TY  - INPR
A1  - Sednev, Maksim V.
A1  - Mykhailiuk, Volodymyr
A1  - Choudhury, Priyanka
A1  - Halang, Julia
A1  - Sloan, Katherine E.
A1  - Bohnsack, Markus T.
A1  - Höbartner, Claudia
T1  - N\(^6\)-methyladenosine-sensitive RNA-cleaving deoxyribozymes
T2  - Angewandte Chemie, International Edition
N2  - Deoxyribozymes are synthetic enzymes made of DNA that can catalyze the cleavage or formation of phosphodiester bonds and are useful tools for RNA biochemistry. Here we report new RNA-cleaving deoxyribozymes to interrogate the methylation status of target RNAs, thereby providing an alternative method for the biochemical validation of RNA methylation sites containing N\(^6\)-methyladenosine, which is the most wide-spread and extensively investigated natural RNA modification. Using in vitro selection from random DNA, we developed deoxyribozymes that are sensitive to the presence of N\(^6\)-methyladenosine in RNA near the cleavage site. One class of these DNA enzymes shows faster cleavage of methylated RNA, while others are strongly inhibited by the modified nucleotide. The general applicability of the new deoxyribozymes is demonstrated for several examples of natural RNA sequences, including a lncRNA and a set of C/D box snoRNAs, which have been suggested to contain m\(^6\)A as a regulatory element that influences RNA folding and protein binding.
KW  - N6-methyladenosine
KW  - RNA modification
KW  - deoxyribozymes
KW  - in vitro selection
KW  - DNA catalyst
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-171753
N1  - This is the pre-peer reviewed version of the following article: M.V. Sednev, V. Mykhailiuk, P. Choudhury, J. Halang, K. E. Sloan, M. T. Bohnsack, C. Höbartner, Angew. Chem. Int. Ed. 2018, 57, 15117-15121, which has been published in final form at https://doi.org/10.1002/anie.201808745. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.
ER  - 
TY  - INPR
A1  - Höbartner, Claudia
A1  - Steinmetzger, Christian
A1  - Palanisamy, Navaneethan
A1  - Gore, Kiran R.
T1  - A multicolor large Stokes shift fluorogen-activating RNA aptamer with cationic chromophores
T2  - Chemistry - A European Journal
N2  - Large Stokes shift (LSS) fluorescent proteins (FPs) exploit excited state proton transfer pathways to enable fluorescence emission from the phenolate intermediate of their internal 4 hydroxybenzylidene imidazolone (HBI) chromophore. An RNA aptamer named Chili mimics LSS FPs by inducing highly Stokes-shifted emission from several new green and red HBI analogs that are non-fluorescent when free in solution. The ligands are bound by the RNA in their protonated phenol form and feature a cationic aromatic side chain for increased RNA affinity and reduced magnesium dependence. In combination with oxidative functional-ization at the C2 position of the imidazolone, this strategy yielded DMHBO\(^+\), which binds to the Chili aptamer with a low-nanomolar K\(_D\). Because of its highly red-shifted fluorescence emission at 592 nm, the Chili–DMHBO\(^+\) complex is an ideal fluorescence donor for Förster resonance energy transfer (FRET) to the rhodamine dye Atto 590 and will therefore find applications in FRET-based analytical RNA systems.
KW  - RNA Aptamer
KW  - fluorescence
KW  - large Stokes shift
KW  - fluorescent protein
KW  - fluorescent resonance energy transfer
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-174197
N1  - This is the pre-peer reviewed version of the following article: Steinmetzger, C. , Palanisamy, N. , Gore, K. . and Höbartner, C. (2018), A multicolor large Stokes shift fluorogen‐activating RNA aptamer with cationic chromophores. Chem. Eur. J. doi:10.1002/chem.201805882, which has been published in final form at https://doi.org/10.1002/chem.201805882. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.
ER  -