Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

Mieczkowski, Mateusz; Steinmetzger, Christian; Bessi, Irene; Lenz, Ann Kathrin; Schmiedel, Alexander; Holzapfel, Marco; Lambert, Christoph; Peña, Vladimir; Höbartner, Claudia

doi:10.1038/s41467-021-23932-0

Cited by 27 publications

(16 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We note that many small-molecule DNA/RNA complexes fold into duplex–quadruplex structures, such as quadruplex–duplex junction–ligand complexes, − and fluorogenic RNA aptamer–ligand complexes. − However, the interaction mode between DNA/RNA and the ligand in these complexes is different from that in the OBA33–OTA complex. G-Quadruplexes in these complexes are directly involved in the DNA/RNA–ligand interaction through the stacking interaction between the ligand and the G-quartet layer.…”

Section: Discussionmentioning

confidence: 94%

Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer

Jie

et al. 2022

J. Am. Chem. Soc.

View full text Add to dashboard Cite

A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer–OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex–quadruplex structural scaffold stabilized by Mg2+ and Na+ ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through π–π stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.

show abstract

Section: Discussionmentioning

confidence: 94%

Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer

Jie

et al. 2022

J. Am. Chem. Soc.

View full text Add to dashboard Cite

show abstract

“…Like other fluorogenic RNA aptamers, Pepper binds its ligand via a platform generated by a co-planar arrangement of multiple bases, although not using G-quadruplexes as observed in several other aptamers ,,− (Tables S1 and S2). The base quadruple in Pepper appears to be sequence-specific as mutations in the tetrad lead to loss of activity (see below), although the base triple above it is more forgiving.…”

Section: Resultsmentioning

confidence: 99%

“…The out-of-plane system can involve up to three nucleotides, as seen in the malachite green aptamer and Spinach. , Various combinations of nucleobases comprise the two stacking layers and fluorogenic aptamers fall broadly into two categories. Those that use a G-quadruplex fold to form one of the stacking layers include Spinach, , Mango, ,, Chili, and Corn, and those that do not, include the malachite green aptamer, DIR2, Squash, and Pepper . The latter category of aptamers uses a base triple or base quadruple.…”

Section: Discussionmentioning

confidence: 99%

Structural Basis for Fluorescence Activation by Pepper RNA

Rees

Gogacz

et al. 2022

ACS Chem. Biol.

View full text Add to dashboard Cite

Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K+ dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg2+ ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper’s function may expand to allow the in vivo detection of other small molecules and metals.

show abstract

“…47 Search models were double-stranded RNA A-form helix fragments as described previously. 23 Here we used the 7-bp bottom stem from the Chili RNA aptamer 48 (PDB: 7OAX, chain A nt 2-8/45-51), searched for three copies in the ensemble and obtained a MR solution with a Z-score (TFZ) of 14.4 (TFZ >8 indicates a definite solution). The initial electron density map obtained from Phaser was used for automated model building with the AutoBuild module in Phenix.…”

Section: Data Collection and Structure Determinationmentioning

confidence: 99%

Structure and mechanism of the methyltransferase ribozyme MTR1

et al. 2022

Self Cite

View full text Add to dashboard Cite

RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the sitespecific synthesis of 1-methyladenosine (m 1 A) in RNA, using O 6 -methylguanine (m 6 G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m 1 A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-Omethylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.

show abstract

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

Cited by 27 publications

References 69 publications

Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer

Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer

Structural Basis for Fluorescence Activation by Pepper RNA

Structure and mechanism of the methyltransferase ribozyme MTR1

Contact Info

Product

Resources

About