GTP aptamer

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Timeline

2002

The GTP RNA aptamer was selected for the first time[1]

2004

To compare the structures and activities of eleven distinct GTP-binding RNAs[2]

2006

Present the solution structure of the 41-nt Class I GTP aptamer (Kd = 75 nM) as determined by NMR[3]

2013

Using in vitro selection to search a GTP RNA aptamers,including one (the "G motif") with a G-quadruplex structure[4]

2014

Reporting the discovery and characterization of a second class of naturally occurring GTP aptamer, the “CA motif”[5]

2016

Solution NMR demonstrates class V aptamer binds GTP via a two-layered G-quadruplex, folding upon ligand addition[6]

2017

Report the NMR solution structure of an in vitro selected GTP-binding RNA aptamer bound to GTP with an intricate tertiary structure[7]

2019

The NMR-based structure determination of the high-affinity binding GTP-aptamer 9-12[8]

2023

Selection for ATP binding we isolate specific ATP- or GTP-binding aptamers with low micromolar affinities[9]

Description

 In 2002, Davis et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for GTP. Then,Davis et al. demonstrated significantly enhanced GTP binding, spanning three orders of magnitude in binding affinity. In 2006, James etal elucidated the structure of the aptamer complexed with GTP using multidimensional nuclear magnetic resonance spectroscopy and molecular dynamics calculations[1].

SELEX

Aptamers, RNA sequences that bind to target ligands, are typically isolated by in vitro selection from RNA libraries containing completely random sequences. To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. Because stem-loops are common motifs in previously characterized aptamers, we designed the partially structured library to contain a centrally located stable stem-loop. We used an off-rate selection protocol designed to maximize the enrichment of high-affinity aptamers. The selection produced a surprisingly large number of distinct sequence motifs and secondary structures, including seven different aptamers with Kds ranging from 500 to 25 nanomolar. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool[1].
Detailed information are accessible on SELEX page.



Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information[3].

5'-GGGACGAAGUGGUUGGGCGCUUCGGCGUGUGAAAACGUCCC-3'

 drawing

3D visualisation

James m. carothers and Jonathan h. davis elucidate the solution structure of the 41-nt Class I GTP aptamer (Kd = 75 nM) using multidimensional NMR spectroscopy and molecular dynamics calculations. The PDB ID of this structure is 2AU4[3].
Additional available structures that have been solved and detailed information are accessible on Structures page.

(Clicking the "Settings/Controls info" to turn Spin off)      
drawing PDBe Molstar




Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 2AU4 by NMR. GTP(Guanosine-5'-triphosphate)(shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with GTP.

drawing drawing


Ligand information

SELEX ligand

Jonathan H. Davis and Jack W. Szostak use ultrafiltration Kd assays to determine binding assays[3]. The affinity of the aptamer is shown in the figure below.

drawing

Structure ligand

GTP is a guanosine 5'-phosphate and a purine ribonucleoside 5'-triphosphate. It has a role as an Escherichia coli metabolite, a mouse metabolite and an uncoupling protein inhibitor. It is a conjugate acid of a GTP.-----from PubChem
PubChem CID Molecular Formula MW CAS Solubility Drugbank ID
135398633 C10H16N5O14P3 523.18 g/mol 86-01-1 100 mg/mL in water DB04137
drawing drawing

Similar compound

We screened the compounds with great similarity to GTP by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available, we will supplement them with Pubchem CID.
Zinc_id Named CAS Pubchem CID Structure
ZINC14881082 9beta-D-Arabinofuranosylguanosine 5'-Triphosphate 72490-81-4 135544356 drawing
ZINC100054067 6-Thioguanosine-5'- O- Triphosphate NA 131769948 drawing
ZINC37868676 Phosphoaminophosphonic Acid Guanylate Ester 34273-04-6 135403657 drawing
ZINC8215530 Inosine triphosphate 132-06-9 135398643 drawing
ZINC13436579 2'-Deoxyguanosine-5'-Triphosphate 2564-35-4 135398599 drawing
ZINC95618747 6-Thioguanosine 5'-triphosphate 17670-19-8 10143562 drawing
ZINC53683954 7-Methyl-Guanosine-5'-Triphosphate 26554-26-7 135419182 drawing
ZINC44221439 Guanidinetriphosphate NA 135440071 drawing


References

[1] Isolation of high-affinity GTP aptamers from partially structured RNA libraries.
Jonathan H. Davis and Jack W. Szostak.
PNAS, 99 (18) 11616-11621 (2002)
[2] Informational Complexity and Functional Activity of RNA Structures.
James M. Carothers, Stephanie C. Oestreich‡, Jonathan H. Davis, and Jack W. Szostak.
JACS, 126(16) 5130–5137 (2004)
[3] Solution structure of an informationally complex high-affinity RNA aptamer to GTP.
Carothers, J. M., Davis, J. H., Chou, J. J., & Szostak, J. W.
RNA, 12(4), 567-579 (2006)
[4] Discovery of widespread GTP-binding motifs in genomic DNA and RNA.
Curtis, E. A., & Liu, D. R.
Chemistry & biology, 20(4), 521-532 (2013)
[5] A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats.
Curtis, Edward A., and David R. Liu
RNA biology, 11(6), 682-692 (2014)
[6] An intermolecular G-quadruplex as the basis for GTP recognition in the class V–GTP aptamer.
Nasiri, A. H., Wurm, J. P., Immer, C., Weickhmann, A. K., & Wöhnert, J.
RNA, 22(11), 1750-1759. (2016)
[7] A stably protonated adenine nucleotide with a highly shifted pKa value stabilizes the tertiary structure of a GTP‐binding RNA aptamer.
Wolter, A. C., Weickhmann, A. K., Nasiri, A. H., Hantke, K., Ohlenschläger, O., Wunderlich, C. H. & Wöhnert, J.
Angewandte Chemie International Edition, 56(1), 401-404. (2017)
[8] NMR resonance assignments for the GTP-binding RNA aptamer 9-12 in complex with GTP.
Wolter, A. C., Pianu, A., Kremser, J., Strebitzer, E., Schnieders, R., Fürtig, B.& Wöhnert, J.
Biomolecular NMR Assignments, 13, 281-286 (2019)
[9] Emergence of ATP‐and GTP‐Binding Aptamers from Single RNA Sequences by Error‐Prone Replication and Selection.
Wachowius, F., Porebski, B. T., Johnson, C. M., & Holliger, P.
ChemSystemsChem, 5(5), e202300006. (2023)