Group of dna minor groove. Medical search. Frequent questions

The interactions shown, caused the DNA to bend, extending the minor groove. (wikipedia.org)
The distorted DNA causes the complementary major groove to form interactions between the side chains. (wikipedia.org)
Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. (nature.com)
These characteristics give insight regarding how strongly solvated DNA duplexes containing cationic alkylpurines with minor groove or major groove lesions are, electrostatic/ionic atmosphere changes associated with these modifications, base stacking/pairing interactions, and general B-form conformational stability. (hhs.gov)
High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. (embl.de)
Two novel nucleotides are proposed to further elucidate minor groove interactions of DNA with polymerase molecules. (umn.edu)
DNA minor-groove binding drugs have been extensively studied in the last years in order to influence the regulation of gene expression in neoplastic disorders by means of specific interactions with DNA bases. (najah.edu)
For this reason many groups applied heterocyclic substitutions extensively, in order to either modify the reactivity profile or introduce extra interactions within the minor groove, thus changing the binding site or modulating the binding sequence. (najah.edu)
This functional group texture strongly influences the molecular function of the DNA as it participates in DNA-protein interactions providing donor or acceptor sites for intermolecular hydrogen bonding networks. (brc.hu)
Transcription factors (TFs) are central proteins for transcriptional regulation, and interactions between TFs and their DNA targets (TFBSs) are important for downstream genes' expression. (biomedcentral.com)
To expand the knowledge about interactions between TFs and TFBSs, three biological features (sequence feature, structure feature, and evolution feature) were utilized to build TFBS identification models for studying binding preference between TFs and their DNA targets in mammals. (biomedcentral.com)
Since the discovery of DNA and our knowledge of its basic physical properties such as the double helix, we have progressed a great deal to learning about the chemical properties of DNA and interactions between DNA and its environment. (exploredna.co.uk)
The propynyl groups occupy a large part of the major groove and make favourable van der Waals interactions with their nearest neighbours and the atoms of the rings. (ox.ac.uk)
In the present study, we adopted MO calculations to investigate interactions between FMs and eight DNA hexamers with sequences such as AAAAAA, TTTTTT, AAATTT, TTTAAA, ATATAT, TATATA, GGGGGG and CCCCCC. (int-conf-chem-structures.org)

The AT-hook is a DNA-binding motif present in many proteins, including the high mobility group (HMG) proteins, DNA-binding proteins from plants and hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex. (wikipedia.org)
AT-hook proteins can form hydrogen bonds between NH groups of Gly37 and Arg38 on the main-chain and thymine oxygen atoms in the minor groove, which bends the DNA and widens the minor groove. (wikipedia.org)
The binding to the minor groove facilitates binding of other proteins in the major groove. (wikipedia.org)
The AT-hooks have also been proposed to anchor chromatin-modifying proteins to AT-rich DNA sequences through their association with chromatin remodeling, histone modifications, and chromatin insulator function. (wikipedia.org)
The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. (wikipedia.org)
Since it has an amine-reactive succinimidyl group, fluorescein derived from CFSE can covalently bond to proteins or other amino groups in the cell or on the cell membrane. (dojindo.com)
DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. (embl.de)
AT-hook motifs identified in a wide variety of DNA-binding proteins. (embl.de)
The AT-hook is a small DNA-binding protein motif which was first described in the high mobility group non-histone chromosomal protein HMG-I(Y). Since its discovery, this motif has been observed in other DNA-binding proteins from a wide range of organisms. (embl.de)
Furthermore, AT-hook motifs are frequently associated with known functional domains seen in chromatin proteins and in DNA-binding proteins (e.g. histone folds, homeodomains and zinc fingers). (embl.de)
It is most interesting that this motif seems to be quite specific to known or predicted chromosomal/DNA-binding proteins, suggesting that it may act as a versatile minor groove tether. (embl.de)
The HMG family of proteins comprises members with multiple HMG domains that bind DNA with low sequence specificity, and members with single HMG domains that recognize specific nucleotide sequences. (embl.de)
Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
Proteins perform a vast array of functions within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli providing structure to cells and organisms, and molecules from one location to another. (transectscience.org)
Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. (transectscience.org)
The information storage function of DNA is a highly controlled process accomplished by numerous distinct nucleotide motifs mostly responsible for anchoring regulatory proteins. (brc.hu)
Transcription factors (TFs) are important functional proteins, which play central roles in transcriptional regulation by interacting with specific DNA targets. (biomedcentral.com)
The genetic information of life on Earth have been conserved in natural nucleotides-A, G, C, T(U) forming two exclusive sets of base pairs A-T(U) & G-C, that complementing to the fundamental processes of DNA replication & RNA transcription by several polymerases and translation to functional proteins via ribosomal reactions. (fortuneonline.org)
RNA plays several important roles in the processes of translating genetic information from deoxyribonucleic acid ( DNA ) into proteins . (wikidoc.org)
Unlike DNA, this structure is not just limited to long double-stranded helices but rather collections of short helices packed together into structures akin to proteins. (wikidoc.org)
DNA-binding motifs, first described in one of the HMGA PROTEINS: HMG-I(Y) PROTEIN. (lookformedical.com)
Characterisation of a cluster of genes encoding Theileria annulata AT hook DNA-binding proteins and evidence for localisation to the host cell nucleus. (lookformedical.com)
Major and minor grooves are structures to allow for necessary proteins in your body to make contact with bases. (exploredna.co.uk)
As such, these DNA grooves seen in the structure of DNA facilitate the binding of proteins like transcription factors, which then serves to keep the cellular processes occurring effectively within your body. (exploredna.co.uk)
The antisense strand is the DNA strand that carries important information to make proteins by binding to the RNA. (exploredna.co.uk)
The possibility for such recognition is critical since proteins must be able to recognize specific DNA sequences on which to bind in order for the proper functions of the body and cell to be carried out. (microbenotes.com)

DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
Solvation differences between F-F and T-T therefore support the steric exclusion model for nucleotide incorporation in DNA replication. (umn.edu)
The encoded protein also functions in mitochondrial DNA replication and repair. (nih.gov)
Ideal for classroom demonstration, the model can be used to demonstrate DNA replication as well as complementary base pairing. (labworld.co.uk)

Ab initio study of naphtho-homologated DNA bases. (irbbarcelona.org)
Large differences in the orientation of minor groove functional groups, in addition to differences in solvation, further rationalize why F bases present during DNA extension events induce stalls. (umn.edu)
This molecule is designed to covalently bind to the C2-amino groups of guanine bases WBP4 in the minor groove of DNA to form mono-adducts. (monossabios.com)
Except for the functional groups sited within the major or minor grooves, the bases of B-DNA are quite protected from the external environment. (elsevierpure.com)
Forming a right-handed double helix, the model displays bases containing nitrogen as well as pentoses and phosphate groups from which DNA is composed. (labworld.co.uk)
The unnatural base pairs formed by recognition and interaction of these unnatural bases are able to maintain the standard Watson and crick structure of DNA as well. (fortuneonline.org)
Several groups have developed synthetic unnatural nucleotides that can form unnatural base pairs with their complementary synthetic bases. (fortuneonline.org)
High-precision flow linear dichroism (LD) here confirms that MB is coplanar with the DNA bases at low dyeDNA binding ratios and low ionic strengths. (ac.ir)
In DNA, bases are specific in that an adenine base, for example, only pairs with a thymine base. (exploredna.co.uk)
Since the major and minor grooves expose the edges of the bases, the grooves can be used to tell the base sequence of a specific DNA molecule. (microbenotes.com)

The AT-hook binds to the minor groove of adenine-thymine (AT) rich DNA, hence the AT in the name. (wikipedia.org)
Dynemicin A (1), a member of the enediyne family of natural products, binds to double-stranded DNA (K_B ∼ 10^4 M^(-1)) and in the presence of millimolar concentrations of a reducing cofactor such as NADPH or GSH reacts to cleave DNA. (caltech.edu)
Carboxyl-terminal domain III of the delta' subunit of the DNA polymerase III holoenzyme binds delta. (colorado.edu)
The 3' MGB moiety binds non-covalently to the minor groove and stabilises the target-probe duplex, effectively increasing the T m of the duplex. (biosearchtech.com)

