RNA loop aptamer

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Description

 In 1997, Bongrae Cho and colleagues used the systematic evolution of ligands by exponential enrichment (SELEX) to isolate high affinity RNA aptamers that bind to the RNA stem-loop. The RNA used for selection was a small stem-loop which was prepared by in vitro transcription[1].

SELEX

In 1997, Bongrae Cho and colleagues used a blocking deoxynucleotide to select against species in the RNA library which bound to the target RNA stem-loop by W-C base pairing. The winning RNA aptamer was identified by affinity chromatography and gel-shift[1].
Detailed information are accessible on SELEX page.



Structure

g18_04 aptamer was the aptamer sequence mainly studied in the article, which had a high affinity with RNA stem-loop. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].

5'-GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGGGUCUGUGCGCAAAACCAUCGGCCCUGGUGCCUAUGUGCGUCUACAUGGAUCCUCA-3'

 drawing


Ligand information

SELEX ligand

The target stem-loop RNA was designed by the authors themselves. The target stem-loop RNA designed by the author includes the stem sequence is the same as that of Bacillus subtilis RNase P RNA P5.1 domain. Although the stem-loop RNA is 3 nt longer than the latter.

Name Gene ID Pfam MW Nucleic acid sequences PDB
RNA stem-loop NA RF00011 105.48 kDa GCGAGCCUAGCGAAGUCAUAAGCUAGGGCAGUCUUUAGAGGCUGACGGCAGGAAAAAAGCCUACGUCUUCGGAUAUGGCUGAGUAUCCUUGAAAGUGCCACAGUGACGAAGUCUCACUAGAAAUGGUGAGAGUGGAACGCGGUAAACCCCUCGCA NA

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

Name Sequence Ligand Affinity
g18_04 GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGGGUCUGUGCGCAAAACCAUCGGCCCUGGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop 70 nM
g18_01 GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGGGUCUGUGCGCAAAACCAUCGUCCCGGGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop NA
g18_06 GGGAGAAUUCCGACCAGAAGCUUUUCCUUAGGGGUUCAGUUGUUUCGCGCAUGAACGGCAUCAGUGCACCGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop NA
g18_09 GGGAGAAUUCCGACCAGAAGCUUAGUUGAUCGAGCGUGUUAGUUCUCCAAUCUCUGUGUAGCGUGGAGCUGGGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop NA
g18_10 GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGUGUCUGUGCGCAAAACCAUCGGCCCGGGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop NA
g18_11 GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGGGUCUGUGCGCAAAACCAUCGGCCCGGGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop NA
g18_12 GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGUGUCUGUGCGCAAAACCAUAGGCCCGGGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop NA
g12_03 GGGAGAAUUCCGACCAGAAGCUUCCGAAGCAUUCCGGCGUAGGGGUCUGUGCGCAAAACUAUCGGCCCGGGUGCCUAUGUGCGUCUACAUGGAUCCUCA RNA stem-loop 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
2A64-A 8-404 326.8
3DHS-A 8-255 181.4
1NBS-A 1-154 145.9
1NBS-B 1-154 145.9


References

[1] Interacting RNA species identified by combinatorial selection.
Cho, B., Taylor, D. C., Nicholas, H. B., Jr, & Schmidt, F. J.
Bioorganic & medicinal chemistry, 5(6), 1107–1113. (1997)