109.2-3 aptamer

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Description

 In 2000, Robert R. Rando 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, Robert R. Rando 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].
Detailed information are accessible on SELEX page.



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.

5'-GGGAGAAUUCCGACCAGAAGCUUCUCCUGCCGCGCGAUUUUACGCCGACAAGGGUGGCAUGAUGAUGUGUCUNUAUAUAGGGGGGGCAUAUGUGCGUCUACAUGGAUCCUCA-3'

 drawing


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

Name Gene ID Pfam MW Nucleic acid sequences PDB
16S rRNA decoding region 8923219 RF00177 9.31 kDa GGCGUCACACCUUCGGGUGAAGUCGCC 1PBR

Some isolated sequences bind to the affinity of the nucleic acid.

Name Sequence Ligand Affinity
109.2-3 GGGAGAAUUCCGACCAGAAGCUUCUCCUGCCGCGCGAUUUUACGCCGACAAGGGUGGCAUGAUGAUGUGUCUNUAUAUAGGGGGGGCAUAUGUGCGUCUACAUGGAUCCUCA 16S rRNA decoding region 1.236 μM
109.1-7 GGGAGAAUUCCGACCAGAAGC UUUUAGGGCGGGACUUUUGGCCGCAAAGGUUGGUGUGAGGGUUCUCAAUAAUGGCCCAAG CAUAUGUGCGUCUACAUGGAUCCUCA 16S rRNA decoding region 1.446 μM
109.2-15 GGGAGAAUUCCGACCAGAAGCGGCGUUCCGCAUCGGCAACUGGCGAGGAGUUGUAUUCGGCGGAAACGGGUUGAGGUCCGACAUAUGUGCGUCUACAUGGAUCCUCA 16S rRNA decoding region 1.655 μM
69.1-4 GGGAGAAUUCCGACCAGAAGCAGUGGAAGAGCCGGGUUGGGCAUAUGUGCGUCUACAUGGAUCCUCA 16S rRNA decoding region 2.946 μM
69.1-11 GGGAGAAUUCCGACCAGAAGCAGCGGAACGGCCGACUUCAACAUAUGUGCGUCUACAUGGAUCCUCA 16S rRNA decoding region 2.786 μM
drawing

Similar compound

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. Bit score is a relative score used to measure the similarity of a sequence alignment. 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 Residues Bit score
8UU9-a 1-1550 1642.7
8UU4-a 1-1550 1642.7
8UU5-a 1-1550 1642.7
8UU6-a 1-1550 1642.7
8UU7-a 1-1550 1642.7
8UU8-a 1-1550 1642.7
8Buu-a 2-1551 1641.0
7QH4-W 3-1552 1639.1
6HA8-a 2-1551 1639.1
8CDU-A 2-1551 1639.1


References

[1] RNA aptamers that specifically bind to a 16S ribosomal RNA decoding region construct.
Tok, J. B., Cho, J., & Rando, R. R.
Nucleic acids research, 28(15), 2902–2910. (2000)