Fluorescent dyes with aromatic amino or guanidine groups, such as propidium iodide (PI), diaminophenylindole (DAPI), acridine orange (AO), and Hoechst dyes, interact with nucleotides to emit fluorescence. (dojindo.com)
Furthermore, these unnatural nucleotides developed by various groups have the ability to store and transcribe the information just like the natural DNA. (fortuneonline.org)
Thus, while inculcating the UBPs in a DNA structure, their aromatic scaffolds must exhibit hydrophobic packing and must have hydrogen bond donor groups for the artificial nucleotides to interact with polymerases for their efficient incorporation in the non-template strand to bind with their UB partner in template strand [1-3]. (fortuneonline.org)
RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and RNA uses the nucleotide uracil in its composition, instead of thymine which is present in DNA. (wikidoc.org)
First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. (wikidoc.org)
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. (lookformedical.com)
A long polymer, DNA is made up of smaller units called nucleotides. (exploredna.co.uk)
The two DNA strands are called polynucleotides, as they are made of simpler monomer units called nucleotides. (microbenotes.com)
DNA strands are composed of monomers called nucleotides. (microbenotes.com)
The addition of the propynyl group at the 5 position of pyrimidine nucleotides is highly stabilising. (ox.ac.uk)

DNA in chromatin is organized in arrays of nucleosomes 1 .Two copies of each histone protein, H2A, H2B, H3 and H4, are assembled into an octamer that has 145?147 base pairs (bp) of DNA wrapped around it to form a nucleosome core (of relative molecular mass 206K). (nature.com)
Furthermore, the role of DNA thermodynamic "signatures" in lesion recognition by DNA repair enzymes, such as DNA glycosylases, is poorly understood, again because such enzymes catalyze the repair of these lesions, precluding their biochemical/structural study in corresponding protein/DNA complexes. (hhs.gov)
Neocarzinostatin is composed of a labile chromophore with DNA-cleaving activity and a stabilizing protein. (caltech.edu)
In general, it appears that the AT-hook motif is an auxiliary protein motif cooperating with other DNA-binding activities and facilitating changes in the structure of the DNA either as a polypeptide on its own [e.g. (embl.de)
Motif Plotter tool displays the base readout information of agglomerative binding site descriptions like PFMs by using a novel functional group based representation that can help for identifying the conserved functional groups in the ambiguous sequence motifs of protein binding DNA segments. (brc.hu)
Provide schematic and 3D views of the interacting surface of DNA-protein complexes. (brc.hu)
Interface Plotter combines the visualisation elements of DNA Plotter with the available 3D information about DNA-protein contact sites, and projects the intermolecular hydrogen bonding pattern of the 3D structure to a simplified 2D chemical functional group texture of the major and minor grooves. (brc.hu)
Interface Plotter module also provides realistic 3D views preconfigured for the visualisation of the functional elements participating in the establishment of the DNA-protein contact interfaces. (brc.hu)
This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. (ibecbarcelona.eu)
One type of RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes , others form vital portions of the structure of ribosomes, act as essential carrier molecules for amino acids to be used in protein synthesis, or change which genes are active. (wikidoc.org)
They act to fasten the protein to an AT RICH SEQUENCE in the DNA. (lookformedical.com)

Particularly, alkylation damage along the major groove of DNA (such as at N7 of guanine and adenine) may affect DNA structure and dynamics very differently than alkylation along sites located in the minor groove (such as N3 of guanine and adenine). (hhs.gov)

Al-Mahamad LLG, El-Zubir O, Smith DG, Horrocks BR, Houlton A. A coordination polymer for the site-specific integration of semiconducting sequences into DNA-based materials . (ncl.ac.uk)
DNA Plotter provides a comprehensive view about the direct and indirect specificity determining features of the native DNA that can be used for identifying matching functional group positions in different sequences or to visualise the physicochemical and conformational descriptor fingerprint of a DNA segment. (brc.hu)
Molecular dynamics simulations (AMBER, PME electrostatics) of fully solvated, cation neutralized, DNA sequences containing 8-oxoguanine (8OG) and of appropriate normal (control) DNAs have been carried out. (elsevierpure.com)

On the other hand, AO can form complexes with either double-stranded DNA or single-stranded DNA and RNA. (dojindo.com)
As the programs for the simulations such as Amber, CHARMM, BOSS and so on have good parameters for DNA, they succeeded in producing dynamic features of complexes of DNA and fluorescent materials (FMs).However, it is necessary to always make parameters for each FM when new FMs are designed for a specific DNA sequence. (int-conf-chem-structures.org)

