• These inverted repeats contain a sequence of DNA in one strand that is repeated in the opposite direction on the other strand. (wikipedia.org)
  • 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)
  • Closely spaced long inverted repeats, also known as DNA palindromes, can undergo intrastrand annealing to form DNA hairpins. (biomedcentral.com)
  • The mechanism of cruciform extrusion occurs through the opening of double stranded DNA to allow for intrastrand base pairing. (wikipedia.org)
  • Unlike C-type, S-type cruciform formation requires salt for extrusion. (wikipedia.org)
  • 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)
  • 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)
  • They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the protein the viral capsid is made of. (mdwiki.org)
  • 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)
  • 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)
  • We developed a new protocol to identify palindromes that couples the S1 nuclease treated Cot0 DNA (GAPF) with high-throughput sequencing (GAP-Seq). (biomedcentral.com)
  • Long DNA palindromes are difficult to directly analyze using standard molecular genetics methods. (biomedcentral.com)
  • Palindromes longer than 200 bp cannot be amplified by traditional PCR using DNA polymerases with low strand displacement activity, nor can they be stably maintained in Escherichia coli . (biomedcentral.com)
  • 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)
  • We have explored alternative methods for systematically analyzing palindromes in the genome and here we report our analysis of de novo DNA palindromes from the MCF-7 breast cancer cell line [ 15 ]. (biomedcentral.com)
  • 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)
  • If inverted repeat sequences were present, then double-stranded DNA was speculated to form branches and loops. (wikipedia.org)
  • Unlike earlier protocols, it does not involve restriction enzymatic digestion prior to DNA snap-back thereby preserving longer DNA sequences. (biomedcentral.com)
  • Among the changes incorporated into the enhanced-sensitivity bDNA (ES bDNA) assay to reduce the background level and enhance the signal are the use of shorter overhang sequences of target probes for capture, the cruciform design of target probes for amplification, and the addition of preamplifier molecules. (ox.ac.uk)
  • Parvoviruses have linear, single-stranded DNA (ssDNA) genomes that are about 4-6 kilobases (kb) in length. (mdwiki.org)
  • They sequencedamplicons from inverse PCRs using that DNA as a template to identifythe transposon insertion sites in the mycoplasma genomes. (fullblog.com.ar)
  • Folded cruciform structures are characterized by the formation of acute angles between adjacent arms and main strand DNA. (wikipedia.org)
  • Unfolded cruciform structures have square planar geometry and 4-fold symmetry in which the two arms of the cruciform are perpendicular to each other. (wikipedia.org)
  • 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)
  • The first theoretical description of cruciform-forming DNA structures was hypothesized in the early 1960s. (wikipedia.org)
  • 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)
  • 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)
  • Damage can often be repaired (DNA REPAIR). (lookformedical.com)
  • 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)
  • A type of chromosomal aberration involving DNA BREAKS. (lookformedical.com)
  • Cruciform DNA is a form of non-B DNA, or an alternative DNA structure. (wikipedia.org)
  • This leads to the formation of a cruciform structure. (wikipedia.org)
  • At high sodium ion concentration and in the absence of magnesium ions, a compact, folded cruciform structure is formed. (wikipedia.org)
  • The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. (lookformedical.com)
  • Thus, with its lack of genomic redundancy and contingenciesfor different environmental conditions, M. genitalium is already closeto being a minimal bacterial cell. (fullblog.com.ar)
  • Additionally, the presence or absence of sodium and magnesium ions can affect the conformation of cruciform adopted. (wikipedia.org)
  • Here, the stems form acute angles with the main DNA strand instead of sharing 90° between them. (wikipedia.org)
  • Two mechanisms for the formation of cruciform DNA have been described: C-type and S-type. (wikipedia.org)
  • C-type cruciform formation is marked by a large initial opening in the double-stranded DNA. (wikipedia.org)
  • C-type cruciform formation is temperature dependent because of higher entropy and enthalpy of activation than S-type. (wikipedia.org)
  • An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. (ox.ac.uk)
  • The branched-DNA (bDNA) assay provides a reliable method for the quantification of HIV-1 RNA in human plasma and is considered one of the most reproducible assays ready for use in clinical trials. (ox.ac.uk)
  • Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. (nih.gov)
  • Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study. (uams.edu)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • Effect of in vitro transcription on cruciform stability. (ecu.edu)
  • We have investigated the effect of in vitro transcription on cruciform stability. (ecu.edu)
  • 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)
  • Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway. (uams.edu)
  • 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)
  • 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)
  • 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)
  • Here, the stems form acute angles with the main DNA strand instead of sharing 90° between them. (wikipedia.org)
  • 4. Identification of complex genomic breakpoint junctions in the t(9;11) MLL-AF9 fusion gene in acute leukemia. (nih.gov)
  • 12. MLL-SEPTIN6 fusion recurs in novel translocation of chromosomes 3, X, and 11 in infant acute myelomonocytic leukaemia and in t(X;11) in infant acute myeloid leukaemia, and MLL genomic breakpoint in complex MLL-SEPTIN6 rearrangement is a DNA topoisomerase II cleavage site. (nih.gov)
  • The mechanism of cruciform extrusion occurs through the opening of double stranded DNA to allow for intrastrand base pairing. (wikipedia.org)
  • 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)
  • 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)
  • 13. 11q23 translocations split the "AT-hook" cruciform DNA-binding region and the transcriptional repression domain from the activation domain of the mixed-lineage leukemia (MLL) gene. (nih.gov)
  • 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)
  • 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)