Chemical synthesis of long RNAs with terminal 5′‐phosphate groups

Pradère, Ugo; Halloy, François; Hall, Jonathan

doi:10.1002/chem.201700514

Cited by 17 publications

(15 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Other phosphorylation agents exist. [29] Several routes to the target molecules of Figure 1 were considered. Conventional solid-phase peptide synthesis is performed from C-to N-terminus, so generating the peptide on the preassembled RNA chain, as in the synthesis of aminoacyl oligonucleotides [30,31] would require an unconventional approach, with carboxy-protected building blocks.…”

Section: Resultsmentioning

confidence: 99%

Synthesis of Peptido RNAs from Unprotected Peptides and Oligoribonucleotides via Coupling in Aqueous Solution

2020

View full text Add to dashboard Cite

Peptido RNAs are hybrid molecules with a phosphoramidate link between the N‐terminus of a peptide and the 5'‐phosphate of an oligoribonucleotide. Such species are formed in spontaneous co‐oligomerizations of amino acids and ribonucleotides in aqueous condensation buffer. To shed light on the properties of these fascinating molecules, a synthetic method for their preparation in monodisperse form is needed. Herein, we report how peptido RNAs can be prepared via solution‐phase coupling of unprotected peptides and oligoribonucleotides in aqueous solution. The preferred protocol uses pre‐activation of the 5'‐phosphate of the RNA as an imidazolide at pH 6.5, followed by precipitation and coupling to the peptide at pH 8 with an organocatalyst. The procedure gave peptido RNAs from water‐soluble peptides and synthetic oligoribonucleotides in up to 68 % yield. The method is convenient and inexpensive and can produce NMR quantities, opening the door to the systematic exploration of the chemistry of peptido RNAs.

show abstract

Section: Resultsmentioning

confidence: 99%

Synthesis of Peptido RNAs from Unprotected Peptides and Oligoribonucleotides via Coupling in Aqueous Solution

2020

View full text Add to dashboard Cite

show abstract

“…Upon completion of the automated solid-phase synthesis, oligoribonucleotides were cleaved from the solid support and deprotected with aqueous ammonia/methylamine solution, followed by standard desilylation protocol. After HPLC purification in the DMT-on mode and removal of the DMT group, the click reaction in solution with Cy5 azide 3 was performed as described, 52 followed by the HPLC purification in the DMT-off mode.…”

Section: Methodsmentioning

confidence: 99%

Site-Specific Fluorophore Labeling of Guanosines in RNA G-Quadruplexes

et al. 2019

Self Cite

View full text Add to dashboard Cite

RNA G-quadruplexes are RNA secondary structures that are implicated in many cellular processes. Although conventional biophysical techniques are widely used for their in vitro characterization, more advanced methods are needed to study complex equilibria and the kinetics of their folding. We have developed a new Förster resonance energy-transfer-based method to detect the folding of RNA G-quadruplexes, which is enabled by labeling the 2′-positions of participating guanosines with fluorophores. Importantly, this does not interfere with the required anti conformation of the nucleobase in a quadruplex with parallel topology. Sequential click reactions on the solid phase and in solution using a stop-and-go strategy circumvented the issue of unselective cross-labeling. We exemplified the method on a series of sequences under different assay conditions. In contrast to the commonly used end-labeling approach, our internal labeling strategy would also allow the study of G-quadruplex formation in long functional RNAs.

show abstract

“…A 5′-phosphorothioate cap was introduced via a dinitrobenzhydryl-phosphporamidite (DNB) as described previously in combination with a sulfurization step. 44 The 5′-DNB photocage was removed after sapphire deposition through irradiation at 365 nm for 30 min/side. All oligonucleotide sequences are given in 5′–3′ direction.…”

Section: Experimental Sectionmentioning

confidence: 99%

One- and Two-Dimensional High-Resolution NMR from Flat Surfaces

et al. 2019

Self Cite

View full text Add to dashboard Cite

Determining atomic-level characteristics of molecules on two-dimensional surfaces is one of the fundamental challenges in chemistry. High-resolution nuclear magnetic resonance (NMR) could deliver rich structural information, but its application to two-dimensional materials has been prevented by intrinsically low sensitivity. Here we obtain high-resolution one- and two-dimensional 31 P NMR spectra from as little as 160 picomoles of oligonucleotide functionalities deposited onto silicate glass and sapphire wafers. This is enabled by a factor >10 5 improvement in sensitivity compared to typical NMR approaches from combining dynamic nuclear polarization methods, multiple-echo acquisition, and optimized sample formulation. We demonstrate that, with this ultrahigh NMR sensitivity, 31 P NMR can be used to observe DNA bound to miRNA, to sense conformational changes due to ion binding, and to follow photochemical degradation reactions.

show abstract

Chemical synthesis of long RNAs with terminal 5′‐phosphate groups

Cited by 17 publications

References 21 publications

Synthesis of Peptido RNAs from Unprotected Peptides and Oligoribonucleotides via Coupling in Aqueous Solution

Synthesis of Peptido RNAs from Unprotected Peptides and Oligoribonucleotides via Coupling in Aqueous Solution

Site-Specific Fluorophore Labeling of Guanosines in RNA G-Quadruplexes

One- and Two-Dimensional High-Resolution NMR from Flat Surfaces

Contact Info

Product

Resources

About