A mildly inducible and selective cross-link methodology for RNA duplexes

Carrette, Lieselot L. G.; Gyssels, Ellen; Loncke, Joke; Madder, Annemieke

doi:10.1039/c3ob42374c

Cited by 26 publications

(37 citation statements)

References 33 publications

(32 reference statements)

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“…A versatile crosslinking approach based on furans was recently introduced by Madder and co‐workers, and has been employed to study a large variety of biomolecular interactions, including DNA–DNA,2 RNA–RNA,3 protein–DNA4 and protein–RNA 5. This crosslinking chemistry is based on the pronounced propensity of furans to undergo oxidative conversion to highly electrophilic ene‐1,4‐diones in an aqueous environment; these readily react with DNA and RNA nucleobases bearing exocyclic amino groups (Scheme ) 2b.…”

Section: Methodsmentioning

confidence: 99%

Seaweed‐Derived Heteroatom‐Doped Highly Porous Carbon as an Electrocatalyst for the Oxygen Reduction Reaction

et al. 2014

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We report the template-free pyrolysis of easily available natural seaweed, Undaria pinnatifida, as a single precursor, which results in "seaweed carbon" (SCup). Interestingly, thus-obtained SCup not only contains heteroatoms such as nitrogen and sulfur in its framework, but it also possesses a well-developed porous structure with high surface area. The heteroatoms in SCup originate from the nitrogen- and sulfur-containing ingredients in seaweed, whereas the porosity is created by removal of salts inherently present in the seaweed. These essential and fundamental properties make seaweed a prime choice as a precursor for heteroatom-containing highly porous carbon as a metal-free efficient electrocatalyst. As-synthesized SCup showed excellent electrocatalytic activity in the oxygen reduction reaction (ORR) in alkaline medium, which can be addressed in terms of the presence of the nitrogen and sulfur heteroatoms, the well-developed porosity, and the electrical conductivity in the carbon framework. The pyrolysis temperature was a key controlling parameter that determined the trade-off between heteroatom doping, surface properties, and electrical conductivity. In particular, SCup prepared at 1000 °C showed the best ORR performance. Additionally, SCup exhibited enhanced durability and methanol tolerance relative to the state of the art commercial Pt catalyst, which demonstrates that SCup is a promising alternative to costly Pt-based catalysts for the ORR.

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Section: Methodsmentioning

confidence: 99%

Seaweed‐Derived Heteroatom‐Doped Highly Porous Carbon as an Electrocatalyst for the Oxygen Reduction Reaction

et al. 2014

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“…The crosslinking reaction occurred specifically with the A and C nucleobases of the DNA targets in a 13–57 % yield [20] . Similar crosslinking reactions were also applicable to RNA targets, and a specific crosslinking product was observed with a complementary C base in a 42 % yield [21] . Furthermore, crosslinkable ODN probes were applied to target double‐stranded DNA by triplex formation [22] .…”

Section: Introductionmentioning

confidence: 90%

Pyrrolidinyl Peptide Nucleic Acid Probes Capable of Crosslinking with DNA: Effects of Terminal and Internal Modifications on Crosslink Efficiency

Muangkaew

Vilaivan

2020

ChemBioChem

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In this study, we describe a furan-modified acpcPNA as a probe that can form an interstrand crosslink (ICL) with its DNA target upon activation with N-bromosuccinimide (NBS). To overcome the problem of furan instability under acidic conditions, a simple and versatile post-synthetic methodology for the attachment of the furan group to the PNA probe was developed. Unlike in other designs, the furan was placed at the end of the PNA molecule or tethered to the PNA backbone with all the base pairs in the PNA • DNA duplexes fully preserved. Hence, the true reactivity of each nucleobase towards the crosslinking could be compared. We show that all DNA bases except T could participate in the crosslinking reaction when the furan was placed at the end of the PNA strand. The crosslinking process was sensitive to mispairing, and lower crosslinking efficiency was observed in the presence of a base-mismatch in the PNA • DNA duplex. In contrast, when the furan was placed at internal positions of the acpcPNA • DNA duplex, no ICL was observed; this was explained by the inability of a hydrogenbonded nucleobase to participate in the crosslinking reaction. The crosslinking efficiency was considerably improved, despite lower duplex stability, when an unpaired base (in the form of Cinsertion) was present in the complementary DNA strand close to the furan modification site.

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“…In recent years, applications of ODNs have extended to emerging areas such as nanotechnology [8–9], antisense drug development [10–12], DNA damage and repair [13–14], DNA methylation and demethylation [15–18], DNA–protein interactions [19–20], CRISPR genome editing [21–23], DNA data storage [24–25], synthetic biology [26], bioconjugation [27] and others [28–30]. These applications frequently require modified ODNs that contain a wide variety of functional groups including those that cannot survive known ODN synthesis, cleavage and deprotection conditions.…”

Section: Introductionmentioning

confidence: 99%

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

Shahsavari¹,

Eriyagama²,

Halami³

et al. 2019

Beilstein J. Org. Chem.

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Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, α-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within the ODN sequences without using any sequence- or functionality-specific conditions and procedures.

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A mildly inducible and selective cross-link methodology for RNA duplexes

Cited by 26 publications

References 33 publications

Seaweed‐Derived Heteroatom‐Doped Highly Porous Carbon as an Electrocatalyst for the Oxygen Reduction Reaction

Seaweed‐Derived Heteroatom‐Doped Highly Porous Carbon as an Electrocatalyst for the Oxygen Reduction Reaction

Pyrrolidinyl Peptide Nucleic Acid Probes Capable of Crosslinking with DNA: Effects of Terminal and Internal Modifications on Crosslink Efficiency

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

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