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At least 55 records · Page 3Linked to original sources
PubMed2026

Defective RNA Polymerase III sensing of mitochondrial DNA in pulmonary epithelial cells impairs type I IFN immunity to SARS-CoV-2.

The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection ranges from asymptomatic cases to critical COVID-19 pneumonia. To investigate the role of host genetics in susceptibility to critical COVID-19 and identify pathophysiological mechanisms and pathways, we analyzed whole-exome and whole-genome sequencing data from the COVID Human Genetic Effort. We identified 10 rare, monoallelic predicted loss-of-function variants in 18 patients in POLR3A and POLR3C encoding two subunits of RNA polymerase III (POL III), a nuclear multisubunit enzyme, which has been implicated in cytosolic DNA sensing. These variants were deleterious for expression of full-length POLR3A and POLR3C proteins. We demonstrate that human pulmonary A549-hACE2 cells with reduced POLR3A or POLR3C expression exhibit impaired type I IFN responses to transfected mitochondrial DNA (mtDNA) or SARS-CoV-2 infection, together with increased viral replication. Mechanistically, we show that SARS-CoV-2 induces cellular mtDNA release via oligomerization of the mitochondrial voltage-dependent anion channel under virus-induced oxidative stress, enabling POL III-mtDNA interaction. These findings establish POL III as a sensor of endogenous mtDNA released during viral infection and indicate that autosomal dominant POL III haploinsufficiency may predispose individuals to critical COVID-19.

Humans↗
PubMed2005

Electrochemical impedance sensing of DNA hybridization on conducting polymer film-modified diamond.

The impedimetric sensing of DNA hybridization on polyaniline/polyacrylate (PANI/PAA)-modified boron-doped diamond (BDD) electrode has been investigated. An ultrathin film of PANI-PAA copolymer was electropolymerized onto the diamond surfaces to provide carboxylic groups for tethering to DNA sensing probes. The electrochemical impedance and the intrinsic electroactivity of the polymer-diamond interface were analyzed after the hybridization reaction with target and non-target DNA. The impedance measurement shows changes in the impedance modulus as well as electron-transfer resistance at the stage of probe DNA immobilization (single-strand), as well as after hybridization with target DNA (double-strand). DNA hybridization increases the capacitance of the polymer-DNA layer and reduces the overall impedance of the DNA-polymer-diamond stack significantly. The polymer-modified BDD electrode shows no detectable nonspecific adsorption, with good selectivity between the complementary DNA targets and the one-base mismatch targets. The detection limit was measured to be 2 x 10(-8) M at 1000 Hz. Denaturing test on the hybridized probe and subsequent reuse of the probe indicates chemical robustness of the sensor. Our results suggest that electropolymerization followed by the immobilization of biomolecules is a simple and effective way of creating a functional biomolecular scaffold on the diamond surface. In addition, label-free electrochemical impedance method can provide direct and noninvasive sensing of DNA hybridization on BDD.

Boron↗
PubMed2004

Electrochemical study of quercetin-DNA interactions: part II. In situ sensing with DNA biosensors.

Quercetin interaction with dsDNA was investigated electrochemically using two types of DNA biosensor in order to evaluate the occurrence of DNA damage caused by oxidized quercetin. The results showed that quercetin binds to dsDNA where it can undergo oxidation. The radicals formed during quercetin oxidation cause breaks of the hydrogen bonds in the dsDNA finally giving rise to 8-oxoguanine since the DNA guanosine and adenosine nucleotides in contact with the electrode surface can easily be oxidized. A mechanism for oxidized quercetin-induced damage to dsDNA immobilized onto a glassy carbon electrode surface is proposed and the formation of 8-oxoguanine is explained. The importance of DNA-electrochemical biosensors in the determination of the interaction mechanism between DNA and quercetin is clearly demonstrated.

Biosensing Techniques↗
PubMed1998

DNA polymerase II (epsilon) of Saccharomyces cerevisiae dissociates from the DNA template by sensing single-stranded DNA.

