A procedure is presented for copper(I)-catalyzed [3+2] cycloaddition of nucleosides and nucleotides in near-quantitative yield. Azido-alkyne cycloaddition was applied for the preparation of a range of adenosine dimers and derivatives with versatile functionality, as well as for the smooth condensation of two oligonucleotide strands. The described technology may find valuable application in the synthesis of oligonucleotide dimers and conjugates.

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Abstract:Copper-free click chemistry between cyclooctynes and azide is a mild, fast and selective technology for conjugation of oligonucleotides. However, technology for site-specific introduction of the requisite probes by automated protocols is scarce, while the reported cyclooctynes are large and hydrophobic. In this work, it is demonstrated that the introduction of bicyclo[6.1.0]nonyne (BCN) into synthetic oligonucleotides is feasible by standard solid-phase phosphoramidite chemistry. A range of phosphoramidite building blocks is presented for incoporation of BCN or azide, either on-support or in solution. The usefulness of the approach is demonstrated by the straightforward and high-yielding conjugation of the resulting oligonucleotides, including biotinylation, fluorescent labeling, dimerization and attachment to polymer.

The stabilizing effect of 7-propynylated 7-deazapurine nucleosides on DNA-hairpins and DNA-duplexes containing d(GA) mismatches was investigated. The corresponding oligonucleotides were synthesized using solid-phase synthesis. For this purpose, the phosphoramidite of 7-deaza-7-propynyl-2'-deoxyadenosine (3c) was prepared. The incorporation of 3c instead of dA into the tandem d(GA) base pair of a DNA-hairpin alters the secondary structure, but has a positive effect on the duplex stability. A complete replacement of the canonical nucleosides of the tandem d(GA) base pair by 3c and 7-deaza-7-propynyl-2'-deoxyguanosine results in a significant base pair stabilization.

.net)The syntheses and the fluorescence properties of 7H-3,6-dihydro-1,2,3-triazolo[4,5-d]pyrimidin-7-one 2'-deoxy-b-d-ribonucleosides ( 2'-deoxy-8-azainosine) 3 (N 3 ), 15 (N 2 ), and 16 (N 1 ) as well as of 1,2,3-benzotriazole 2'-O-methyl-b-or -a-d-ribofuranosides 6 (N 1 ) and 24 (N 1 ) are described. Also the fluorescence properties of 1,2,3-benzotriazole 2'-deoxy-b-d-ribofuranosides 4 (N 1 ) and 5 (N 2 ) are evaluated. From the nucleosides 3 ± 6, the phosphoramidites 19, 26a, 26b, and 28 are prepared and employed in solid-phase oligonucleotide synthesis. In 12-mer DNA duplexes, compound 3 shows similar ambiguous base-pairing properties as 2'-deoxyinosine (1), while the nucleosides 4 ± 6 show strong pairing with each other and discriminate very little the four canonical DNA constituents.Introduction. ± DNA-Duplex stability does not only depend on the horizontal interactions of the bases (H-bonding), but also vertical interactions (base stacking) are of utmost importance [1 ± 6]. These interactions are controlled by the properties of the nucleobases (regular or modified ones) but also by the structure of the sugar ± phosphate backbone (N or S sugar conformation, PNA, LNA) and the environmental conditions such as counter ions and H 2 O molecules. Within the series of base-modified oligonucleotides, a number of heterocyclic systems (hydrophilic or hydrophobic) were synthesized and incorporated in DNA or RNA for various purposes [6 ± 13]. This led to the development of the so-called universal or ambiguous nucleosides which are categorized into two types: i) those forming base pairs by H-bonding and ii) those stabilizing duplexes by stacking.The 2'-deoxyinosine (1) is one of the most widely used universal nucleosides for primers and probes in DNA technology. It forms H-bonds with all four natural constituents of DNA; however, a wide range of T m values is noticed [9] [10]. Earlier, we have studied the ambiguous base-pairing properties of the related 2'-deoxy-7-deazainosine (2) in DNA duplexes [11]. The oligonucleotides incorporating 2 show similar base-pairing properties to those of 2'-deoxyinosine (1), and 2 emerges also as a universal nucleoside. As almost all of the universal nucleosides decrease the T m values of the oligonucleotide duplexes, we were looking for analogous compounds not showing such drawbacks. Recently, it was reported that an additional N-atom in the 8-position of purines leads to duplex stabilization compared to the parent purines [12 ± 15]. This prompted us to synthesize 2'-deoxy-8-azainosine ( 7H-3,6-dihydro-1,2,3-triazolo[4,5-d]pyrimidin-7-one 2'-deoxy-b-d-ribonucleoside; 3; systematic numbering

