method based on metal-enhanced quantum dot fluorescence on a gold colloid formed film for target DNA detection.

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