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DNA, CruciformDNA, SuperhelicalNucleic Acid ConformationBase SequenceMolecular Sequence DataPlasmidsInverted Repeat SequencesDNARepetitive Sequences, Nucleic AcidHolliday Junction ResolvasesDNA, BacterialSingle-Strand Specific DNA and RNA EndonucleasesAT Rich SequenceCloning, MolecularGenomic InstabilitySequence Analysis, DNAEndodeoxyribonucleasesPsoralensDNA Restriction EnzymesGenomic LibraryAcetaldehydeOsmium TetroxideBase CompositionPolymerase Chain ReactionEscherichia coliTrioxsalenRestriction MappingAmino Acid SequenceEndonucleasesNucleic Acid HybridizationElectrophoresis, Agar GelGenomicsPhylogenyComparative Genomic HybridizationGenomeBlotting, SouthernBacteriocin PlasmidsMutationChromosome MappingExonsDNA, CircularDeoxyribonuclease BamHIDNA, Single-StrandedChromosome BreakpointsGenome, HumanChromosome InversionDNA-Binding ProteinsSequence Homology, Nucleic AcidDNA, ViralDNA, RecombinantTranscription, GeneticGenomic IslandsDNA, FungalDNA ReplicationGenome, BacterialIntronsModels, GeneticPoly dA-dTGenesOligodeoxyribonucleotidesPromoter Regions, GeneticSaccharomyces cerevisiaeDiethyl PyrocarbonateDNA PrimersSequence AlignmentDNA, RibosomalRecombination, GeneticSodium ChlorideDNA, ComplementaryRNA, Ribosomal, 16SReplication OriginGenotypeNucleic Acid DenaturationSpecies SpecificityGenomic ImprintingPhenanthrolinesSequence DeletionSequence Homology, Amino AcidTemperatureGenetic VariationTranslocation, GeneticKineticsRNA, MessengerLac OperonPhenotypeDNA Mutational AnalysisGene LibraryMultigene FamilyGene DosageDeoxyribonucleasesOligonucleotide Array Sequence AnalysisAllelesPolymorphism, Restriction Fragment LengthBinding SitesFormatesEvolution, MolecularSaltsPolymorphism, GeneticThermodynamicsPolymorphism, Single Nucleotide
Inverted repeatsHairpin structuresInstabilityReplicationDouble-strandGeneDonorMoleculeSequencesSequenceChromosomesDamageSegmentBasesCellsLackTemplateBreaksLongHumanLeftInstabilityNucleotide sequenceProteinsConformationQuadruplexGenesRecombinationTRANSPOSABLE ELEMENTSMotifsHairpinsChromatin structureDouble-strandedMechanismComplexesTargetsSite in the genomeMechanismsProteinRegionsAlternativeRepairFormSitesDirectLevels
Inverted repeats3
  • Again, the orientation of two of the recombining sites within the donor DNA molecule relative to the asymmetry of the intervening DNA cleavage sequences, known as the crossover region, is pivotal to the formation of either inverted repeats or direct repeats. (wikipedia.org)
  • Terminal inverted repeats have been observed in the DNA of various eukaryotic transposons, even though their source remains unknown. (wikipedia.org)
  • Closely spaced long inverted repeats, also known as DNA palindromes, can undergo intrastrand annealing to form DNA hairpins. (biomedcentral.com)
Hairpin structures2
  • This is because perfect and near perfect palindromes, where a sequence is immediately followed by its exact inverse complement with very little or no spacer, are able to intrastrand anneal to form hairpin structures. (biomedcentral.com)
  • However, HIV-lhNef demonstrated a severe production and replication defect, which we were able to solve by selecting spontaneous virus variants with truncated hairpin structures. (biomedcentral.com)
Instability3
Replication3
  • A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. (lookformedical.com)
  • Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. (lookformedical.com)
  • Nonetheless,some of the putatively disrupted genes, such as isoleucyl andtyrosyl-tRNA synthetases (MG345 & MG455), DNA replication gene dnaA(MG469), and DNA polymerase HI, subunit alpha (MG261) are thought toperform essential functions. (fullblog.com.ar)
Double-strand3
  • In this report, we described the application of CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 (endonuclease) system for efficient genetic editing in E. tenella , and showed that the CRISPR/Cas9 system mediates site-specific double-strand DNA breaks with a single guide RNA. (biomedcentral.com)
  • The CRISPR/Cas9 system introduces site-specific double-strand DNA breaks (DSBs) with endonuclease Cas9 in a target sequence that is homologous to the single guide RNA (sgRNA). (biomedcentral.com)
  • The formation of RAD51/DMC1 filaments on single-stranded (ss)DNAs essential for homology search and strand exchange in DNA double-strand break (DSB) repair is tightly regulated. (bvsalud.org)
Gene3