In 1997 structural studies using NMR determined that a DNA-bound AT-hook adopted a crescent or hook shape around the minor groove of a target DNA strand (pictured at right). (wikipedia.org)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases. (irbbarcelona.org)
I propose preparation and incorporation of methylated ribonucleotides 3-methyladenosine (3mA) and 7- methylguanosine (7mG, in place of their "normal", deoxyribose counterparts) into duplex DNA, as analogues with stabilized glycosidic bonds for biophysical, biochemical, and structural studies. (hhs.gov)
These properties will then be compared to biochemical data, such as equilibrium binding constants to DNA glycosylases AAG and AlkD, and will be utilized as structural probes to gain insight regarding recognition and excision mechanisms employed by these enzymes. (hhs.gov)
Sherer, EC & Cramer, CJ 2004, ' Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs ', Theoretical Chemistry Accounts , vol. 111, no. 2-6, pp. 311-327. (umn.edu)
Display various physical, chemical, and structural properties of the input DNA. (brc.hu)
In addition, coordinated display of colour stripes representing an extensive set of physicochemical and structural DNA descriptors helps to identify the corresponding components of direct and indirect readout mechanisms. (brc.hu)
CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. (ibecbarcelona.eu)
In 1990, Steven Benner and his group were successful in creating structural analogues of the G-C pair by exchanging the carbonyl and amino positions and forming non-standard hydrogen bonding patterns, yielding the isoG-isoC base pair (Figure 1). (fortuneonline.org)
RNA is very similar to DNA, but differs in a few important structural details: RNA is usually single stranded, while DNA is usually double stranded. (wikidoc.org)
The most important structural feature of RNA, that distinguishes it from DNA is the presence of a hydroxyl group at the 2'-position of the ribose sugar. (wikidoc.org)
The sugar-phosphate backbone forms the structural framework of nucleic acids, including DNA. (microbenotes.com)

The geometry of this "accidental" dimer is consistent with a location of the nonintercalated MB in the minor groove, bridging the strands by the positively charged amino groups directed towards phosphate groups. (ac.ir)
The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule. (wikidoc.org)
This backbone is composed of alternating sugar and phosphate groups and defines the directionality of the molecule. (microbenotes.com)

One of the most significant current discussions in Cu biochemistry relates to the mechanisms of the positive and negative actions of Cu ions based on the generation of reactive oxygen species, including radicals that can interact with DNA molecules. (mdpi.com)
Calcein and BCECF can be converted into electrically neutral molecules by the addition of acetyl or acetoxymethyl groups to their phenolic OH or carboxylic groups, which allows them to freely permeate into the cell. (dojindo.com)
PI molecules intercalate inside the DNA double helix. (dojindo.com)
DAPI and Hoechst dye molecules attach at the minor groove of the DNA double helix. (dojindo.com)
Thermodynamic characteristics of interest include the number of moles of hydrating water molecules per mole of DNA, the number of moles of associated counterions, B-to-A form DNA transition propensity (measured in relative humidity upon addition of trifluoroethanol), and DNA duplex melting temperature. (hhs.gov)
The title compound, (4S,5S,8R,10Z)-2,2,5,6,8,10- hexamethyl-4-phenyl-l,3-dioxa-6-aza-2-silacycloundec- 10-en-7-one, crystallizes with two virtually identical molecules in the asymmetric unit, each with the same absolute configuration. (caltech.edu)
In living organisms such as humans, DNA exists as a pair of molecules rather than a single molecule. (exploredna.co.uk)

Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. (cdc.gov)
Synthesis of RNA is usually catalyzed by an enzyme - RNA polymerase , using DNA as a template. (wikidoc.org)

