tRNA aptamer

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Description

 In 1999, Daniela Scarabino and colleagues employed in vitro selection to identify RNA sequences that bind with high affinity to a T7 transcript corresponding to phenylalanine tRNA of Saccharomyces cerevisiae. One aptamer is shown to form a classical ‘kissing complex’ with full base-pairing of complementary hairpin loops[1].

SELEX

In 1999, Daniela Scarabino and colleagues used a pool with an 80 nucleotide (nt) region of fully random sequence to isolate aptamers that can bind to yeast phenylalanine tRNA. Selection was performed using a phenylalanine tRNA affinity matrix containing 3 mM tRNA[1].
Detailed information are accessible on SELEX page.



Structure

B2 was the aptamer sequence mainly studied in the article, which had a high affinity with yeast phenylalanine tRNA. The 2D structure of the figure is based on the prediction results of the RNA fold website by ribodraw tool to draw.

5'-GGGAAUUCCGCGUGUGCUACGUAUCUUCAGGCGGUAACUAACUGUGCUGAGUCUAAUCUUUGUGAGGGACGGUAACAUAUGGUUCCCGCGUGGUCCGUUCGGGAUCCUC-3'

 drawing


Ligand information

SELEX ligand

Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins. Transfer RNA (tRNA) does this by carrying an amino acid to the protein-synthesizing machinery of a cell called the ribosome. Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code.-----From Rfam

Name Gene ID Pfam MW Nucleic acid sequences PDB
Yeast phenylalanine tRNA 55752253 RF00005 25.2 kDa GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA 1EHZ

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

Name Sequence Ligand Affinity
B2 GGGAAUUCCGCGUGUGCUACGUAUCUUCAGGCGGUAACUAACUGUGCUGAGUCUAAUCUUUGUGAGGGACGGUAACAUAUGGUUCCCGCGUGGUCCGUUCGGGAUCCUC Yeast phenylalanine tRNA 12 nM
B3 GGGAAUUCCGCGUGUGCAAGCCUGUCGUGUGAACCUUGGUAGUCUUCAGAUACCAUUCUAGCCACGAGAGACUACGACACUGCUCCGUCGCCCGUCCGUUCGGGAUCCUC Yeast phenylalanine tRNA 26 nM
B4 GGGAAUUCCGCGUGUGCUCGGUCACGCAUCUUCACGUCGAAAGCUACAUCGGUCUGCUGACGGUGAUGGCAUUUGCGCGGCUUACGCCGGUCGUGGUCCGUUCGGGAUCCUC Yeast phenylalanine tRNA NA
B6 GGGAAUUCCGCGUGUGCAGAGUGGCCGGGCCUCCAUUCGGGGGUUAUCUUCACCUACGGGCCCCACGCGUUAUUUAGUGUUGUACCGUAGGGCUGUGUCCGUUCGGGAUCCUC Yeast phenylalanine tRNA NA
B7 GGGAAUUCCGCGUGUGCGGGUCUUCACAGACUUGGCAAUUACCAGAACAUGUGCCUGGUAUACGUCAAUACGUCUGGUGGUUAAUACCGCCGUGGUCCGUUCGGGAUCCUC Yeast phenylalanine tRNA NA
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
5EL5-1K 1-73 78.5
8BHN-5 1-73 78.5
5IB8-1K 1-73 78.5
5EL6-1L 1-73 78.5
5UYQ-Y 1-73 78.5
5EL4-3K 1-73 78.5
5E7K-3L 1-73 78.5
5EL7-1K 1-73 78.5
5IB8-3K 1-73 78.5
5IB7-1L 1-73 78.5


References

[1] tRNA prefers to kiss.
Scarabino, D., Crisari, A., Lorenzini, S., Williams, K., & Tocchini-Valentini, G. P.
The EMBO journal, 18(16), 4571–4578. (1999)