  • These repeated DNA sequences often range from a pair of nucleotides to a whole gene, while the proximity of the repeat sequences varies between widely dispersed and simple tandem arrays. (wikipedia.org)
  • In order to solve this problem, we constructed an HIV-1 variant with a 300 bp long hairpin structure in the 3' part of the genome corresponding to the Nef gene (HIV-lhNef). (biomedcentral.com)
  • An alternative method to inhibit HIV-1 is the use of gene constructs encoding HIV-1-specific long hairpin RNAs (lhRNAs, transcripts folding an extended hairpin structure) or long double-stranded RNAs (dsRNAs, two complementary transcripts that form an extended duplex). (biomedcentral.com)
Donor2
  • The limited recombination of the sequences between two distinct sequence elements known as conservative site-specific recombination (CSSR) results in inversions of the DNA segment, based on the arrangement of the recombination recognition sequences on the donor DNA and recipient DNA. (wikipedia.org)
  • Subsequent repair of the DSBs is carried out by the host cell through either non-homologous end-joining pathway (NHEJ), leading to insertion and deletion mutations in the targeted genes, or homologous direct repair (HDR) in the presence of a DNA donor template. (biomedcentral.com)
Molecule1
  • The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. (lookformedical.com)
Sequences3
  • Some elements of the genome with unique sequences function as exons, introns and regulatory DNA. (wikipedia.org)
  • Though the most familiar loci of the repetitive sequences are the centromere and the telomere, a large portion of the repeated sequences in the genome are found among the noncoding DNA. (wikipedia.org)
  • Unlike earlier protocols, it does not involve restriction enzymatic digestion prior to DNA snap-back thereby preserving longer DNA sequences. (biomedcentral.com)
Sequence2
  • Thus, recombination occurring at a pair of inverted sites will invert the DNA sequence between the two sites. (wikipedia.org)
  • Mei5-Sae3 shows sequence similarity to fission yeast Sfr1-Swi5, which stimulates DNA strand exchanges by Rad51 as well as Dmc1. (bvsalud.org)
Chromosomes1
Damage4
  • Damage can often be repaired (DNA REPAIR). (lookformedical.com)
  • 8-oxoG) in DNA, we examined levels of oxidative DNA damage produced in normally growing cells. (bvsalud.org)
  • The level of 8-oxoG DNA damage was about 9- and 63-fold higher in cells grown in M9-glucose and M9-glycerol media, respectively, than in those grown in LB medium. (bvsalud.org)
  • We also found that about 14-fold more 8-oxoG DNA damage was produced in cells grown in about 0.1% oxygen than in those grown in the normal atmosphere. (bvsalud.org)
Segment1
  • Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. (lookformedical.com)
Bases1
  • The most common repeats include the dinucleotide repeats, which have the bases AC on one DNA strand, and GT on the complementary strand. (wikipedia.org)
Cells1
  • In that report, the authors grewTn4001 transformed cells in mixed pools for several weeks, and thenisolated genomic DNA from those mixtures of mutants. (fullblog.com.ar)
Lack1
  • Due to a lack of systematic approaches to identify and characterize palindromes from genomes, little is known about the distribution of DNA palindromes nor their association with human diseases. (biomedcentral.com)
Template1
  • They sequencedamplicons from inverse PCRs using that DNA as a template to identifythe transposon insertion sites in the mycoplasma genomes. (fullblog.com.ar)
Breaks1
Long1
  • Long DNA palindromes are difficult to directly analyze using standard molecular genetics methods. (biomedcentral.com)
Human1
  • Previous nanoscale imaging by atomic force microscopy (AFM) showed that the ring-like structure of the human Mre11/Rad50 complex transiently opens at the zinc hook of Rad50. (bvsalud.org)
Left1
  • HN - 2008 BX - Lateral Sinus MH - Atrial Septum UI - D054087 MN - A07.541.459.249 MS - The thin membrane-like muscular structure separating the right and the left upper chambers (HEART ATRIA) of a heart. (bvsalud.org)
Instability5
  • Cruciform structures can increase genomic instability and are involved in the formation of various diseases, such as cancer and Werner's Disease. (wikipedia.org)
  • A second major focus of the lab is to understand how repetitive DNA causes genomic instability, including DNA breaks and fork stalling, and the cellular mechanisms used to overcome these barriers to genome integrity. (tufts.edu)