DAPI (diamidino-2-phenylindole) is a blue fluorescent probe that fluoresces brightly upon selectively binding to the minor groove of double stranded DNA, where its fluorescence is approximately 20-fold greater than in the nonbound state. (thermofisher.com)
One molecule of AO can intercalate with three base pairs of double-stranded DNA to emit green fluorescence with the maximum wavelength at 526 nm. (dojindo.com)
Goldberg and coworkers first demonstrated that the reaction of the isolated chromophore (1) with thiols in the presence of double-stranded DNA leads to DNA cleavage by a free-radical mechanism. (caltech.edu)
Experiments establishing the intermediacy of the cumulene 3 and the biradical 4 in the cleavage of double-stranded DNA by neocarzinostatin chromophore (1) and methyl thioglycolate (2) are described. (caltech.edu)
It is shown that double-stranded calf thymus DNA and the water-soluble 1,4-cyclohexadiene derivative 14 are approximately equally effective in trapping of the biradical intermediate at concentrations of 5 mM (base pairs) and 1 M, respectively, supporting the idea that the biradical is generated as a DNA-bound species. (caltech.edu)
Furthermore, single-stranded DNA and heterogeneous cellular RNA are shown to serve as effective hydrogen atom donors for quenching of the biradical product of thiol activation, suggesting that biopolymers other than double-stranded DNA are potential targets for neocarzinostatin-induced damage. (caltech.edu)
The reaction of calicheamicin γ_1 (1) with glutathione (GSH) has been studied in the presence of double-stranded DNA and is shown to produce initially all four products arising from S-S bond exchange between the calicheamicin γ_1 trisulfide group and the thiol function of glutathione. (caltech.edu)
The kinetics of cleavage of double-stranded DNA by 1 and GSH, determined by polyacrylamide gel electrophoretic (PAGE) analysis is found to parallel the kinetics of formation of 3 and is characterized by a two-stage process. (caltech.edu)
Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs are extensively base paired to form double stranded helices. (wikidoc.org)

DNA fragments usually are defined by a particular sequence of four characters (A,C,G,T) representing the nucleotide monomers building up one strand of the highly ordered double helical DNA structure. (brc.hu)
On sub-nucleotide level however, a more complex sequence dependent molecular pattern can be observed along the DNA major and minor grooves. (brc.hu)
Although the functional group pattern and the conformational and physico-chemical parameters can be directly deduced from the nucleotide sequence, the conventional four letter DNA representation keep these important functional components mostly obscured. (brc.hu)
Reveal the chemical functional group pattern of DNA motifs containing ambiguous nucleotide positions. (brc.hu)
The Motif Plotter tool allows the user to visualise the functional group distribution pattern in major and minor groves of DNA represented by the input ambiguous nucleotide motif. (brc.hu)
Thirdly, the complementary nucleotide to adenine is not thymine , as it is in DNA, but rather uracil , which is an unmethylated form of thymine. (wikidoc.org)
In turn, each nucleotide consists of a phosphate group, a sugar and a nitrogenous base. (exploredna.co.uk)

We have determined the thermodynamic stability of the DNA.RNA hybrid r(GAAGAGAAGC)*d(GC(p)U(p)U(p)C(p)U(p) C(p)U(p)U(p)C) where p is the propynyl group at the 5 position and compared it with that of the unmodified duplex and the effects of methyl substitutions. (ox.ac.uk)

The (Z)-allene-ene-yne 10, a precursor to a reactive α,3-dehydrotoluene biradical, was covalently linked to a minor groove binding element, and the resultant conjugate (9) was shown to bind and cleave DNA with sequence selectivity. (caltech.edu)
The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. (ibecbarcelona.eu)
This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. (tumorportal.org)
The dihedral angle of the MB pairs, corresponding to a left-handed helix, is opposite to that with acridine orange and proflavine on DNA, indicating that the latter ligands bind to DNA in a different way. (ac.ir)

Bioinformatics uses sophisticated analyses of large amounts of genetic information to clarify the relationships between species, explain the evolution of groups of genes, and assemble information from genome sequencing projects. (cdc.gov)
It is presumed that Dri, like Osa, which is a member of the Trithorax Group of genes implicated in the modification of chromatin structures required for epigenetic regulation (Vazquez, 1999), is acting to establish stable chromatin structures. (sdbonline.org)
These targets are named as transcription factor binding sites (TFBSs), which are short DNA fragments mainly located in promoter regions of genes. (biomedcentral.com)

Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex. (irbbarcelona.org)
Using a combination of biophysical techniques such as circular dichroism, differential scanning calorimetry, and thermal melting experiments, I will characterize the effects that methyl groups - a common DNA alkyl lesion - have into the major and minor groove of duplex DNA (where 7mG and 3mA provide methyl groups located in the major and minor grooves, respectively). (hhs.gov)
Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. (ibecbarcelona.eu)
The incorporation of the propyne group at the 5 position gives rise to a very large stabilisation of the hybrid duplex compared with the analogous 5-Me modification. (ox.ac.uk)

The figure shows the position of the main chain to allow hydrogen bonds with the minor groove thymine oxygen atoms. (wikipedia.org)

Ryan initally moved to Huddersfield (England) for his PhD studies, researching antimicrobial minor groove binders with a focus on gram-negative bacterial infections and combatting common resistance mechanisms under the supervision of Dr. Fraser Scott and Prof. Colin Suckling. (burleylabs.co.uk)

Moreover, the CpG site methylation is mediated by DNA methyltransferases (DNMTs), which catalyze the addition of a methyl group to cytosine ( 13 , 14 ). (spandidos-publications.com)
The rate-determining step in the damage of DNA by neocarzinostatin chromophore and the thiols glutathione (GSH), cysteine (CySH), or methyl thioglycolate at physiologically relevant concentrations and pH values is shown to be thiol addition to the chromophore. (caltech.edu)
The duplexes have been characterised by gel electrophoresis and NMR spectroscopy, which indicate that methyl substitutions have a smaller influence on local and global conformation than the propynyl groups. (ox.ac.uk)

One molecule of AO can also interact with one phosphate group of single-stranded DNA or RNA to form an aggregated, or stacked, structure that emits red fluorescence with the maximum wavelength at 650 nm. (dojindo.com)
It is shown that thiol activation of 1 in the presence of single-stranded calf thymus DNA or a heterogeneous mixture of cellular RNA, but not bovine serum albumin, likely occurs as a ternary complex with the biopolymer. (caltech.edu)

Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. (nature.com)
The lackof uniformity between multiple histone/DNA-binding sites causesthe DNA to deviate from ideal superhelix geometry. (nature.com)
The repeating nucleosome cores further assemble into higher-order structures which are stabilized by the linker histone H1 and these compact linear DNA overall by a factor of 30?40. (nature.com)
The high-mobility group (HMG) domain is a DNA-binding motif that is shared abundant non-histone components of chromatin and by specific regulators of transcription and cell differentiation. (embl.de)

This gene encodes a key mitochondrial transcription factor containing two high mobility group motifs. (nih.gov)
Recently, we described the characterisation of a parasite gene (TashAT2), whose polypeptide product bears AT hook DNA-binding motifs and may be transported from the parasite to the host nucleus. (lookformedical.com)

A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone. (wikidoc.org)
Secondly, while DNA contains deoxyribose , RNA contains ribose , (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA, whereas RNA has two hydroxyl groups). (wikidoc.org)
These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis . (wikidoc.org)
Each strand has a 5′end (with a phosphate group) and a 3′end (with a hydroxyl group). (microbenotes.com)
Furthermore, the simulations show a spine of hydration in the major groove as well as in the minor groove involving the RNA hydroxyl groups. (ox.ac.uk)

Each DNA double helix thus has a simple construction: wherever one strand has an A, the other strand has a T, and each C is matched with a G. (microbenotes.com)

DNA-bound 2 rearranges to the biradical B, which then abstracts hydrogen atoms from the ribose backbone of DNA. (caltech.edu)
A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. (wikidoc.org)
Deoxyribose is the sugar component of DNA, just as ribose serves that role in RNA (ribonucleic acid). (microbenotes.com)

Dodson, ML & Lloyd, RS 2001, ' Backbone dynamics of DNA containing 8-oxoguanine: Importance for substrate recognition by base excision repair glycosylases ', Mutation Research - DNA Repair , vol. 487, no. 3-4, pp. 93-108. (elsevierpure.com)

DNA can be in a relaxed or coiled state and it is this coiling that allows our extremely long strands of DNA to fit or 'pack' into the comparatively much smaller cells in our bodies. (exploredna.co.uk)
The three-dimensional structure of DNA, first proposed by James D. Watson and Francis H. C. Crick in 1953, consists of two long helical strands that are coiled around a common axis to form a double helix. (microbenotes.com)
Each DNA molecule is comprised of two biopolymer strands coiling around each other. (microbenotes.com)

