Nucleic Acid Driven DNA Machineries Synthesizing Mg2+-Dependent DNAzymes: An Interplay between DNA Sensing and Logic-Gate Operations

2012 ◽  
Vol 18 (46) ◽  
pp. 14689-14694 ◽  
Author(s):  
Ron Orbach ◽  
Lena Mostinski ◽  
Fuan Wang ◽  
Itamar Willner
Keyword(s):  
Nucleic Acid ◽  
Logic Gate ◽  
Dna Sensing

Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing

2020 ◽  
Vol 18 (30) ◽  
pp. 5951-5962
Author(s):  
Chayan Charoenpakdee ◽  
Tirayut Vilaivan
Keyword(s):  
Nucleic Acid ◽  
Electrostatic Interaction ◽  
Peptide Nucleic Acid ◽  
Dna Sensing ◽  
Complementary Dna

Oligodeoxyguanosine effectively quenches the fluorescence of PNA probes via electrostatic interaction, and the signal is restored by the addition of complementary DNA targets.

scholarly journals A nucleic acid logic gate system that distinguishes different sets of inputs from one miRNA collection with shared members

RSC Advances ◽  
2017 ◽  
Vol 7 (67) ◽  
pp. 42345-42349 ◽  
Author(s):  
You Zhang ◽  
Xiangjiang Zheng ◽  
Lian Xia ◽  
Jinmao You ◽  
Rui Ren
Keyword(s):  
Nucleic Acid ◽  
Logic Gate ◽  
Gate System ◽  
Proof Of Principle ◽  
Logic System

A proof-of-principle logic system was established to process multi-input and multi-output logic relationships with the aim of identifying the tissue origins of cancer in light of their established relationships with miRNA distributions.

Magnetic Manipulation of Nucleic Acid Base Microcrystals for DNA Sensing

2014 ◽  
Vol 50 (11) ◽  
pp. 1-4 ◽  
Author(s):  
Yuri Mizukawa ◽  
Kentaro Suzuki ◽  
Shigefumi Yamamura ◽  
Yoko Sugawara ◽  
Tadashi Sugawara ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Sensing ◽  
Acid Base ◽  
Magnetic Manipulation ◽  
Nucleic Acid Base

scholarly journals Penaeus monodon Interferon Regulatory Factor (PmIRF) Activates IFNs and Antimicrobial Peptide Expression via a STING-Dependent DNA Sensing Pathway

2022 ◽  
Vol 12 ◽  
Author(s):  
Suthinee Soponpong ◽  
Piti Amparyup ◽  
Taro Kawai ◽  
Anchalee Tassanakajon
Keyword(s):  
Nucleic Acid ◽  
Penaeus Monodon ◽  
Poly I:C ◽  
Dna Sensing ◽  
Dead Box ◽  
Polycytidylic Acid ◽  
Acid Sodium Salt ◽  
Peptide Expression ◽  
Immune Related Genes ◽  
Antimicrobial Peptide Expression

Interferon regulatory factors (IRFs) are transcription factors found in both vertebrates and invertebrates that were recently identified and found to play an important role in antiviral immunity in black tiger shrimp Penaeus monodon. In this study, we investigated the mechanism by which P. monodon IRF (PmIRF) regulates the immune-related genes downstream of the cytosolic DNA sensing pathway. Depletion of PmIRF by double-stranded RNA-mediated gene silencing significantly reduced the mRNA expression levels of the IFN-like factors PmVago1, PmVago4, and PmVago5 and antilipopolysaccharide factor 6 (ALFPm6) in shrimp. In human embryonic kidney (HEK293T) cells transfected with PmIRF or co-transfected with DEAD-box polypeptide (PmDDX41) and simulator of IFN genes (PmSTING) expression plasmids, the promoter activity of IFN-β, nuclear factor (NF-κB), and ALFPm6 was synergistically enhanced following stimulation with the nucleic acid mimics deoxyadenylic–deoxythymidylic acid sodium salt [poly(dA:dT)] and high molecular weight (HMW) polyinosinic–polycytidylic acid [poly(I:C)]. Both nucleic acid mimics also significantly induced PmSTING, PmIRF, and ALFPm6 gene expression. Co-immunoprecipitation experiments showed that PmIRF interacted with PmSTING in cells stimulated with poly(dA:dT). PmSTING, PmIRF, and PmDDX41 were localized in the cytoplasm of unstimulated HEK293T cells and PmIRF and PmDDX41 were translocated to the nucleus upon stimulation with the nucleic acid mimics while PmSTING remained in the cytoplasm. These results indicate that PmIRF transduces the pathogen signal via the PmDDX41–PmSTING DNA sensing pathway to induce downstream production of interferon-like molecules and antimicrobial peptides.