  • We are actively studying pathways of DNA repair that impact repeat instability and their mechanism of action. (tufts.edu)
  • 11. Comparison of proliferation and genomic instability responses to WRN silencing in hematopoietic HL60 and TK6 cells. (nih.gov)
  • 14. Structure of the helicase core of Werner helicase, a key target in microsatellite instability cancers. (nih.gov)
Nucleotide sequence1
  • Cruciform DNA structures require at least a six nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. (wikipedia.org)
Proteins9
  • They also serve a function in epigenetic regulation along with biological implications such as DNA supercoiling, double strand breaks, and targets for cruciform-binding proteins. (wikipedia.org)
  • Alfred Gierer was one of the first scientists to propose an interaction between proteins and the grooves of specific double-stranded DNA nucleotide sequences. (wikipedia.org)
  • Proteins were hypothesized to bind to these branched DNA structures and cause regulation in gene expression. (wikipedia.org)
  • The binding association between proteins and branch-forming DNA was suggested due to the structure and function of tRNA. (wikipedia.org)
  • Starting in the early 1980s, recognition sites of DNA that formed hairpin structures for a range of cellular proteins were characterized. (wikipedia.org)
  • We use a combination of genetic and physical assays to study the types of proteins that mediate replication of structure-forming repeats and repair of repeat-induced chromosomal damage. (tufts.edu)
  • however, the proteins are thought to play a role in chromatin structure. (nih.gov)
  • Also the HMG domain has been found in many DNA binding proteins that regulate transcription. (nih.gov)
  • The genetic information of organisms is stored into deoxyribonucleic acid (DNA), which is generally arranged in a supercoiled form, further stabilized by ancillary proteins. (frontiersin.org)
Conformation4
  • Therefore, a protocruciform is seen as an intermediate step before the final cruciform conformation produced. (wikipedia.org)
  • Additionally, the presence or absence of sodium and magnesium ions can affect the conformation of cruciform adopted. (wikipedia.org)
  • At lower sodium ion concentration and in the absence of magnesium ions, the cruciform adopts a symmetrical, square planar conformation with fully extended stems. (wikipedia.org)
  • First, a network approach was applied to predict novel genes/genomic regions/SNPs, playing a role in longevity, which integrated three-dimensional (3D) chromosome conformation data (Hi-C) and two GWAS datasets. (ntu.ac.uk)
Quadruplex2
  • We have previously shown that human virus genomes are enriched in G-rich sequences that fold in four-stranded nucleic acid secondary structures, the G-quadruplexes.Here, by extensive bioinformatics analysis on all available genomes, we showed that human viruses are enriched in highly conserved multiple A (and T or U) tracts, with such an array that they could in principle form quadruplex structures. (frontiersin.org)
  • Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study. (uams.edu)
Genes4
  • The developmental time and location of [beta]-galactosidase expression then is determined by regulatory signals of the genes that contain the inserted [beta]-element DNA. (nih.gov)
  • In this study we hypothesised that co-location of novel genes/genomic regions with genes, known to be associated with longevity, that share biological function with co-located genes, make them good candidates for novel genomic regions, linked to longevity. (ntu.ac.uk)
  • Networks were created using genes/genomic regions, known to associate with longevity, as original nodes with additional nodes (regions) later added to these networks if they strongly interacted (i.e. came into close proximity as measured by the Hi-C data) with the original nodes. (ntu.ac.uk)
  • Are There Hidden Genes in DNA/RNA Vaccines? (osu.eu)
Recombination3
  • Cruciform DNA is found in both prokaryotes and eukaryotes and has a role in DNA transcription and DNA replication, double strand repair, DNA translocation and recombination. (wikipedia.org)
  • These inversions are genomic polymorphisms that facilitate misalignment and abnormal recombination between flanking segmental duplications. (nih.gov)
  • Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway. (uams.edu)
TRANSPOSABLE ELEMENTS1
  • DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (nih.gov)
Motifs2
  • Each TF typically recognises a collection of often dissimilar DNA motifs. (ntu.ac.uk)
