A new AgNC fluorescence regulation mechanism caused by coiled DNA and its applications in constructing molecular beacons with low background and large signal enhancement

2017 ◽  
Vol 53 (91) ◽  
pp. 12290-12293 ◽  
Author(s):  
Weijun Zhou ◽  
Shaojun Dong
Keyword(s):  
Dna Sequence ◽  
Dna Detection ◽  
Signal Enhancement ◽  
Molecular Beacons ◽  
Regulation Mechanism ◽  
Large Signal ◽  
Low Background ◽  
Target Dna

A AgNC fluorescence interference strategy caused by a coiled DNA sequence (A) and its applications in target DNA detection (B).

scholarly journals Progress toward Ultrafast DNA Sequencing Using Solid-State Nanopores

2007 ◽  
Vol 53 (11) ◽  
pp. 1996-2001 ◽  
Author(s):  
Gautam V Soni ◽  
Amit Meller
Keyword(s):  
Solid State ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Large Scale ◽  
Optical Detection ◽  
Ionic Current ◽  
Molecular Beacons ◽  
Single Nucleotide ◽  
Dual Color ◽  
Target Dna

Abstract Background: Measurements of the ionic current flowing through nanometer-scale pores (nanopores) have been used to analyze single DNA and RNA molecules, with the ultimate goal of achieving ultrafast DNA sequencing. However, attempts at purely electronic measurements have not achieved the signal contrast required for single nucleotide differentiation. In this report we propose a novel method of optical detection of DNA sequence translocating through a nanopore. Methods: Each base of the target DNA sequence is 1st mapped onto a 2-unit code, 2 10-bp nucleotide sequence, by biochemical conversion into Designed DNA Polymers. These 2-unit codes are then hybridized to complementary, fluorescently labeled, and self-quenching molecular beacons. As the molecular beacons are sequentially unzipped during translocation through a <2-nm-wide nanopore, their fluorescent tags are unquenched and are detected by a custom-built dual-color total internal reflection fluorescence (TIRF) microscope. The 2-color optical signal is then correlated to the target DNA sequence. Results: A dual-color TIRFM microscope with single-molecule resolution was constructed, and controlled fabrication of 1-dimensional and 2-dimensional arrays of solid-state nanopores was performed. A nanofluidic cell assembly was constructed for TIRF-based optical detection of voltage-driven DNA translocation through a nanopore. Conclusions: We present a novel nanopore-based DNA sequencing technique that uses an optical readout of DNA translocating unzipping through a nanopore. Our technique offers better single nucleotide differentiation in sequence readout, as well as the possibility of large-scale parallelism using nanopore arrays.

scholarly journals A Novel Position-Specific Encoding Algorithm (SeqPose) of Nucleotide Sequences and Its Application for Detecting Enhancers

2021 ◽  
Vol 22 (6) ◽  
pp. 3079
Author(s):  
Xuechen Mu ◽  
Yueying Wang ◽  
Meiyu Duan ◽  
Shuai Liu ◽  
Fei Li ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Dna Sequence ◽  
Prediction Models ◽  
Nucleotide Sequences ◽  
Attention Mechanism ◽  
Training Dataset ◽  
Regulation Mechanism ◽  
Independent Test ◽  
Regulation Strength ◽  
Enhancer Detection

Enhancers are short genomic regions exerting tissue-specific regulatory roles, usually for remote coding regions. Enhancers are observed in both prokaryotic and eukaryotic genomes, and their detections facilitate a better understanding of the transcriptional regulation mechanism. The accurate detection and transcriptional regulation strength evaluation of the enhancers remain a major bioinformatics challenge. Most of the current studies utilized the statistical features of short fixed-length nucleotide sequences. This study introduces the location information of each k-mer (SeqPose) into the encoding strategy of a DNA sequence and employs the attention mechanism in the two-layer bi-directional long-short term memory (BD-LSTM) model (spEnhancer) for the enhancer detection problem. The first layer of the delivered classifier discriminates between enhancers and non-enhancers, and the second layer evaluates the transcriptional regulation strength of the detected enhancer. The SeqPose-encoded features are selected by the Chi-squared test, and 45 positions are removed from further analysis. The existing studies may focus on selecting the statistical DNA sequence descriptors with large contributions to the prediction models. This study does not utilize these statistical DNA sequence descriptors. Then the word vector of the SeqPose-encoded features is obtained by using the word embedding layer. This study hypothesizes that different word vector features may contribute differently to the enhancer detection model, and assigns different weights to these word vectors through the attention mechanism in the BD-LSTM model. The previous study generously provided the training and independent test datasets, and the proposed spEnhancer is compared with the three existing state-of-the-art studies using the same experimental procedure. The leave-one-out validation data on the training dataset shows that the proposed spEnhancer achieves similar detection performances as the three existing studies. While spEnhancer achieves the best overall performance metric MCC for both of the two binary classification problems on the independent test dataset. The experimental data shows that the strategy of removing redundant positions (SeqPose) may help improve the DNA sequence-based prediction models. spEnhancer may serve well as a complementary model to the existing studies, especially for the novel query enhancers that are not included in the training dataset.

Sensitive mutant DNA biomarker detection based on magnetic nanoparticles and nicking endonuclease assisted fluorescence signal amplification

RSC Advances ◽  
2015 ◽  
Vol 5 (26) ◽  
pp. 20020-20024 ◽  
Author(s):  
Na Li ◽  
Zhong Feng Gao ◽  
Bei Hua Kang ◽  
Nian Bing Li ◽  
Hong Qun Luo
Keyword(s):  
Magnetic Nanoparticles ◽  
Signal Amplification ◽  
Fluorescence Signal ◽  
Biomarker Detection ◽  
Background Signal ◽  
Sensitive Mutant ◽  
Nicking Endonuclease ◽  
Low Background ◽  
Target Dna ◽  
Fluorescence Signal Amplification

Amplified fluorescence target DNA detection was developed combining nicking endonuclease assisted target recycling and magnetic nanoparticles with low background signal.

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 light-regulated bZIP module, photozipper, induces the binding of fused proteins to the target DNA sequence in a blue light-dependent manner

2015 ◽  
Vol 14 (11) ◽  
pp. 1998-2006 ◽  
Author(s):  
Osamu Hisatomi ◽  
Keigo Furuya
Keyword(s):  
Dna Sequence ◽  
Blue Light ◽  
Fluorescent Protein ◽  
Yellow Fluorescent Protein ◽  
Dependent Manner ◽  
Target Dna

Yellow fluorescent protein or mCherry protein fused with the Photozipper underwent blue light-induced dimerization, which enhanced their affinities for the target DNA.

Triplex Molecular Beacons as Modular Probes for DNA Detection

2007 ◽  
Vol 46 (27) ◽  
pp. 5223-5225 ◽  
Author(s):  
Tom N. Grossmann ◽  
Lars Röglin ◽  
Oliver Seitz
Keyword(s):  
Dna Detection ◽  
Molecular Beacons

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.

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