Locus-patterned sequence oriented enrichment for multi-dimensional gene analysis
TL;DR: A locus-patterned sequence oriented enrichment was proposed to analyze the gene sequence, locus variation and molecular abundance of heterogeneous genes.
read more
Abstract: Multi-dimensional gene analysis provides in-depth insights into gene sequence, locus variations and molecular abundance, whereas it is vulnerable to the perturbation of complex reaction networks and always compromises on the discrimination of analogous sequences. Here, we present a sequence oriented enrichment method patterned by the prescribed locus without crosstalk between concurrent reactions. Energetically favourable structures of nucleic acid probes are theoretically derived and oriented to a specific gene locus. We designed a pair of universal probes for multiple conserved loci to avoid side reactions from undesired interactions among increased probe sets. Furthermore, competitive probes were customized to sink analogues for differentiating the reaction equilibrium and kinetics of sequence enrichment from the target, so variant loci can be synchronously identified with nucleotide-level resolution. Thus, the gene locus guides sequence enrichment and combinatorial signals to create unique codes, which provides access to multidimensional and precise information for gene decoding.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal.
TL;DR: In this article, the authors reviewed the major methods that emerged in recent years on the design of DNA-based biosensors and their applications, and briefly discussed the possible future direction of DNA based sensors design.
58
Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal
01 Feb 2022
TL;DR: In this article , the authors reviewed the major methods that emerged in recent years on the design of DNA-based biosensors and their applications, and briefly discussed the possible future direction of DNA based sensors design.
20
Homogeneous and universal transduction of various nucleic acids to an off-shelf device based on programmable toehold switch sensing.
TL;DR: Through a rational construction of an RNA toehold switch sensor, the glucometer-based detection of nucleic acids was innovatively simplified into a completely homogeneous and label-free process, which is more robust, user-friendly, reagent-saving, and reproducible.
17
Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus.
Yue Zhao,X. Fang,Huahang Yu,You-hui Fu,Yonghua Zhao +4 more
TL;DR: The feasibility of multilocus detection was validated using various mutation-prone genes, demonstrating a significant potential for accurate analysis of SARS-CoV-2 and holding great promise for the clinical diagnosis of other infectious diseases.
8
Hydrogel-compartmentalized heterogeneous amplification for viral digital genotyping
TL;DR: In this article , a hydrogel-compartmentalized nucleic acid amplification and restriction enzyme was introduced to establish a competitive amplification reaction for hepatitis B virus genotyping.
3
References
Loop-mediated isothermal amplification of DNA
Tsugunori Notomi,Hiroto Okayama,Harumi Otawara-shi Masubuchi,Toshihiro Yonekawa,Keiko Watanabe,Nobuyuki Amino,Tetsu Hase +6 more
TL;DR: A novel method that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions that employs a DNA polymerase and a set of four specially designed primers that recognize a total of six distinct sequences on the target DNA.
Control of DNA Strand Displacement Kinetics Using Toehold Exchange
David Y. Zhang,Erik Winfree +1 more
TL;DR: This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.
1.4K
Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity
Kristen M. Turner,Viraj Deshpande,Doruk Beyter,Tomoyuki Koga,Jessica M. Rusert,Catherine Lee,Bin Li,Karen C. Arden,Bing Ren,David Nathanson,Harley I. Kornblum,Harley I. Kornblum,Michael D. Taylor,Sharmeela Kaushal,Webster K. Cavenee,Robert J. Wechsler-Reya,Frank B. Furnari,Scott R. VandenBerg,P. Nagesh Rao,Geoffrey M. Wahl,Vineet Bafna,Paul S. Mischel +21 more
TL;DR: It is shown that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells, and the results suggest that ec DNA contributes to accelerated evolution in cancer.
Microfluidic single-cell whole-transcriptome sequencing
Aaron M. Streets,Xiannian Zhang,Chen Cao,Yuhong Pang,Xinglong Wu,Liang Xiong,Lu Yang,Yusi Fu,Liang Zhao,Fuchou Tang,Yanyi Huang +10 more
TL;DR: It is shown that the benefits of combining microfluidic technology with high-throughput sequencing will be valuable for large-scale efforts in single-cell transcriptome analysis and enhanced measurement precision, detection sensitivity, and experimental throughput aided the distinction between biological variability and technical noise.
289
Hepatitis B virus genotype assignment using restriction fragment length polymorphism patterns.
Masashi Mizokami,Tatsunori Nakano,Etsuro Orito,Yasuhito Tanaka,Hiroshi Sakugawa,Motokazu Mukaide,Betty H. Robertson +6 more
TL;DR: This HBV genotyping system using restriction fragment length polymorphism (RFLP) was confirmed to be correct when the PCR products of the S gene in 23 isolates collected from various countries were digested with this method.
252