Top 10 similar words or synonyms for nonamer

decamer    0.823142

heptamer    0.812062

nonamers    0.776482

octamers    0.761602

undecamer    0.749129

heptamers    0.743190

dodecamer    0.731894

octamer    0.726240

decamers    0.707739

hexamer    0.707371

Top 30 analogous words or synonyms for nonamer

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Article Example
Signal peptide peptidase In mice, a nonamer peptide originating from the SPP protein serves as minor histocompatibility antigen HM13 that plays a role in transplant rejection
V(D)J recombination To maintain the specificity of recombination, V(D)J recombinase recognizes and binds to Recombination Signal Sequences (RSSs) flanking the variable (V), diversity (D), and joining (J) genes segments. RSSs are composed of three elements: a heptamer of seven conserved nucleotides, a spacer region of 12 or 23 basepairs in length, and a nonamer of nine conserved nucleotides. While the majority of RSSs vary in sequence, the consensus heptamer and nonamer sequences are CACAGTG and ACAAAAACC, respectively; and although the sequence of the spacer region is poorly conserved, the length is highly conserved. The length of the spacer region corresponds to approximately one (12 basepairs) or two turns (23 basepairs) of the DNA helix. Following what is known as the 12/23 Rule, gene segments to be recombined are usually adjacent to RSSs of different spacer lengths ("i.e.", one has a "12RSS" and one has a "23RSS"). This is an important feature in the regulation of V(D)J recombination.
Butyrate kinase The investigators of the study that produced the crystallization of 1X9J hypothesized that the enzyme was an octomer formed from dimers. The crystallized form has a radius of 7.5 nm which corresponded to a molecular weight of 380kDa. Because a monomer of "buk2" is about 43kDa, it was believed that the enzyme itself was either an octomer or a nonamer. Investigators hypothesized that the enzyme was an octomer since most of the proteins within the ASHKA super family form dimers.
Recombination-activating gene A recent study published in Cell and featured in Global Medical Discovery solved the cryo-EM structures of synaptic RAG in complex with various forms of DNA intermediates and products, at near-atomic resolutions (3.4 Å resolution). The structures of the synaptic RAG complexes reveal a closed dimer conformation with generation of new intermolecular interactions between two RAG1-RAG2 monomers upon DNA binding, compared to the Apo-RAG complex which constitutes as an open conformation. Both RAG1 molecules in the closed dimer are involved in the cooperative binding of the 12-RSS and 23-RSS intermediates with base specific interactions in the heptamer of the signal end. The first base of the heptamer in the signal end is flipped out to avoid the clash in the active center. Each coding end of the nicked-RSS intermediate is stabilized exclusively by one RAG1-RAG2 monomer with non-specific protein-DNA interactions. The coding end is highly distorted with one base flipped out from the DNA duplex in the active center, which facilitates the hairpin formation by a potential two-metal ion catalytic mechanism. The 12-RSS and 23-RSS intermediates are highly bent and asymmetrically bound to the synaptic RAG complex with the nonamer binding domain dimer tilts towards the nonamer of the 12-RSS but away from the nonamer of the 23-RSS, which emphasizes the 12/23 rule. Two HMGB1 molecules bind at each side of 12-RSS and 23-RSS to stabilize the highly bent RSSs. These structures elaborate the molecular mechanisms for DNA recognition, catalysis and the unique synapsis underlying the 12/23 rule, provide new insights into the RAG-associated human diseases, and represent a most complete set of complexes in the catalytic pathways of any DDE family recombinases, transposases or integrases.
Recombination signal sequences RSSs are made up of conserved heptamer sequences (7 base pairs), spacer sequences, and conserved nonamer sequences (9 base pairs) that are adjacent to the V, D and J sequences in the heavy-chain region of DNA and the V and J sequences in the light-chain DNA region. Spacer sequences are located between heptamer and nonamer sequences and exhibit base pair variety but are always either 12 base pairs or 23 base pairs long. Unlike spacer sequences, heptamer sequences are usually CACAGTG, and the first three nucleotides are highly conserved. Nonamers are usually ACAAAAACC, and the A/T basepairs are also highly conserved. The RAG1/RAG2 enzyme complex follows the 12-23 rule when joining V,D, and J segments, pairing 12-bp spacer RSSs to 23-bp spacer RSSs. This prevents two different genes coding for the same region from recombining (ex. V-V recombination). RSSs are located between V,D, and J segments of the germ-line DNA of maturing B and T lymphocytes and are permanently spliced out of the final Ig mRNA product after V(D)J recombination is complete.
HM13 The minor histocompatibility antigen 13 is a nonamer peptide that originates from a protein encoded by the "H13" gene. The peptide is generated by the cytosol by the proteasome, enters the endoplasmic reticulum (ER) lumen by the transporter associated with antigen processing (TAP) and is presented on the cell surface on H2-D major histocompatibility anigen I (MHC I) molecules. The alloreactivity, which leads to transplant rejection in mice, is conferred by Val/Ile polymorphism in the ‘SSV(V/I)GVWYL’ peptide. The orthologue gene in humans is called HM13. If a related polymorphism exists, and if the HM13 serves as a Minor histocompatibility antigen, however, remains to be addressed.
Organization and expression of immunoglobulin genes It is understood that rearrangement occurs between specific sites on the DNA called recombination signal sequences (RSSs). The signal sequences are composed of a conserved palindromic heptamer and a conserved AT- rich nonamer. These signal sequences are separated by non-conserved spacers of 12 or 23 base pairs called one-turn and two-turn respectively. They are within the lambda chain, k-chain and The processes of rearrangement in these regions are catalyzed by two recombination-activating genes: RAG-1 and RAG-2 and other enzymes and proteins. The segments joined due to signals generated RSSs that flank each V, D, and J segments. Only genes flank by 12 -bp that join to the genes flank by 23-bp spacer during the rearrangements and combinations to maintain VL-JL and VH-DH-JH joining.
Polony sequencing The fluorophore-tagged nonamers anneal with differential success to the tag sequences according to a strategy similar to that of degenerate primers, but instead of submission to polymerases, nonamers are selectively ligated onto adjoining DNA- the anchor primer. The fixation of the fluorophore molecule provides a fluorescent signal that indicates whether there is an A, C, G, or T at the query position on the genomic DNA tag. After four-colour imaging, the anchor primer/nonamer complexes are stripped off and a new cycle is begun by replacing the anchor primer. A new mixture of the fluorescently tagged nonamers is introduced, for which the query position is shifted one base further into the genomic DNA tag.
Recombination-activating gene As with many enzymes, RAG proteins are fairly large. For example, mouse RAG-1 contains 1040 amino acids and mouse RAG-2 contains 527 amino acids. The enzymatic activity of the RAG proteins is concentrated largely in a core region; Residues 384–1008 of RAG-1 and residues 1–387 of RAG-2 retain most of the DNA cleavage activity. The RAG-1 core contains three acidic residues (D, D, and E) in what is called the DDE motif, the major active site for DNA cleavage. These residues are critical for nicking the DNA strand and for forming the DNA hairpin. Residues 384–454 of RAG-1 comprise a nonamer-binding region (NBR) that specifically binds the conserved nonomer (9 nucleotides) of the RSS and the central domain (amino acids 528–760) of RAG-1 binds specifically to the RSS heptamer. The core region of RAG-2 is predicted to form a six-bladed beta-propeller structure that appears less specific than RAG-1 for its target.