Two forms of DNA polymerase II (epsilon) of Saccharomyces cerevisiae, Pol II* and Pol II, were purified to near homogeneity from yeast cells. Pol II* is a four-subunit complex containing a 256-kDa catalytic polypeptide, whereas Pol II consists solely of a 145-kDa polypeptide derived from the N-terminal half of the 256-kDa polypeptide of Pol II*. We show that Pol II* and Pol II are indistinguishable with respect to the processivity and rate of DNA-chain elongation. The equilibrium dissociation constants of the complexes of Pol II* and Pol II with the DNA template showed that the stability of these complexes is almost the same. However, when the rates of dissociation of the Pol II* and Pol II from the DNA template were measured using single-stranded DNA as a trap for the dissociated polymerase, Pol II* dissociated 75-fold faster than Pol II. Furthermore, the rate of dissociation of Pol II* from the DNA template became faster as the concentration of the single-stranded DNA was increased. These results indicate that the rapid dissociation of Pol II* from the DNA template is actively promoted by single-stranded DNA. The dissociation of Pol II from the DNA template was also shown to be promoted by single-stranded DNA, although at a much slower rate. These results suggest that the site for sensing single-stranded DNA resides within the 145-kDa N-terminal portion of the catalytic subunit and that the efficiency for sensing single-stranded DNA by this site is positively modulated by either the C-terminal half of the catalytic subunit and/or the other subunits.

Amino Acid Sequence↗
PubMed2004

Role of p53 in sensing oxidative DNA damage in response to reactive oxygen species-generating agents.

The tumor suppressor p53 plays an important role in the regulation of cellular response to DNA damage. Recent studies suggest that p53 is able to bind DNA with certain structural alterations in a sequence-independent manner and to interact with several molecules involved in DNA repair. This study was undertaken to test the hypothesis that p53 may participate in sensing oxidative DNA damage, the most frequently occurring spontaneous DNA lesion, and modulate its repair by the base excision repair (BER) machinery. Using synthetic DNA containing 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxoG), we showed that p53 was pulled down together with two BER proteins, human 8-oxoguanine glycosylase (hOGG1) and AP endonuclease (APE). Functional analysis showed that p53 significantly enhanced the sequential activities of hOGG1 and APE in excising the 8-oxoG nucleotide from DNA in vitro. The ability of p53 to enhance the removal of oxidized DNA bases was further demonstrated in vivo using a pair of p53 isogenic lines. HCT116 p53+/+ cells exhibit a more rapid removal of 8-oxoG from DNA than p53-/- cells exposed to the same levels of reactive oxygen species (ROS) stress. Together, these results suggest that p53 participates in sensing oxidative DNA damage and modulates BER function in response to persistent ROS stress.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2001

Phosphorylation of proteins and apoptosis induced by c-Jun N-terminal kinase1 activation in rat cardiomyocytes by H(2)O(2) stimulation.

Cytokines and various cellular stresses are known to activate c-Jun N-terminal kinase-1 (JNK1), which is involved in physiological function. Here, we investigate the activation of JNK1 by oxidative stress in H9c2 cells derived from rat cardiomyocytes. H(2)O(2) (100 microM) significantly induces the tyrosine phosphorylation of JNK1 with a peak 25 min after the stimulation. The amount of JNK1 protein remains almost constant during stimulation. Immunocytochemical observation shows that JNK1 staining in the nucleus is enhanced after H(2)O(2) stimulation. To clarify the physiological role of JNK1 activation under these conditions, we transfected antisense JNK1 DNA into H9c2 cells. The antisense DNA (2 microM) inhibits JNK1 expression by 80% as compared with expression in the presence of the sense DNA, and significantly blocks H(2)O(2)-induced cell death. Consistent with the decrease in cell number, we detected condensation of the nuclei, a hallmark of apoptosis, 3 h after H(2)O(2) stimulation in the presence of the sense DNA for JNK1. The antisense DNA of JNK1 inhibits the condensation of nuclei by H(2)O(2). Under these conditions, the H(2)O(2)-induced phosphorylation of proteins with molecular masses of 55, 72, and 78 kDa is blocked by treatment with the antisense DNA for JNK1 as compared with the sense DNA for JNK1. These findings suggest that JNK1 induces apoptotic cell death in response to H(2)O(2), and that the cell death may be involved in the phosphorylations of 55, 72, and 78 kDa proteins induced by JNK1 activation.

Animals↗
PubMed1985

Bidirectional transcription of maize streak virus DNA and identification of the coat protein gene.

Three RNA transcripts encoded by maize streak virus DNA were detected in polyadenylated RNA from virus-infected maize leaves. Two of the transcripts, a major 0.9 kb and a minor 1.05 kb RNA, were mapped on the virion (+) sense DNA and the other minor transcript of 1.2 kb was mapped on the complementary (-) sense DNA, demonstrating that transcription of MSV DNA was bidirectional. The two virion sense transcripts were 3' coterminal at nucleotide 1114 but had 5' termini at nucleotides 2682 and 163 respectively. Virus-specific polyadenylated RNA translated in vitro to produce a 28,000 MW polypeptide, specifically immunoprecipitable by antiserum raised against whole virus. The mRNA for this protein was mapped by hybrid-arrested translation to the long open reading frame in virion sense DNA whose potential amino acid composition, calculated from nucleotide sequence data, closely agreed with that determined experimentally for the coat protein.

