Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first in fungi and archaea. Moreover, we have uncovered natural examples "type II" hammerheads, our findings reveal permuted form occurs bacteria as frequently type I III architectures. We also identified a commonly occurring...

G-quadruplexes (G4s) are non-canonical structures involved in many important cellular processes. To date, the prediction of potential G-quadruplex (PG4s) has been based almost exclusively on sequence interest agreeing with algorithm Gx-N-1–7-Gx-N1–7-Gx-N1–7-Gx (where x ≥ 3 and N = A, U, G or C). However, sequences this do not form G4s considered false-positive predictions. Here we show RNA PG4 candidate 3′-untranslated region (UTR) TTYH1 gene to be one such false positive. Specifically, G4...

The Y genes encode small noncoding RNAs whose functions remain elusive, numbers vary between species, and major property is to be bound by the Ro60 protein (or its ortholog in other species). To better understand evolution of gene family, we performed a homology search 27 different genomes along with structural using RNA specific motifs. These searches confirmed that are well conserved animal kingdom resulted detection several new genes, including first insects second detected Caenorhabditis...

Abstract On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch contains a regulatory pause site in initiation region acts as checkpoint expression. By biochemically probing transcription complexes halted defined positions, find narrow window metabolite binding, which downstream boundary...

Rolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds thousands samples are required daily. This work presents first research date on direct, real-time label-free isothermal monitoring using microcavity in-line Mach-Zehnder interferometer (μIMZI) fabricated in an optical fiber. The solution based μIMZI offers...

ABSTRACT We have investigated the secondary structure of peach latent mosaic viroid (PLMVd) in solution, and we present here first description a branched solution. Different PLMVd transcripts plus polarity were produced by using circularly permuted RNA method exploitation internal to position 5′ 3′ termini studied nuclease mapping binding shift assays DNA oligonucleotides. show that folds into complex, structure. In general, this is similar reported previously, which was based on sequence...

Abstract The B urkholderia cepacia complex ( Bcc ) comprises strains with a virulence potential toward immunocompromised patients as well plant growth–promoting rhizobacteria PGPR ). Owing to the link between quorum sensing QS and virulence, most studies among species have been directed of pathogenic bacteria. We investigated . ambifaria , only infrequently recovered from patients. cepI gene, responsible for synthesis main signaling molecule N ‐octanoylhomoserine lactone (C 8 ‐ HSL ), was...

Recent observations have suggested that nonionizing radiation in the microwave and terahertz (THz; far-infrared) regimes could an effect on double-stranded DNA (dsDNA). These are of significance owing to omnipresence emitters our daily lives (e.g., food preparation, telecommunication, wireless Internet) increasing prevalence THz for imaging concealed weapon detection airports, skin cancer screenings) communication technologies. By examining multiple nanostructures as well two plasmid DNAs,...

Toehold mediated strand displacement reaction (TMSDR) offers a rapid, enzyme-free amplification strategy, providing advantages over traditional methods like RT-PCR, and RT-LAMP. Optimizing TMSDR can significantly enhance sensitivity in point-of-care biosensor applications for target nucleic acid detection. However, achieving optimal performance requires meticulous probe design stringent quality control. We developed TMSDR-based system targeting specific SARS-CoV-2 RNA sequence through...

Site-specific endonucleases that exclusively cut single-stranded DNA have hitherto never been described and constitute a barrier to the development of ssDNA-based technologies. We identify characterize one such family, from GIY-YIG superfamily, widely distributed site-specific nucleases (Ssn) exhibiting unique ssDNA cleavage properties. By first comprehensively studying Ssn homolog Neisseria meningitidis, we demonstrate it interacts specifically with sequence (called NTS) present in hundreds...

RNA structure plays a crucial role in its function. With the advancement of deep sequencing technology, numerous new ncRNA sequences have been discovered. However, functional analysis these is lagging. Traditionally, mutations are designed to affect and prepared one by for experimental assessment For large scale characterization structure/function relationship many RNAs, we developed program: Structure Mutation Designer (SMDesigner) which makes both disruptive compensatory according...

Nucleic acid-based regulatory elements capable of modulating gene expression in response to specific molecular cues have gained increasing attention synthetic biology. These systems, which include riboswitches, allosteric DNAzymes, and aptazymes, function as Gene Expression Allosteric actuators (GENAs) by coupling recognition with genetic regulation. Their versatility can enable applications diagnostics, therapeutics, metabolic engineering. This study presents a novel "semi-trans"...

ABSTRACT We characterized the peach latent mosaic viroid (PLMVd) replication intermediates that accumulate in infected leaves and determined tissue subcellular localization of RNA species. Using situ hybridization, we showed PLMVd strands both plus minus polarities concentrate cells forming palisade parenchyma. At cellular level, was found to predominantly chloroplasts. Northern blot analyses demonstrated replicates via a symmetric mode involving accumulation circular linear monomeric...

We report the characterization in human genome of 966 pseudogenes derived from four Y (hY) RNAs, components Ro/SS-A autoantigen. About 95% RNA are found corresponding locations on chimpanzee and chromosomes. On contrary, mice both infrequent different genomic regions. In addition to this rodent/primate discrepancy, conservation hY relative genes suggests that they occurred after divergence. Flanking regions contain convincing evidence for involvement L1 retrotransposition machinery. Although...

Transducers made from graphene-type materials are widely used in sensing applications. However, utilization of graphene oxide obtained electrochemical exfoliation graphite (EGO) has remained relatively unexplored. In this study, cocaine aptasensors based on large-size EGO flakes were investigated. particular, the influence following parameters sensor performance was examined: (i) aptamer's terminal group (-NH2 vs -OH), (ii) functionalization with aptamer via physical adsorption and covalent...

Cationic antimicrobial peptides (CAMPs) occur naturally in numerous organisms and are considered as a class of antibiotics with promising potential against multi-resistant bacteria. Herein, we report strategy that can lead to the discovery novel small CAMPs greatly enhanced activity retained antibiofilm potential. We geared our efforts towards i) N-terminal cysteine functionalization previously reported synthetic cationic peptide (peptide 1037, KRFRIRVRV-NH2), ii) its dimerization through...

We present a new publicly accessible web-service, RiboSoft, which implements comprehensive hammerhead ribozyme design procedure. It accepts as input target sequence (and some parameters) then generates set of ranked ribozymes, the sequence. This paper describes implemented procedure, takes into consideration multiple objectives leading to multi-objective ranking computer-generated ribozymes. Many ribozymes were assayed and validated, including four targeting transcript disease-causing gene...

Oculopharyngeal muscular dystrophy (OPMD) is caused by a small expansion of short polyalanine (polyAla) tract in the poly(A)-binding protein nuclear 1 (PABPN1). Despite monogenic nature OPMD, no treatment currently available. Here we report an RNA replacement strategy that has therapeutic potential cell and C. elegans OPMD models. We develop selective microRNAs (miRNAs) against PABPN1, miRNAs our previously developed hammerhead ribozymes (hhRzs) are capable reducing expression both mRNA...