Hoogsteen-based parallel-stranded duplexes of DNA. (irbbarcelona.org)
The relative flexibility of B-DNA and A-RNA duplexes: database analysis. (irbbarcelona.org)

Frontiers in molecular dynamics simulations of DNA. (irbbarcelona.org)
Molecular dynamics simulations of double-helical DNA oligomers have been performed to investigate differences in the structure, dynamics, and hydration of F-F and T-T mispairs. (umn.edu)

The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
The mechanism of action of aclarubicin is based on its capacity to insert its trisaccharide chain into the minor DNA groove: poison of topoisomerase I, inhibitor of topoisomerase II, eviction of histones from nucleosomes, but also inhibitor of the 20S proteasome. (rxreasoner.com)
Explain the chemical characteristics of DNA and the histones that allows them to form a complex. (exploredna.co.uk)

Moreover, in the ketamine group, the level of Ten‑Eleven‑Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription‑quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. (spandidos-publications.com)
Since transcription factors interact physically with their DNA targets, it is reasonable to depict binding preference between TFs and TFBSs through conformational and physicochemical information. (biomedcentral.com)

DNA), and also for larger, micrometer-sized structures. (nanosurf.net)

The major and minor groove edges of the T-T pairs were observed to be solvated at exposed carbonyl positions by at least one water molecule, while F-F pairs lacked solvating waters. (umn.edu)

The DNA dodecamer has eight consecutive AT base pairs, allowing the AT-hook to be positioned in several positions, with the preferred position being at one of the AATT regions to fully occupy the minor groove. (wikipedia.org)
TheX-raycrystalstructureofthenucleosomecoreparticleofchromatinshowsinatomicdetailhowthehistoneprotein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. (nature.com)
The standard Watson-Crick DNA model justifies the size-complementarity and the hydrogen bonding patterns responsible for the crystal structure which is necessary for the amplification of genetic information and specificity to the formation of base pairs [6]. (fortuneonline.org)
To get a sense of just how long a DNA polymer is, consider that just one human chromosome is several hundred million base pairs long. (exploredna.co.uk)

Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. (cdc.gov)

Towards the right-center among the coils, a prosthetic group called a home group (shown in gray) with a bound oxygen molecule (red). (transectscience.org)
These conjugates find use in single molecule DNA sequencing and other applications. (justia.com)
DNA stands for Deoxyribonucleic acid, a molecule that contains the instructions an organism needs to develop, live and reproduce. (microbenotes.com)
As a result of the double-helical nature of DNA, the molecule has two asymmetric grooves. (microbenotes.com)

Thermo Scientific Pierce DAPI Nuclear Counterstains are high-purity forms of diamidino-2-phenylindole dye for fixed-cell, fluorescent staining of DNA content and nuclei for cellular imaging techniques. (thermofisher.com)
Minor Groove Binder (MGB) Probes are dual-labeled 5' hydrolysis probes consisting of a 5' fluorescent reporter dye and a 3' Eclipse Dark Quencher (EDQ) conjugated to a MGB moiety. (biosearchtech.com)
The interaction between DNA and a fluorescent material has been investigated for a long time. (int-conf-chem-structures.org)

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? (irbbarcelona.org)

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes, some of them guided by non-coding RNAs . (wikidoc.org)
These conformations interact with enzymes in your body and are also involved in aspects such as DNA repair. (exploredna.co.uk)

In addition to the molecular patterns of the DNA grooves, the local conformational and physico-chemical properties of DNA can also strongly influence the functional characteristics of a DNA fragment. (brc.hu)
Can somebody please tell me at least 5 or more characteristics/facts about DNA? (exploredna.co.uk)
One of the areas of human identification is Cheiloscopy, the name given to the study of the lips, their characteristics (such as thickness, position of the grooves and grooves) and the record of the impressions left by them. (bvsalud.org)

The experimental evidence suggests that the cumulene intermediate undergoes cycloaromatization while bound to DNA and that the biradical formed in this cycloaromatization reaction is a highly reactive and poorly selective intermediate. (caltech.edu)
Similarly studies with Emodin and Aloe emodin derivatives have also revealed greater therapeutic potential, DNA intercalation property, and reactive oxygen species generation and thereby induction of apoptosis in cancer cells [ 12 ]. (longdom.org)

