Nucleosides and Oligonucleotides with Diynyl Side Chains: Base Pairing and Functionalization of 2′‐Deoxyuridine Derivatives by the Copper(I)‐Catalyzed AlkyneAzide ‘Click’ Cycloaddition

Abstract

Oligonucleotides containing the 5‐substituted 2′‐deoxyuridines 1b or 1d bearing side chains with terminal CC bonds are described, and their duplex stability is compared with oligonucleotides containing the 5‐alkynyl compounds 1a or 1c with only one nonterminal CC bond in the side chain. For this, 5‐iodo‐2′‐deoxyuridine (3) and diynes or alkynes were employed as starting materials in the Sonogashira cross‐coupling reaction (Scheme 1). Phosphoramidites 2b–d were prepared (Scheme 3) and used as building blocks in solid‐phase synthesis. Tm Measurements demonstrated that DNA duplexes containing the octa‐1,7‐diynyl side chain or a diprop‐2‐ynyl ether residue, i.e., containing 1b or 1d, are more stable than those containing only one triple bond, i.e., 1a or 1c (Table 3). The diyne‐modified nucleosides were employed in further functionalization reactions by using the protocol of the CuI‐catalyzed Huisgen–Meldal–Sharpless [2+3] cycloaddition (‘click chemistry’) (Scheme 2). An aliphatic azide, i. e., 3′‐azido‐3′‐deoxythymidine (AZT; 4), as well as the aromatic azido compound 5 were linked to the terminal alkyne group resulting in 1H‐1,2,3‐triazole‐modified derivatives 6 and 7, respectively (Scheme 2), of which 6 forms a stable duplex DNA (Table 3). The Husigen–Meldal–Sharpless cycloaddition was also performed with oligonucleotides (Schemes 4 and 5).

Click chemistry with DNA

“…Melting experiments indicated that in all cases the octa-1,7-diynyl nucleosides have a positive influence on DNA duplex stability, more so than oligonucleotides functionalised with single alkynes. 22,23 Oligonucleotides containing the octadiynyl derivative of dU were also used in CuAAC reactions on solidphase and in solution to link the DNA strands to 3 0 -azidothymidine (AZT) and to an aromatic azide-compound. 22 In a related study, 7-alkynyl-7-deaza-2 0 -deoxyinosine was synthesised and used as a universal nucleoside.…”

“…22,23 Oligonucleotides containing the octadiynyl derivative of dU were also used in CuAAC reactions on solidphase and in solution to link the DNA strands to 3 0 -azidothymidine (AZT) and to an aromatic azide-compound. 22 In a related study, 7-alkynyl-7-deaza-2 0 -deoxyinosine was synthesised and used as a universal nucleoside. 24 The hypoxanthine base of deoxyinosine, which lacks the 2-amino-group of guanine, can form stable base pairs with guanine, thymidine and adenine, and to a lesser extent with cytosine.…”

Biocompatible artificial DNA linker that is read through by DNA polymerases and is functional in Escherichia coli

“…We recently described a highyielding DNA ligation method (click ligation) based on the CuAAC reaction (15,16). Click chemistry has been used extensively in the nucleic acids field (17)(18)(19)(20)(21) and it fulfils all the above criteria (22)(23)(24). We demonstrated that although the DNA triazole linkage is read through by PCR (Fig.…”

Crosslinking of viral nanoparticles with “clickable” fluorescent crosslinkers at the interface

“…This reaction has been extensively used in materials development [6][7][8][9], polymer synthesis [10,11], dendrimer synthesis [12][13][14][15][16] and drug discovery [17][18][19]. CuAAC reaction serves as a great tool for bioconjugation applications [20][21][22][23][24][25][26][27][28][29], mainly due to (i) facile synthesis and easy incorporation of alkyne and azide moieties into biomolecular frameworks, (ii) compatibility to other functionalities yielding highly specific products, (iii) compatibility to water which is crucial for biomolecular systems, (iv) mild reaction conditions which will help maintaining the properties of biomolecules, and (v) stability of the resulting triazole ring to the hydrolytic cleavage, oxidation and reduction [2,3,9].…”