TY  - JOUR
A1  - Mieczkowski, Mateusz
A1  - Steinmetzger, Christian
A1  - Bessi, Irene
A1  - Lenz, Ann-Kathrin
A1  - Schmiedel, Alexander
A1  - Holzapfel, Marco
A1  - Lambert, Christoph
A1  - Pena, Vladimir
A1  - Höbartner, Claudia
T1  - Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine
JF  - Nature Communications
N2  - Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.
KW  - Fluorogenic RNA Aptamers
KW  - Synthetic Functional RNAs
KW  - Chili RNA Aptamer
KW  - Co-Crystal Structures of Chili RNA
KW  - RNA
KW  - Optical Spectroscopy
KW  - Structural Biology
KW  - X-ray Crystallography
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-254527
VL  - 12
ER  - 
TY  - JOUR
A1  - Mieczkowski, Mateusz
A1  - Steinmetzger, Christian
A1  - Bessi, Irene
A1  - Lenz, Ann-Kathrin
A1  - Schmiedel, Alexander
A1  - Holzapfel, Marco
A1  - Lambert, Christoph
A1  - Pena, Vladimir
A1  - Höbartner, Claudia
T1  - Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine
JF  - Nature Communications
N2  - Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.
KW  - RNA
KW  - optical spectroscopy
KW  - structural biology
KW  - X-ray crystallography
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-270274
VL  - 12
ER  - 
TY  - JOUR
A1  - Okuda, Takumi
A1  - Lenz, Ann-Kathrin
A1  - Seitz, Florian
A1  - Vogel, Jörg
A1  - Höbartner, Claudia
T1  - A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells
JF  - Nature Chemistry
N2  - Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.
KW  - Alkyltransferase Ribozyme SAMURI
KW  - Site-specific RNA labelling
KW  - bioorthogonal SAM analogue ProSeDMA
KW  - Chemical modification
KW  - RNA
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-328762
ER  -