The performance of each assay was monitored by running a dilution series (1 x 102 to 1 x 108 copies per reaction) of E. coli genomic DNA in TaqMan™ Fast Advanced Master Mix, following manufacturers recommendations for assay concentrations and cycling conditions. (biosearchtech.com)

The Double Helix Mini DNA Model (22 Segments) is an excellent teaching aids for any classroom. (labworld.co.uk)
The Double Helix Mini DNA Models (22 Segments) is usually delivered within 3 to 5 working days of ordering via UPS courier. (labworld.co.uk)
1) Sequence feature, which is the sequence similarity of DNA segments to a position weight matrix (PWM). (biomedcentral.com)

Ester is a suitable functional group for staining viable cells. (dojindo.com)
Here we provide a tool suitable for the simultaneous visualisation of functional group pattern of an input DNA sequence together with numerous different conformational and physico-chemical DNA parameters. (brc.hu)
The presence of this functional group enforces the C3'-endo sugar conformation (as opposed to the C2'-endo conformation of the deoxyribose sugar in DNA) that causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA. (wikidoc.org)

Its selectivity for DNA and high cell permeability allows efficient staining of nuclei with little background from the cytoplasm. (thermofisher.com)

2) Structure feature, which is conformational and physicochemical information of a DNA segment. (biomedcentral.com)

Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is a pentose sugar (monosaccharide containing five carbon atoms) that is a key component of the nucleic acid deoxyribonucleic acid (DNA). (microbenotes.com)

The variation in this preference along the length of nucleosomal DNA and the intrinsic sequence-dependent bendability of DNA implies that strong translational settings can also occur. (nature.com)

Spoligotype analysis ( 13 ) is a form of DNA sequencing by hybridization. (cdc.gov)

In support of this idea, it is shown that the sequence specificity of DNA cleavage by externally generated cumulene is identical to that of the presumptive cumulene formed in situ from 1 and 2 in the presence of DNA. (caltech.edu)
It is proposed that the species that determines the sequence specificity of DNA cleavage is thecumulene intermediate. (caltech.edu)
Both stages of DNA cleavage proceed with identical sequence specificity. (caltech.edu)

Moreover, DNA hypomethylation of the COX‑2 promoter region located from ‑1,522 to ‑829 bp might contribute to transcriptional regulation of COX‑2 expression and induce a pro‑inflammatory response in KIC. (spandidos-publications.com)

The structure and dynamics of DNA in the gas phase. (irbbarcelona.org)

DAPI is a classic nuclear counterstain for immunofluorescence microscopy, as well as an important component of high-content screening methods requiring cell-based quantitation of DNA content. (thermofisher.com)

Failure to repair DNA alkylation damage may lead to either or both mutagenesis or cytotoxicity. (hhs.gov)
Pyrrolo[2,1-c][1,4]benzodiazepines (PBDs), CC-1065 and distamycins are three classes of minor-groove alkylating agents which showed interesting cytotoxicity profiles, but they cannot be used in humans for various toxicity problems. (najah.edu)

Anatomy3

Organisms2

Chemicals and Drugs137

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Phenomena and Processes59

Disciplines and Occupations5

Technology, Industry, Agriculture1

Information Science6

Named Groups1

Health Care1

Interactions14

Proteins27

Replication4

Bases10

Binds4

Nucleotides10

Protein11

Guanine1

Sequences3

Complexes2

Structural12

Phosphate groups3

Molecules7

Polymerase2

Double-stranded9

Nucleotide7

Thermodynamic1

Bind4

Genes3

Duplex4

Thymine1

Binders1

Methyl3

Single-stranded2

Histone4

Motifs2

Hydroxyl5

Strand1

Ribose3

Backbone1

Strands3

Duplexes2

Simulations2

Histones3

Transcription2

Structures1

Major and m1

Base pairs4

Fingerprint1

Molecule4

Fluorescent3

Hydrogen bonds1

Enzymes2

Characteristics3

Reactive2

Genomic1

Segments3

Functional group3

Selectivity1

Physicochemical1

Deoxyribonucleic1

Sequence-dependent1

Hybridization1

Specificity3

Transcriptional1

Structure and dyna1

DAPI1

Cytotoxicity2