5 research outputs found
Copper-free dual labeling of DNA by triazines and cyclopropenes as minimal orthogonal and bioorthogonal functions
Two different and small functions for inverse electron demand Diels-Alder reactions were applied for dual labeling of DNA: the 1,2,4-triazine was attached to the 5-position of 2'-deoxyuridine triphosphate, and the 1-methylcyclopropene to the 7-position of 7-deaza-2'-deoxyadenosine triphosphate. These two modified nucleotides were sequence-selectively incorporated into oligonucleotides by DNA polymerases. These products were labeled by two different fluorescent dyes using postsynthetic reactions that are not only bioorthogonal in general, but also mutually orthogonal.status: publishe
Scope and limitations of typical copper-free bioorthogonal reactions with DNA: Reactive 2â-deoxyuridine triphosphates for postsynthetic labeling
Four triphosphates
of 2âČ-deoxyuridine that carried the following
bioorthogonally reactive groups were synthesized by organicâchemical
methods. Two triphosphates with tetrazines and one with a cyclopropene
moiety were designed for DielsâAlder reactions with inverse
electron demand, and one triphosphate with a tetrazole core was designed
for the âphotoclickâ cycloaddition. These triphosphates
were not only successfully applied for oligonucleotide preparation
by standard DNA polymerases, including Hemo KlenTaq, Vent, and Deep
Vent, but also bypassed for full length primer extension products.
Fluorescent labeling of the primer extension products was achieved
by fluorophores with reactive counterparts and analyzed by polyacrylamide
gel electrophoresis mobility shifts. The tetrazineâoligonucleotide
conjugates were reacted with carboxymethylmonobenzocyclooctyne- and
bicyclononyne-modified fluorophores. The yield of these postsynthetic
reactions could significantly be improved by a more stable but still
reactive nicotinic acid-derived tetrazine and by changing the key
experimental conditions, mainly the pH of 7.2 and the temperature
of 45â55 °C. The cyclopropeneâoligonucleotide conjugate
could be successfully labeled with a tetrazine-modified rhodamine
in very good yields. The âphotoclickâ cycloaddition
between tetrazoleâoligonucleotide conjugates and a maleimide-modified
dye worked quantitatively. The combination of primer extension, bypass,
and bioorthogonal modification works also for double and triple labeling
using the cyclopropene-modified 2âČ-deoxyuridine triphosphate