  • Here we hypothesised that TFs may recognise a certain structure, e.g. non-B DNA structures, rather than sequence motifs. (ntu.ac.uk)
Hairpins1
  • As a result, inverted repeats are self-complementary and can give rise to structures such as hairpins and cruciforms. (wikipedia.org)
Chromatin structure1
  • DNA repair takes place in the context of chromatin structure, and CAG/CTG repeat sequence is an especially strong nucleosome positioning sequence. (tufts.edu)
Double-stranded3
  • The mechanism of cruciform extrusion occurs through the opening of double stranded DNA to allow for intrastrand base pairing. (wikipedia.org)
  • C-type cruciform formation is marked by a large initial opening in the double-stranded DNA. (wikipedia.org)
  • Contrary to human host cells, viruses display a diverse array of nucleic acid types, which include DNA or RNA in single-stranded or double-stranded conformations. (frontiersin.org)
Mechanism1
  • This study expands on the presence and mechanism of nucleic acid secondary structures in human viruses and provides a new direction for antiviral research. (frontiersin.org)
Complexes1
  • 8. WRN helicase and mismatch repair complexes independently and synergistically disrupt cruciform DNA structures. (nih.gov)
Targets1
  • Non-canonical nucleic acid secondary structures are being investigated as pharmacological targets in the treatment of multiple human diseases, such as cancer, neurodegenerative disorders, and infectious diseases ( Tateishi-Karimata and Sugimoto, 2020 ). (frontiersin.org)
Site in the genome2
  • Elements that are transcribed into RNA , reverse-transcribed into DNA and then inserted into a new site in the genome. (nih.gov)
  • Discrete segments of DNA which can excise and reintegrate to another site in the genome. (nih.gov)
Mechanisms4
  • Two mechanisms for the formation of cruciform DNA have been described: C-type and S-type. (wikipedia.org)
  • The overall goal of my research is to understand mechanisms of genome stability that operate at repetitive DNA, and how they collaborate to protect against repeat expansions and chromosome fragility. (tufts.edu)
  • The DNA secondary structures that deviate from the classic Watson and Crick base pairing are increasingly being reported to form transiently in the cell and regulate specific cellular mechanisms. (frontiersin.org)
  • Unconventional DNA structures are normally formed transiently and promote (or prevent) certain cellular mechanisms, thus being strictly involved in the life cycle of cell. (frontiersin.org)
Protein3
  • 13. The Werner syndrome protein contributes to induction of p53 by DNA damage. (nih.gov)
  • Twenty high-affinity and 13 low-affinity NK-2 binding sites were found in 2.2 kb of DNA from the 5 -upstream region of the NK-2 gene, which suggests that NK-2 protein may be required to maintain the expression of the NK-2 gene. (nih.gov)
  • Clone 393C-2 was shown to encode Drosophila high-mobility-group protein D (HMG-D), a DNA binding protein. (nih.gov)
Regions1
  • The formation of cruciform structures in linear DNA is thermodynamically unfavorable due to the possibility of base unstacking at junction points and open regions at loops. (wikipedia.org)
Alternative1
Repair1
  • We are investigating how these and other histone modifications and chromatin remodelers facilitate genome stability and promote repair with fidelity in the context of structure-forming DNA repeats. (tufts.edu)
Form1
  • Here, the stems form acute angles with the main DNA strand instead of sharing 90° between them. (wikipedia.org)
Sites1
  • DNA flanking the P-element insertion sites were cloned from 15 of the most interesting transgenic fly lines and corresponding cDNA clones were obtained and were sequenced partially. (nih.gov)
Direct2
  • Here we report the crystal structures of multiple domains of RMI1-RMI2, providing direct confirmation of the existence of three oligonucleotide/oligosaccharide binding (OB)-folds in RMI1-RMI2. (nih.gov)
  • Structures such as slipped, cruciform, triplexes and tetraplexes, formed on direct, inverted and mirrored repeats and G-quartets were considered and SNPs residing within these structures were analysed. (ntu.ac.uk)
Levels2
  • Most of the identified A-tracts are in the coding strand, both at the DNA and RNA levels, suggesting their possible relevance during viral translation. (frontiersin.org)
  • Descriptors are arranged in a hierarchical structure, which enables searching at various levels of specificity. (uams.edu)