220230-58-0Relevant articles and documents
Synthesis of spin-labeled riboswitch RNAs using convertible nucleosides and DNA-catalyzed RNA ligation
Büttner, Lea,Seikowski, Jan,Wawrzyniak, Katarzyna,Ochmann, Anne,H?bartner, Claudia
, p. 6171 - 6180 (2013)
Chemically stable nitroxide radicals that can be monitored by electron paramagnetic resonance (EPR) spectroscopy can provide information on structural and dynamic properties of functional RNA such as riboswitches. The convertible nucleoside approach is used to install 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) and 2,2,5,5-tetramethylpyrrolidin-1-oxyl (proxyl) labels at the exocyclic N4-amino group of cytidine and 2′-O-methylcytidine nucleotides in RNA. To obtain site-specifically labeled long riboswitch RNAs beyond the limit of solid-phase synthesis, we report the ligation of spin-labeled RNA using an in vitro selected deoxyribozyme as catalyst, and demonstrate the synthesis of TEMPO-labeled 53 nt SAM-III and 118 nt SAM-I riboswitch domains (SAM = S-adenosylmethionine).
Measurement of Angstrom to Nanometer Molecular Distances with 19F Nuclear Spins by EPR/ENDOR Spectroscopy
Meyer, Andreas,Dechert, Sebastian,Dey, Surjendu,H?bartner, Claudia,Bennati, Marina
, p. 373 - 379 (2020)
Spectroscopic and biophysical methods for structural determination at atomic resolution are fundamental in studies of biological function. Here we introduce an approach to measure molecular distances in bio-macromolecules using 19F nuclear spins and nitroxide radicals in combination with high-frequency (94 GHz/3.4 T) electron–nuclear double resonance (ENDOR). The small size and large gyromagnetic ratio of the 19F label enables to access distances up to about 1.5 nm with an accuracy of 0.1–1 ?. The experiment is not limited by the size of the bio-macromolecule. Performance is illustrated on synthesized fluorinated model compounds as well as spin-labelled RNA duplexes. The results demonstrate that our simple but strategic spin-labelling procedure combined with state-of-the-art spectroscopy accesses a distance range crucial to elucidate active sites of nucleic acids or proteins in the solution state.
A U-tetrad stabilizes human telomeric RNA G-quadruplex structure
Xu, Yan,Ishizuka, Takumi,Kimura, Takashi,Komiyama, Makoto
, p. 7231 - 7233 (2010)
Telomeric repeat-containing RNA is a new noncoding RNA molecule recently discovered in mammalian cells. Here we report the structural features of human telomere RNA r(UAGGGU) in the presence of K+ and Na+. We demonstrated for the first time that a novel U-tetrad is formed at the 3- end of a parallel human telomeric RNA G-quadruplex. The U-tetrad dramatically stabilizes human telomeric RNA G-quadruplex structure, leading to an increase in melting temperature (Tm) of 29 °C. The U-tetrad-stabilized telomeric RNA G-quadruplex structure adds considerably to our understanding of the diversity of RNA G-quadruplex architectures. It shows that the structure of base "quartets" is important in RNA assembly. The structural information will be invaluable for understanding the function of human telomere RNA.
Efficient photoactivation of a Diels-Alderase ribozyme
Nierth, Alexander,Singer, Marco,Jaeschke, Andres
, p. 7975 - 7977 (2010)
Here we report the first example of a photoactivatable ribozyme which catalyzes a bimolecular reaction of two small organic molecules with multiple turnover, under control of a photo-cleavable protecting group by exploiting the structural significance of
Reliable chemical synthesis of oligoribonucleotides (RNA) with 2′-O-[(triisopropylsilyl)oxy]methyl(2′-O-tom)-protected phosphoramidites
Pitsch, Stefan,Weiss, Patrick A.,Jenny, Luzi,Stutz, Alfred,Wu, Xiaolin
, p. 3773 - 3795 (2007/10/03)
A method for the introduction of the 2′-O-[(triisopropylsilyl)oxy]methyl (=tom) group into N-acetylated, 5′-O-dimethoxytritylated ribonucleosides is presented. The corresponding 2′-O-tom-protected phosphoramidite building blocks were obtained in pure form and were successfully employed for the routine synthesis of oligoribonucleotides on DNA synthesizers. Under DNA coupling conditions (2.5 min coupling time for a 1.5-μmol synthesis scale) and with 5-(benzylthio)-1H-tetrazole (BTT) as activator, 2′-O-tom-protected phosphoramidites exhibited average coupling yields >99.4%. The combination of N-acetyl and 2′-O-tom protecting groups allowed a reliable and complete two-step deprotection, first with MeNH2 in EtOH/H2O and then with Bu4NF in THF, without concomitant destruction of the product RNA sequences.
Fast and reliable automated synthesis of RNA and partially 2'-O- protected precursors ('caged RNA') based on two navel, orthogonal 2'-O- protecting groups. Preliminary communication
Pitsch, Stefan,Weiss, Patrick A.,Wu, Xiaolin,Ackermann, Damian,Honegger, Thomas
, p. 1753 - 1761 (2007/10/03)
Two sets of RNA phosphoramidites, carrying the (fluoride-labile) 2'-O- [(triisopropylsilyl)oxy]methyl (=tom) group and the (photolabile) [(R)-1-(2- nitrophenyl)ethoxy]methyl (= (R)-npeom) group, were prepared (see 1-4 and 5- 8, resp.). The two protecting groups were completely orthogonal to each other. Three ribozyme-substrate constructs, protected each by a (R)-npeom group, were synthesized; on photolysis, efficient cleavage of this remaining protecting group occurred (Scheme 3). It could be demonstrated that the presence of one (R)-npeom group within a RNA strand has only a minor influence on the pairing properties of corresponding duplexes.
