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

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.