The cell nucleus is a highly organized cellular organelle that contains the genetic material. study of nuclear architecture has become an important field biology. Extracting quantitative data from 3D fluorescence imaging helps understand functions different compartments. However, such approaches are limited by requirement for processing and analyzing large sets images.Here, we describe Tools Analysis Nuclear Genome Organization (TANGO), image analysis tool dedicated to architecture. TANGO...

The restriction endonuclease EcoRV can rapidly locate a short recognition site within long non-cognate DNA using 'facilitated diffusion'. This process has been attributed to sliding mechanism, in which the enzyme first binds via nonspecific interaction and then moves along by 1D diffusion. Recent studies, however, provided evidence that 3D translocations (hopping/jumping) also help its target site. Here we report direct observation of jumping individual molecules DNA. Using fluorescence...

UV-absorption spectrophotometry and molecular modeling have been used to study the influence of chemical nature sugars (ribose or deoxyribose) on triple helix stability. For Pyrimidine.Purine* Pyrimidine motif, all eight combinations were tested with each three strands composed either DNA RNA. The has a dramatic double composition, more stable was formed when third strand RNA rather than DNA. No detected polypurine sequence made Energy minimization studies using JUMNA program suggested that...

Oligonucleotide analogs with N3'-->P5' phosphoramidate linkages bind to the major groove of double-helical DNA at specific oligopurine.oligopyrimidine sequences. These triple-helical complexes are much more stable than those formed by oligonucleotides natural phosphodiester linkages. phosphoramidates containing thymine and cytosine or thymine, cytosine, guanine strongly polypurine tract human immunodeficiency virus proviral under physiological conditions. Site-specific cleavage Dra I...

DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. However, the poor stability of some these structures might limit their use under physiological conditions. Specific ligands can intercalate into and stabilize them. Molecular modeling thermal denaturation experiments suggest that benzo[f]pyrido[3,4-b]quinoxaline derivatives by stacking preferentially with Hoogsteen-paired bases. Based on this model, it was predicted a benzo[f]quino[3,4-b]quinoxaline...

Observation of DNA–protein interactions by single molecule fluorescence microscopy is usually performed using fluorescent DNA binding agents. However, such dyes have been shown to induce cleavage the and perturb its with proteins. A new method for detection surface-attached molecules introduced in this paper. Biotin- and/or digoxigenin-modified fragments are covalently linked at both extremities a via sequence-specific hybridization ligation. After modified stretched on glass surface, their...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective Stabilization of DNA Triple Helixes by Benzopyridoindole DerivativesChristophe Escude, Chi Hung Nguyen, Jean-Louis Mergny, Jian-Sheng Sun, Emile Bisagni, Therese Garestier, and Claude HeleneCite this: J. Am. Chem. Soc. 1995, 117, 41, 10212–10219Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October...

A 16-base pair oligo(purine)-oligo(pyrimidine) sequence present in the coding region of two HIV 1 proviral genes (pol and nef) was chosen as a target for triplex-forming oligonucleotides vitro transcription assays. Inhibition elongation observed with oligonucleotide-acridine conjugates (Acr-15-TCG:5'-Acr-T4CT4G6-3' Acr-9-TC:5'-Acr-T4CT4-3' where C is 5-methylcytosine) under conditions unsubstituted oligomers did not exhibit any inhibitory effect. Both SP6 bacteriophage RNA polymerase...

An oligonucleotide was circularized around double-stranded DNA thanks to triple helix formation. Short oligonucleotides are known be able form helices by binding into the major groove at an oligopurine.oligopyrimidine sequence. After sequence-specific recognition of a target through formation, ends triplex-forming were joined action T4 ligase, thus creating circular molecule catenated plasmid containing The labeling sequence has been carried out without any chemical or enzymatic modification...

Alpha satellite is the major repeated DNA element of primate centromeres. Evolution these tandemly sequences has led to existence numerous families monomers exhibiting specific organizational patterns. The limited amount information available in non-human primates a restriction understanding evolutionary dynamics alpha DNA. We carried out targeted high-throughput sequencing and dimers from Cercopithecus solatus genome, an Old World monkey Cercopithecini tribe. Computational approaches were...

We have recently described a new method for attaching padlock oligonucleotides to supercoiled plasmid DNA at specific sequences. A variant of this has been developed in order allow the coupling targeting moieties plasmids using convenient strategy. After sequence-specific winding around double-stranded target sequence by ligand-induced triple helix formation, extremities triplex-forming oligonucleotide hybridize each other, leaving dangling single-stranded sequence, which is then ligated...

Abstract Background Centromeric regions of human chromosomes contain large numbers tandemly repeated α-satellite sequences. These sequences are covered with constitutive heterochromatin which is enriched in trimethylation histone H3 on lysine 9 (H3K9me3). Although well studied using artificial and global perturbations, the contribution this epigenetic mark to chromatin structure genome stability remains poorly known a more natural context. Results Using transcriptional activator-like...

Labeling of a covalently closed circular double-stranded DNA was achieved using so-called ‘padlock oligonucleotide’. The oligonucleotide targeted to sequence which is present in the replication origin phage f1 and thus numerous commonly used plasmids. After winding around target by ligand-induced triple helix formation, biotinylated circularized T4 ligase this way became catenated plasmid. A gel shift assay developed measure extent plasmid modification padlock oligonucleotide. similar showed...

Catenation of a circular oligonucleotide to supercoiled plasmid can be achieved in high yields by means ligand-induced triple-helix formation. The noncovalent interactions this supramolecular structure modulated triplex-stabilizing agent (TSA; see picture). represents anchor for functionalization.

DNA imaging in living cells usually requires transgenic approaches that modify the genome. Synthetic pyrrole-imidazole polyamides bind specifically to minor groove of double-stranded (dsDNA) represent an attractive approach for in-cell does not necessitate changes Nine hairpin target mouse major satellite were synthesized. Their interactions with synthetic dsDNA fragments studied by thermal denaturation, gel-shift electrophoresis, circular dichroism, and fluorescence spectroscopy. The had...

We have examined the effects of benzopyridoindole derivatives on triple helices with antiparallel third strands. Absorption spectroscopy, footprinting, and gel retardation experiments demonstrate that a derivative (BePI) is able to induce formation helix an (G, T)-containing strand, which does not form in absence this ligand. This triple-helical complex very stable half-dissociation temperature as high 51 degrees C, its pH independent. Antiparallel oligonucleotides containing thymine guanine...