Pieter van Delft

Pieter van Delft
Corbion | CORBION · Analytical sciences

PhD

About

25
Publications
3,917
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
595
Citations

Publications

Publications (25)
Article
Full-text available
In DNA, the loss of a nucleobase by hydrolysis generates an abasic site. Formed as a result of DNA damage, as well as a key intermediate during the base excision repair pathway, abasic sites are frequent DNA lesions that can lead to mutations and strand breaks. Here we present snAP-seq, a chemical approach that selectively exploits the reactive ald...
Article
Full-text available
Background5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. ResultsWe apply the method to generate genom...
Article
Chemically modified bases exist naturally in genomic DNA. Research into these bases has been invigorated by the discovery of several modified bases in the mammalian genome, in particular 5-methylcytosine and its oxidized derivatives, such as 5-(hydroxymethyl)cytosine and 5-formylcytosine, as well as the enzymes that form and process them, such as t...
Article
Full-text available
Chemically modified bases exist naturally in genomic DNA. Research into these bases has been invigorated by the discovery of several modified bases in the mammalian genome, in particular 5-methylcytosine and its oxidized derivatives, such as 5-(hydroxymethyl)cytosine and 5-formylcytosine, as well as the enzymes that form and process them, such as t...
Article
Full-text available
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, dynamic nature and their response to cellular and environmental stress. Mass spectrometry based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they...
Article
Full-text available
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, dynamic nature and their response to cellular and environmental stress. Mass spectrometry based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they...
Article
5-Hydroxymethylcytidine (hm$^{5}$C) was recently identified as a direct metabolite of m$^{5}$C in RNA. We investigated the stability of hm$^{5}$C in human cells using bio-isotopologues and LC-MS/HRMS. This has led to the discovery of a second oxidative metabolite of m$^{5}$C in RNA, namely 2′-$\textit{0}$-methyl-5-hydroxymethylcytidine (hm$^{5}$C$\...
Article
Background 5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. Results We apply the method to generate gen...
Article
Full-text available
5-hydroxymethylcytidine (hm5C) was recently identified as a direct metabolite of m5C in RNA. We investigated the stability of hm5C in human cells using bio-isotopomers and high-resolution tandem LC-MS/MS. This has led to the discovery of a second oxidative metabolite of m5C in RNA, namely 2'-O-methyl-5-hydroxymethylcytidine (hm5Cm). Subsequent quan...
Article
Full-text available
Biopolymers are an attractive alternative to store and circulate information. DNA, for example, combines remarkable longevity with high data storage densities and has been demonstrated as a means for preserving digital information. Inspired by the dynamic, biological regulation of (epi)genetic information, we herein present how binary data can unde...
Article
Full-text available
Biopolymers are an attractive alternative to store and circulate information. DNA, for example, combines remarkable longevity with high data storage densities and has been demonstrated as a means for preserving digital information. Inspired by the dynamic, biological regulation of (epi)genetic information, we herein present how binary data can unde...
Article
Full-text available
Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemical treatment causes strand scission, which depletes the number of sequenceable DNA fragments in a library and thus necessitates PCR amplification. The AT-rich nature of the library generated fro...
Article
The Lewis acid mediated reduction of ribose, arabinose, xylose and lyxose derived methyl- and phenyl-ketofuranoses with triethylsilane as nucleophile was found to proceed with good to excellent stereoselectivity to provide the 1,2-cis addition products. The methyl ketoses reacted in a more stereoselective manner than their phenyl counterparts. The...
Article
Full-text available
RNA methylation is emerging as a regulatory RNA modification that could have important roles in the control and coordination of gene transcription and protein translation. Herein, we describe an in vivo isotope-tracing methodology to demonstrate that the ribonucleoside 5-methylcytidine (m(5) C) is subject to oxidative processing in mammals, forming...
Article
A ribosyltriazole ring‐fused cyclooctyne was prepared and converted into the corresponding phosphoramidite, which was applied in the automated synthesis of DNA and RNA oligomers. Ensuing strain‐promoted alkyne–azide cycloaddition of the obtained oligonucleotides to fluorescent azides yielded the corresponding fluorescent oligonucleotide conjugates....
Article
Lewis acid mediated substitution reactions using [D]triethylsilane as a nucleophile at the anomeric center of the four pentofuranoses, ribose, arabinose, xylose, and lyxose, all proceed with good to excellent stereoselectivity to provide the 1,2-cis adducts. To unravel the stereoelectronic effects underlying the striking stereoselectivity in these...
Article
Lewis acid mediated substitution reactions using [D]triethylsilane as a nucleophile at the anomeric center of the four pentofuranoses, ribose, arabinose, xylose, and lyxose, all proceed with good to excellent stereoselectivity to provide the 1,2-cis adducts. To unravel the stereoelectronic effects underlying the striking stereoselectivity in these...
Article
The synthesis of two ribonucleoprotein fragments of unprecedented complexity is reported. These hybrid biomolecules are prepared combining the use of an automated solid phase peptide and oligonucleotide synthesizer on a single solid support.
Article
A set of four phosphoramidite building blocks containing a strained dibenzocyclooctyne moiety is reported, including one example equipped with a cleavable disulfide linker. Application of these amidites in solid-phase oligonucleotide synthesis yields either 5'-or 3'-cyclooctyne-modified nucleic acids. The strained cyclooctyne-bearing oligonucleotid...
Article
The conjugation of a ribonucleic acid 16-mer with the cationic amphiphilic peptide penetratin and an anionic hyaluronan tetrasaccharide by means of Cu-free "click" chemistry is reported. The alkyne-functionalized 16-mer was prepared by automated solid-phase synthesis, using a newly developed strained cyclooctyne phosphoramidite in the final couplin...
Article
A new method for the construction of pyrophosphates is reported based on the coupling of a sugar phosphate and a nucleoside phosphoramidite. The in situ formed phosphate-phosphite intermediate was subsequently oxidized with tBuOOH. Three UDP-N-acetylglucosamine derivatives were prepared using this one-pot procedure in good yields.

Network

Cited By