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, Szostak, J. W. et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for GTP. Then, Davis, J. H. et al. demonstrated significantly enhanced GTP binding, spanning three orders of magnitude in binding affinity. In 2006, Szostak, J. W. et al. elucidated the structure of the aptamer complexed with GTP using multidimensional nuclear magnetic resonance spectroscopy and molecular dynamics calculations[1,3].



SELEX

A selection process for GTP-binding aptamers was carried out using a mixture of fully random and partially structured libraries. Given that stem-loops are common motifs in previously characterised aptamers, the partially structured library was designed to include a centrally positioned stable stem-loop. An off-rate selection protocol was employed to maximise the enrichment of high-affinity aptamers. This selection process yielded an unexpectedly diverse array of sequence motifs and secondary structures, including seven distinct aptamers with dissociation constants (Kd) ranging from 500 to 25 nanomolar. The engineered stem-loop was present in the three highest-affinity aptamers and in 12 of the 13 independent isolates sharing a single consensus sequence, suggesting that its incorporation increased the prevalence of high-affinity aptamers in the initial pool[1].

Detailed information are accessible on SELEX page.



Structure

2D representation

Here we used ribodraw to complete the figure, through the 3D structure information. Class I GTP aptamer was named by Szostak, J. W[3].

5'-GGGACGAAGUGGUUGGGCGCUUCGGCGUGUGAAAACGUCCC-3'

drawing

3D visualisation

Szostak, J. W. et al. elucidated the solution structure of the 41-nt Class I GTP aptamer (Kd=75 nM) using multidimensional nuclear magnetic resonance (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 (shown in sticks) is labeled in magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with GTP.

drawing drawing


Ligand information

SELEX ligand

Szostak, J. W. et al. used ultrafiltration Kd assays to determine binding assays[1]. 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(3-).-----From PubChem

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

Drugbank: a comprehensive database with detailed information on drugs and drug targets.

Name PubChem CID Molecular Formula Molecular Weight CAS Solubility Drugbank ID
GTP 135398633 C10H16N5O14P3 523.18 g/mol 86-01-1 100 mg/mL in water DB04137
drawing drawing

Similar compound(s)

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: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

ZINC ID Name 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)