ATP aptamer

Jan 2, 2024 • Zhizhong Lu, Yangyi Ren

Timeline

Description

In 1993, Szostak et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for ATP. Subsequently, they used this motif to design ribozymes displaying polynucleotide kinase activity. In 1996, Dinshaw J. Patel et al. elucidated the structure of the aptamer complexed with AMP using multidimensional nuclear magnetic resonance spectroscopy and molecular dynamics calculations^[1,3].

SELEX

In 1993, Szostak et al. used the SELEX method to isolate a small RNA motif that bound ATP. They initiated the in vitro selection experiments by creating a large pool of random polynucleotide sequences, which were then subjected to repeated cycles of enrichment for those species that exhibited the desired characteristics, followed by amplification of the selected pool. The process began with a pool of 169-nucleotide-long RNAs, which consisted of approximately 10¹⁴ distinct sequences. They isolated RNA molecules capable of binding ATP using affinity chromatography on ATP-agarose columns, where the ATP was attached to the agarose at its C8 position. The RNA molecules that were retained by the ATP-agarose matrix were then eluted with ATP. Following this, the eluted RNA was amplified through reverse transcription and polymerase chain reaction (PCR). They produced an enriched pool of RNAs for the next cycle of selection by in vitro transcription of the double-stranded DNA templates generated in this manner. After six rounds of selection and amplification, a population of RNAs that were specifically eluted with ATP was obtained. From the eighth cycle RNA population, 39 clones were sequenced, revealing 17 distinct sequences^[1].
Detailed information are accessible on SELEX page.

Structure

2D representation

In 1993, Szostak et al. obtained 17 different sequences through SELEX, and designed a 40 nt sequence after comparing the information of 17 sequences. The 40-nt aptamer is characterized by a sequence that forms a distinct secondary structure, as illustrated in the subsequent diagram. Here we utilized RiboDraw to complete the figure, based the 3D structure information^[2].

5'-GGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGCAACCC-3'

3D visualisation

In 1996, Roger A. Jones & Dinshaw J. Patel et al. presented the solution structure of both uniformly and specifically C13, N15-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations. The PDB ID is 1AM0. Subsequently, T Dieckmann & J Feigon et al. presented the three-dimensional solution structure of a 36-nucleotide ATP-binding RNA aptamer complexed with AMP, which was determined from NMR-derived distance and dihedral angle restraints. The PDB ID is 1RAW. Here, only the structural diagram of 1RAW was shown. There was no obvious difference between the structures of 1AM0 and 1RAW^[3,4].
Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 1RAW by NMR. Adenosine monophosphate (AMP) shown in sticks. Right: The hydrogen bonds of binding sites of the aptamer bound with AMP^[3].

Ligand information

SELEX ligand

Szostak and colleagues utilized several methodologies including isocratic elution from ATP-agarose and equilibrium gel filtration techniques to determine the dissociation constant of the RNA-ATP complex both on the column and in solution. These methods were employed to comprehensively assess the stability and affinity of the RNA-ATP interaction under different experimental conditions, allowing for a robust evaluation of the binding affinity and dynamics between RNA molecules and ATP in varied environments. Adenosine triphosphate (ATP), Deoxyadenosine triphosphate (dATP)^[2].

Structure ligand

Adenosine monophosphate, also known as 5'-adenylic acid and abbreviated AMP, is a nucleotide that is found in RNA. It is an ester of phosphoric acid with the nucleoside adenosine. AMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase adenine. AMP is used as a dietary supplement to boost immune activity, and is also used as a substitute sweetener to aid in the maintenance of a low-calorie diet.-----From Drugbank
The PubChem CID is a designation established by the PubChem database, a subsidiary of the NCBI: National Center for Biotechnology Information, for metabolites. The CAS registration number is a unique and unambiguous identifier for a particular substance that can be used for clear communication and, with the help of CAS scientists, to tie together all available data and research on that substance. DrugBank is a comprehensive online database that provides detailed information on drugs and drug targets, including their chemical, pharmacological, and pharmaceutical data.