Capsid↗
PubMed2006

Dendritic-like streptavidin/alkaline phosphatase nanoarchitectures for amplified electrochemical sensing of DNA sequences.

This study describes the development and characterization of a novel dendritic-like signal amplification pathway. Such an analytical strategy relies on the use of streptavidin and biotinylated alkaline phosphatase, which can be simply and conveniently self-assembled to build nanoarchitectures rich in enzyme labels. The performance of this enzyme-based amplification route was demonstrated in connection with the electrochemical sensing of DNA sequences. Compared to the commercially available streptavidin-conjugated alkaline phosphatase labels, a single generation of the streptavidin/biotinylated alkaline phosphatase assembly allowed a 15-20-fold enhancement of the electroanalytical signals. The higher sensitivity allowed by the dendritic-like route was attributed to the lower steric hindrance of the proteins employed for this amplification path. As low as 50 pmol/L of a 388-bp-long amplicon identifying Salmonella spp. was easily detected. The experimental results additionally demonstrated that the sensitivity of the method could be further increased in a linear fashion with the number of protein-enzyme generations.

Alkaline Phosphatase↗
PubMed1989

Specific inhibition of class II MHC gene expression by anti-sense RNA.

We have established an anti-sense RNA system which is capable of regulating expression of the class II (Ia) molecule coded for by the major histocompatibility complex in cultured mouse cells. Various areas of the I-A beta chain gene were subcloned in an anti-sense orientation to the 3' of the dihydrofolate reductase (DHFR) cDNA under the control of the human metallothionein IIa gene promoter. These anti-sense DNA constructs were transfected into M12.4 cells, a BALB/c B lymphoma cell line which expresses both I-A and I-E molecules on the cell surface. I-A expression of selected clones transfected with anti-sense DNA encompassing the 5' untranslated region (UT) (100 or 310 bp) including the translation start site or the poly(A) addition signalling sequence in the 3' UT (250 bp) of the I-A beta chain gene were specifically reduced to less than 5% of the control M12.4 cell surface I-A expression. These clones had normal levels of I-E expression. However, transfection of the anti-sense DNA to the beta 1 domain (510 bp) including the splicing donor and acceptor sequences did not affect the expression of I-A molecules. The same antisense DNA constructs (100 bp of the 5' UT or 250 bp of the 3' UT) without the DHFR cDNA (710 bp) did not down-regulate the expression of I-A molecules, indicating that either the physical length of the anti-sense RNA or specific DHFR cDNA sequences are also important.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Impedance sensing of DNA binding drugs using gold substrates modified with gold nanoparticles.

Interfacial interactions between immobilized DNA probes and DNA-specific sequence binding drugs were investigated using impedance spectroscopy toward the development of a novel biosensing scheme. The impedance measurements are based on the charge-transfer kinetics of the [Fe(CN)6]3-/4- redox couple. Compared to bare gold surfaces, the immobilization of DNA and then the DNA-drug interaction on electrode surfaces altered the capacitance and the interfacial electron resistance and thus diminished the charge-transfer kinetics by reducing the active area of the electrode or by preventing the redox species from approaching the electrode. Electrochemical deposition of gold nanoparticles on a gold electrode surface showed significant improvement in sensitivity. DNA-capped gold nanoparticles on electrodes act as selective sensing interfaces with tunable sensitivity due to higher amounts of DNA probes and the concentric orientation of the DNA self-assembled monolayer. The specificity of the interactions of two classical minor groove binders, mythramycin, a G-C specific-DNA binding anticancer drug, netropsin, an A-T specific-DNA binding drug and an intercalator, nogalamycin on AT-rich DNA-modified substrate and GC-rich DNA-modified substrate are compared. Using gold nanoparticle-deposited substrates, impedance spectroscopy resulted in a 20-40-fold increase in the detection limit. Arrays of deposited gold nanoparticles on gold electrodes offered a convenient tool to subtly control probe immobilization to ensure suitably adsorbed DNA orientation and accessibility of other binding molecules.

DNA↗
PubMed2006

A role for the conserved GAFTGA motif of AAA+ transcription activators in sensing promoter DNA conformation.

