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  - Turkin, Arthur
A1  - Holzapfel, Marco
A1  - Agarwal, Mohit
A1  - Fischermeier, David
A1  - Mitric, Roland
A1  - Schweins, Ralf
A1  - Gröhns, Franziska
A1  - Lambert, Christoph
T1  - Solvent Induced Helix Folding of Defined Indolenine Squaraine Oligomers
JF  - Chemistry—A European Journal
N2  - A protecting group strategy was employed to synthesise a series of indolenine squaraine dye oligomers up to the nonamer. The longer oligomers show a distinct solvent dependence of the absorption spectra, that is, either a strong blue shift or a strong red shift of the lowest energy bands in the near infrared spectral region. This behaviour is explained by exciton coupling theory as being due to H- or J-type coupling of transition moments. The H-type coupling is a consequence of a helix folding in solvents with a small Hansen dispersity index. DOSY NMR, small angle neutron scattering (SANS), quantum chemical and force field calculations agree upon a helix structure with an unusually large pitch and open voids that are filled with solvent molecules, thereby forming a kind of clathrate. The thermodynamic parameters of the folding process were determined by temperature dependent optical absorption spectra.
KW  - UV/Vis spectroscopy
KW  - dye chemistry
KW  - solvent effects
KW  - superstructure
KW  - supramolecular folding
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-256869
VL  - 27
IS  - 32
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  - 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  -