851 research outputs found
Furan-PNA : a mildly inducible irreversible interstrand crosslinking system targeting single and double stranded DNA
We here report on the design and synthesis of tailor-made furan-modified peptide nucleic acid (PNA) probes for covalent targeting of single stranded DNA through a crosslinking strategy. After introducing furan-containing building blocks into a PNA sequence, hybridization and furan-oxidation based crosslinking to DNA is investigated. The structure of the crosslinked products is characterized and preliminary investigations concerning the application of these systems to double stranded DNA are shown
Exploiting double exchange Diels-Alder cycloadditions for immobilization of peptide nucleic acids on gold nanoparticles
The generation of PNA-decorated gold nanoparticles (AuNPs) has revealed to be more difficult as compared to the generation of DNA-functionalized ones. The less polar nature of this artificial nucleic acid system and the associated tendency of the neutral poly-amidic backbone to aspecifically adsorb onto the gold surface rather than forming a covalent bond through gold-thiol interaction, combined with the low solubility of PNAs itself, form the main limiting factors in the functionalization of AuNP. Here, we provide a convenient methodology that allows to easily conjugate PNAs to AuNP. Positively charged PNAs containing a masked furan moiety were immobilized via a double exchange Diels-Alder cycloaddition onto masked maleimide-functionalized AuNPs in a one-pot fashion. Conjugated PNA strands retain their ability to selectively hybridize with target DNA strands. Moreover, the duplexes resulting from hybridization can be detached through a retro-Diels-Alder reaction, thus allowing straightforward catch-and-release of specific nucleic acid targets
Development and validation of ultra-high-performance liquid chromatography-tandem mass spectrometry methods for the simultaneous determination of beauvericin, enniatins (A, A1, B, B1) and cereulide in maize, wheat, pasta and rice
Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce
Automated synthesis of monodisperse oligomers, featuring sequence control and tailored functionalization
Long, multifunctional sequence-defined oligomers were obtairred on solid support from a protecting-group-free two-step iterative protocol, based on the inherent reactivity of a readily available molecule containing an isocyanate and a thiolactone. Aminolysis of the latter entity with an amino alcohol liberates a thiol that reacts with an acrylate or acrylamide, present in the same medium. Subsequently, a new thiolactone can be reinstated by means of an alpha-isocyanato-gamma-thiolactone. Different acrylic compounds were used to incorporate diverse functionalities in the oligomers, which were built up to the level of decanters. The reaction conditions were closely monitored in order to fine-tune the applied strategy as well as facilitate the translation to an automated protocol
Furan-modified oligonucleotides for fast, high-yielding and site-selective DNA inter-strand cross-linking with non-modified complements†
Among the various types of DNA damage, inter-strand cross-links (ICL) represent one of the most cytotoxic lesions. Processes such as transcription and replication can be fully blocked by ICLs, as shown by the mechanism of action of some anticancer drugs. However, repair of ICLs can be a possible cause of resistance. To study the mechanisms of cross-link repair stable, site-specifically cross-linked duplexes are needed. We here report on the synthesis of site-specifically cross-linked DNA using an acyclic furan containing nucleoside. Selective in situ oxidation of the incorporated furan moiety generates a highly reactive oxo-enal that instantly reacts with the complementary base in a non-modified strand, yielding one specific stable cross-linked duplex species. Varying sequence context showed that a strong selectivity for cross-linking to either complementary A or complementary C is operating, without formation of cross-links to neighboring or distant bases. Reaction times are very short and high isolated yields are obtained using only one equivalent of modified strand. The formed covalent link is stable and the isolated cross-linked duplexes can be stored for several months without degradation. Structural characterization of the obtained ICL was possible by comparison to the natural mutagenic adducts of cis-2-butene-1,4-dial, a metabolite of furan primarily responsible for furan carcinogenicity
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