Transcription from sigma54-dependent bacterial promoters can be regarded as a second paradigm for bacterial gene transcription. The initial sigma54-RNA polymerase (RNAP).promoter complex, the closed complex, is transcriptionally silent. The transcriptionally proficient sigma54-RNAP.promoter complex, the open complex, is formed upon remodeling of the closed complex by actions of a specialized activator protein that belongs to the AAA (ATPases associated with various cellular activities) protein family in an ATP hydrolysis-dependent reaction. The integrity of a highly conserved signature motif in the AAA activator (known as the GAFTGA motif) is important for the remodeling activity of the AAA activator and for open complex formation. We now provide evidence that the invariant threo-nine residue of the GAFTGA motif plays a role in sensing the DNA downstream of the sigma54-RNAP-binding site and in coupling this information to sigma54-RNAP via the conserved regulatory Region I domain of sigma54 during open complex formation.

Adenosine Triphosphate↗
PubMed1991

DNA forms of the geminivirus African cassava mosaic virus consistent with a rolling circle mechanism of replication.

We have analysed DNA from African cassava mosaic virus (ACMV)-infected Nicotiana benthamiana by two-dimensional agarose gel electrophoresis and detected ACMV-specific DNAs by blot-hybridisation. ACMV DNA forms including the previously characterised single-stranded, open-circular, linear and supercoiled DNAs along with five previously uncharacterised heterogeneous DNAs (H1-H5) were resolved. The heterogeneous DNAs were characterised by their chromatographic properties on BND-cellulose and their ability to hybridise to strand-specific and double-stranded probes. The data suggest a rolling circle mechanism of DNA replication, based on the sizes and strand specificity of the heterogeneous single-stranded DNA forms and their electrophoretic properties in relation to genome length single-stranded DNAs. Second-strand synthesis on a single-stranded virus-sense template is evident from the position of heterogeneous subgenomic complementary-sense DNA (H3) associated with genome-length virus-sense template (VT) DNA. The position of heterogeneous virus-sense DNA (H5), ranging in size from one to two genome lengths, is consistent with its association with genome-length complementary-sense template (CT) DNA, reflecting virus-sense strand displacement during replication from a double-stranded intermediate. The absence of subgenomic complementary-sense DNA associated with the displaced virus-sense strand suggests that replication proceeds via an obligate single-stranded intermediate. The other species of heterogeneous DNAs comprised concatemeric single-stranded virus-sense DNA (H4), and double-stranded or partially single-stranded DNA (H1 and H2).

Chromatography↗
PubMed2006

Quorum sensing and DNA release in bacterial biofilms.

The multicellular behavior of bacteria has been the subject of much recent interest. This behavior includes coordinated control of virulence, luminescence, competence and biofilm formation; each of these appears to be regulated or influenced by quorum sensing. An understanding of what biofilms constitute, and how they develop, is emerging. It is clear that biofilm formation is a carefully orchestrated process that is dependent on quorum sensing. Somewhat surprisingly, several independent observations have noted an important role for DNA in the structure of biofilms. Recent studies describe a mechanism for linking DNA release to quorum sensing, providing a possible mechanism for the coordinated release of DNA, and its integration into a biofilm. A review of the literature reveals that similar observations have been made for biofilms of both Gram-positive and Gram-negative organisms. Further study will determine whether this is a general trend, however.

4-Butyrolactone↗
PubMed2004

Electrochemical sensing of DNA hybridization based on duplex-specific charge compensation.

A nonlabeling voltammetric detection method for DNA hybridization has been developed, in which [Fe(CN)(6)](3-) in solution can readily approach an electrode surface covered with a charge-compensated DNA duplex layer and thus provides a strong redox-sensing current. Charge compensation for negative charges on the DNA backbone has been specifically accomplished on DNA duplexes by discouraging nonspecific binding of positively charged intercalating molecules with single strands. A pretreatment of DNA-modified electrodes with sodium dodecyl sulfate before the intercalator binding process is essential in preventing the nonspecific binding. Since ferricyanide, the only electrochemically active species, is present in the voltammetric solution, the detection signal can be amplified by increasing its concentration. Combination of the duplex-specific charge compensation with the signal amplification has achieved a remarkable signal difference: in 30 mM [Fe(CN)(6)](3-), the area ratio between cyclic voltammograms of the hybridized and unhybridized electrodes is approximately 200 when 3,6-diaminoacridine is used as the intercalator. High sensitivity of the method has been demonstrated by detecting 10 fM (100 zmol in amount) of a target probe DNA.

Biosensing Techniques↗
PubMed2025

Quorum sensing and DNA methylation play active roles in clinical Burkholderia phase variation.