Name	PubChem CID	Molecular Formula	MW	CAS	Solubility	Drugbank ID
AMP	6083	CH14N5O7P	347.22 g/mol	61-19-8	10000 mg/L (at 20 °C)	DB00131

Similar compound

We screened compounds with a significant resemblance to AMP utilizing the ZINC database and presented some of the compounds' structural diagrams. For instances where some CAS numbers were unavailable, we intended to complement them with PubChem CIDs.
The Zinc_id is the compound identifier used by the ZINC database, which is one of the largest repositories of organic small molecules. Many pre-virtual screenings of drug-like molecules are based on this database. The PubChem CID is a designation established by the PubChem database, a subsidiary of the NCBI: National Center for Biotechnology Information, for metabolites. The CAS registration number is a unique and unambiguous identifier for a particular substance that can be used for clear communication and, with the help of CAS scientists, to tie together all available data and research on that substance.

Zinc_id	Named	CAS	Pubchem CID	Structure
ZINC000002126310	Vidarabine Phosphate	29984-33-6	34768
ZINC000053684016	Alpha-Methylene Adenosine Monophosphate	NA	46936495
ZINC000053684213	6-Chloropurine Riboside, 5'-Monophosphate	NA	70789235
ZINC000004096488	6-Thioinosine-5'-Monophosphate	53-83-8	3034391
ZINC000013543089	6-Methylthiopurine 5'-Monophosphate Ribonucleotide	7021-52-5	3037883
ZINC000003927870	Fludarabine	21679-14-1	657237
ZINC000013543718	Vidarabine Phosphoric Acid	NA	22840996
ZINC000001631259	3'-Adenylic acid	84-21-9	41211

References

[1] An RNA motif that binds ATP.
Sassanfar, M., & Szostak, J. W.
Nature, 364(6437), 550–553 (1993)
[2] In vitro evolution of new ribozymes with polynucleotide kinase activity.
Lorsch, J. R., & Szostak, J. W.
Nature, 371(6492), 31–36 (1994)
[3] Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.
Jiang, F., Kumar, R. A., Jones, R. A., & Patel, D. J.
Nature, 382(6587), 183–186 (1996)
[4] Solution structure of an ATP-binding RNA aptamer reveals a novel fold.
Dieckmann, T., Suzuki, E., Nakamura, G. K., & Feigon, J.
RNA (New York, N.Y.), 2(7), 628–640. (1996)
[5] Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex.
Jiang, F., Patel, D. J., Zhang, X., Zhao, H., & Jones, R. A
Journal of biomolecular NMR, 9(1), 55–62. (1997)
[6] Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.
Lin, C. H., & Patel, D. J.
Chemistry & biology, 4(11), 817–832. (1997)
[7] Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection.
Tang, J., & Breaker, R. R.
RNA (New York, N.Y.), 3(8), 914–925 (1997)
[8] Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex.
Nonin, S., Jiang, F., & Patel, D. J.
Journal of molecular biology, 268(2), 359–374. (1997)
[9] Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer.
Huang, Z., & Szostak, J. W.
RNA (New York, N.Y.), 9(12), 1456–1463. (2003)
[10] A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality.
Vaish, N. K., Larralde, R., Fraley, A. W., Szostak, J. W., & McLaughlin, L. W.
Biochemistry, 42(29), 8842–8851. (2003)
[11] A small aptamer with strong and specific recognition of the triphosphate of ATP.
Sazani, P. L., Larralde, R., & Szostak, J. W.
Journal of the American Chemical Society, 126(27), 8370–8371. (2004)
[12] Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon.
Park, Y., Nim-Anussornkul, D., Vilaivan, T., Morii, T., & Kim, B. H.
Bioorganic & medicinal chemistry letters, 28(2), 77–80. (2018)