PKR-dependent cytosolic cGAS foci are necessary for intracellular DNA sensing

2019 ◽  
Vol 12 (609) ◽  
pp. eaav7934 ◽  
Author(s):  
Siqi Hu ◽  
Hong Sun ◽  
Lijuan Yin ◽  
Jian Li ◽  
Shan Mei ◽  
...  
Keyword(s):  
Phase Separation ◽  
Nucleic Acid ◽  
Cyclic Gmp ◽  
Interferon Response ◽  
Dna Sensing ◽  
Dna Virus ◽  
Virus Particles ◽  
Cytoplasmic Structures ◽  
Interferon Responses ◽  
Cellular Organelles

Cyclic GMP-AMP synthase (cGAS) is a major sensor of cytosolic DNA from invading pathogens and damaged cellular organelles. Activation of cGAS promotes liquid-like phase separation and formation of membraneless cytoplasmic structures. Here, we found that cGAS bound G3BP1, a double-stranded nucleic acid helicase involved in the formation of stress granules. Loss of G3BP1 blocked subcellular cGAS condensation and suppressed the interferon response to intracellular DNA and DNA virus particles in cells. Furthermore, an RNA-dependent association with PKR promoted G3BP1 foci formation and cGAS-dependent interferon responses. Together, these results indicate that PKR promotes the formation of G3BP1-dependent, membraneless cytoplasmic structures necessary for the DNA-sensing function of cGAS in human cells. These data suggest that there is a previously unappreciated link between nucleic acid sensing pathways, which requires the formation of specialized subcellular structures.

Intelligent Nucleic Acid Functionalized Dual-Responsive Gold Nanoflare: Logic-Gate Nanodevice Visualized by Single-Nanoparticle Imaging

2016 ◽  
Vol 1 (3) ◽  
pp. 347-353 ◽  
Author(s):  
Jianbo Liu ◽  
Haining Ji ◽  
Jin Huang ◽  
Li Li ◽  
Qing Wang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Logic Gate ◽  
Dual Responsive ◽  
Single Nanoparticle ◽  
Nanoparticle Imaging

Introduction

1978 ◽  
Vol 36 (3) ◽  
pp. 543-544
Author(s):  
W. Bernard
Keyword(s):  
Molecular Weight ◽  
Electron Microscope ◽  
Nucleic Acid ◽  
Gene Mapping ◽  
Molecular Genetics ◽  
Cell Biology ◽  
Gene Activity ◽  
Close Connection ◽  
Basic Information ◽  
Simple Systems

In comparison to many other fields of ultrastructural research in Cell Biology, the successful exploration of genes and gene activity with the electron microscope in higher organisms is a late conquest. Nucleic acid molecules of Prokaryotes could be successfully visualized already since the early sixties, thanks to the Kleinschmidt spreading technique - and much basic information was obtained concerning the shape, length, molecular weight of viral, mitochondrial and chloroplast nucleic acid. Later, additonal methods revealed denaturation profiles, distinction between single and double strandedness and the use of heteroduplexes-led to gene mapping of relatively simple systems carried out in close connection with other methods of molecular genetics.

Infection of Escherichia coli with bacteriophages

1969 ◽  
Vol 27 ◽  
pp. 370-371
Author(s):  
Manfred E. Bayer
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Cell Surface ◽  
Virus Type ◽  
Infection Process ◽  
Adsorption Site ◽  
The Other ◽  
Specific Receptors ◽  
Bacterial Receptors

The first step in the infection of a bacterium by a virus consists of a collision between cell and bacteriophage. The presence of virus-specific receptors on the cell surface will trigger a number of events leading eventually to release of the phage nucleic acid. The execution of the various "steps" in the infection process varies from one virus-type to the other, depending on the anatomy of the virus. Small viruses like ØX 174 and MS2 adsorb directly with their capsid to the bacterial receptors, while other phages possess attachment organelles of varying complexity. In bacteriophages T3 (Fig. 1) and T7 the small conical processes of their heads point toward the adsorption site; a welldefined baseplate is attached to the head of P22; heads without baseplates are not infective.

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