Description

In 2000, Rando, R. R. and colleagues employed in vitro selection to identify RNA sequences that bind with high affinity to the A-site of the 16S rRNA decoding region. While the A and P sites of the decoding region constitute only a small fraction of 16S rRNA, mini constructs of the decoding region are biochemically active, suggesting that the structure of the decoding region is preserved in the absence of the remainder of the RNA molecule^[1].

SELEX

In 2000, Rando, R. R. and colleagues chose to apply two pools of random RNA library to the target 27-nt A-site of the 16S rRNA decoding region. Each of the pools comprised a stretch of 20 and 60 random nucleotides, respectively, which were flanked by the appropriate primers with a promoter site for T7 polymerase^[1].

Structure

109.2-3 was the aptamer sequence mainly studied in the article, which had a high affinity with 16S rRNA decoding region. The 2D structure of the figure is based on the article by ribodraw tool to draw. The 109.2-3 aptamer was named by Rando, R. R. et al. in the article^[1].

5'-GGGAGAAUUCCGACCAGAAGCUUCUCCUGCCGCGCGAUUUUACGCCGACAAGGGUGGCAUGAUGAUGUGUCUNUAUAUAGGGGGGGCAUAUGUGCGUCUACAUGGAUCCUCA-3'

Ligand information

SELEX ligand

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself.-----From Rfam

SO ID: Sequence Ontology (SO) is a vocabulary used to control the content of genome sequences, aiming to unify the way genome annotation.

Pfam: a widely recognised database of protein families and domains.

Mass: an intrinsic property of a body.

Some isolated sequences bind to the affinity of the nucleic acid^[1].

Similar compound(s)

Researchers generate a mapping between European Nucleotide Archive (ENA), Protein Data Bank (PDB) and Rfam coordinate systems for those sequences which have a structure in the PDB. The ENA provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. It is calculated based on a comparison between the score of the alignment sequence and the expected score of the random model. A higher Bit score means that the comparison results are more similar and likely to be more reliable. The list of neighbours is sorted by Bit score.

PDB: PDB ID+ chain name.

PDB Residues: a specific molecule or part of a molecule within a protein or nucleic acid whose three-dimensional structure is described in the Protein Data Bank (PDB).

Bit score: a relative score used to measure the similarity of a sequence alignment.

References