Phenotypic diversity in bacteria often results from adaptation to changing environmental conditions, exemplified by variable colony morphotypes. In Burkholderia pseudomallei, discrete genomic alterations and modulation of gene expression facilitate adaptation. Adapted variants of species within the Burkholderia cepacia complex (Bcc) often lose the pC3 virulence megaplasmid, impacting their colony morphology and their production of virulence factors. In this study, we characterize variants arising in Burkholderia ambifaria clinical isolates using proteomics and phenotypic tests and show that some of them have retained the pC3, indicating a distinct phase variation mechanism at play in this Bcc species. Interestingly, variants of B. ambifaria strains CEP0996 (pC3-null) and HSJ1 (pC3-positive) still share similarities in phenotypes controlled by the Cep quorum-sensing (QS) system. We further investigated the role of QS in B. ambifaria HSJ1 phase variation and confirmed that the Cep QS system is important for the emergence of variants. Given that DNA methylation is a key epigenetic factor regulating virulence factors in Burkholderia cenocepacia, we hypothesized that adenosine DNA methylation also governs phase variation in B. ambifaria HSJ1. By deleting the genes encoding putative adenosine DNA methyltransferases, we discovered that an orphan type II DNA methyltransferase inhibits the emergence of phase variants. This study is the first to demonstrate that quorum sensing and adenosine DNA methylation are two antagonistic systems independently controlling phase variation in B. ambifaria.IMPORTANCESome Burkholderia species are pathogenic to plants, animals, or humans. In immunocompromised individuals, and people suffering from cystic fibrosis, infection from the Burkholderia cepacia complex (Bcc) can lead to "cepacia syndrome." In northern Australia and southeast Asia, melioidosis caused by Burkholderia pseudomallei is prevalent among native population, particularly among people with diabetes, chronic lung or kidney disease or alcoholism. Burkholderia's phenotypic plasticity, including colony morphotype variation (CMV), enables rapid adaptation to diverse environments, enhancing its survival and pathogenicity. This study reveals phase variation as a new CMV mechanism within the Bcc group and is the first to report that quorum sensing and DNA methylation are involved in phase variation. Understanding the underlying mechanisms of CMV could lead to the development of targeted therapies against these highly antibiotic-tolerant bacteria.

Quorum Sensing↗
PubMed2001

The central MHC gene, BAT1, may encode a protein that down-regulates cytokine production.

BACKGROUND: BAT1 belongs to the DEAD-box family of RNA-binding proteins and is encoded in the central MHC. To determine whether it affects immune responses and hence diseases influenced by MHC haplotypes, U937, THP1 and Jurkat cells were stably transfected with anti-sense DNA corresponding to exons 2-5 of BAT1 using a retroviral vector. RESULTS: Anti-sense transfectants carried anti-sense DNA and expressed anti-sense mRNA. After mitogenic stimulation, they produced higher levels of TNFalpha, IL-1 and IL-6 than equivalent cells carrying the vector alone, suggesting that BAT1 may down-regulate acute phase cytokine production. Polyclonal antibodies raised against a peptide in exon 8 of BAT1 recognized approximately 50 kDa and approximately 38 kDa proteins in all cell lines tested, including the anti-sense transfectants. Expression was localized to the nucleolus in dividing fibroblasts. However the immunochemistry may be confounded by a recently described gene, DDXL, on chromosome 19, which shares a 89% amino acid identity with BAT1. RT-PCR analyses established that BAT1 and DDXL mRNA are expressed in resting U937, THP1 and Jurkat cells. BAT1 and DDXL are divergent in the exons selected for the anti-sense study. CONCLUSIONS: BAT1 is a negative regulator of inflammation. Future studies should address how its functions relate to those of DDXL.

ATP-Binding Cassette Transporters↗
PubMed2006

Signaling networks controlled by the MRN complex and MDC1 during early DNA damage responses.

Cells activate complex signaling networks in response to DNA damage. Several proteins and protein complexes are involved in sensing DNA lesions and initiating the DNA damage response networks. The subsequent DNA damage responses, including the initiation of DNA repair pathways, the activation of cell cycle checkpoint controls and the induction of apoptosis, help maintain genomic stability in mammalian systems. Failure to establish the appropriate DNA damage signaling networks results in genomic instability, which is a known causal factor in tumorigenesis. This review will discuss recent progress in the understanding of the mechanisms by which mammalian cells sense DNA lesions and transduce DNA damage signals during early DNA damage responses.

Adaptor Proteins, Signal Transducing↗