Aryl-1,3-diones represent a promising new class of herbicidal acetyl-CoA carboxylase (ACCase) inhibitors. The original synthesis of this structural motif employed in the research phase involved a selenium oxide mediated oxidation, the use of diazoacetate and aryl lead reagents, and a low temperature oxidation of an aryl lithium intermediate, so it was not well suited to large scale synthesis. For kilogram scale synthesis of the two aryl-1,3-dione building blocks (3 and 4), we developed an alternative route which employs a manganese or manganese−copper catalyzed alkyl Grignard coupling and a semi-pinacol rearrangement of an epoxide as the key steps. The optimized conditions could be of general interest as scalable methods for the synthesis of 2-alkyl substituted benzaldehydes and of 2-aryl-1,3-diones.

2 0 -O-(3-(Furan-2-yl)propyl)adenosine was synthesized and evaluated for interstrand crosslink (ICL) formation in DNA duplexes. In situ oxidation of the furan moiety with NIS showed rapid crosslink formation to dA and dC, while dT and dG were inactive.Oligonucleotides that form interstrand crosslinks (ICLs) have found widespread applications in chemical biology research areas. Therefore, chemical and enzymatic methods have been developed to incorporate crosslinks into helical regions of DNA and RNA. 1 Examples include the synthesis of a duplex incorporating a preformed crosslinked dinucleotide 2,3 or postsynthetic modification of duplexes by bifunctional crosslinking reagents. 4,5 However, in some cases, the site-specific introduction of a crosslink is problematic due to formation of a mixture of monoadducts, intrastrand and interstrand crosslinks. Introduction of reactive moieties at a specific position within the duplex can circumvent the selectivity issue as is shown for photocrosslinking with 4-thiouridine, 6 5-bromouridine, 7 5-methyleneaminouridine 8 or 8-azidoadenosine. 9 Furthermore, a thio-modified oligonucleotide (ON) can form disulfide bonds post-synthetically. 10,11 However such ICLs are highly dependent on the proper positioning of thiol groups and, more importantly, require modification of both strands. More recent studies on site-specific ICL formation involve modified phenylselenyl derivatives of thymidine or 5-methyl-2 0 -deoxycytidine, 12 1,4-dioxobutane abasic lesion, 13 alkyl-connected 2-amino-6-vinylpurine 14 and 4-amino-6-oxo-2-vinylpyrimidine. 15 We have earlier developed a complementary methodology incorporating furan-modified 2 0 -amido-uridine and an acyclic building block to give a site-specific ICL upon oxidation with Nbromosuccinimide (NBS). 16,17 First crosslinking results obtained for the furan-modified 2 0 -amido-uridine with complementary adenine (A) were further extended into a more detailed selectivity study against all canonicals using a more synthetically accessible acyclic furanmodified building block. In the latter case, strong selectivity for crosslinking to its opposite canonical A or cytidine (C) was observed, without formation of crosslinks to neighboring or distant bases. 17 In this context, furan-modification on other canonicals than uridine and the potential impact on the crosslinking process have not been evaluated yet. From this point of view, we became interested in evaluating the scope of furan-modified purines for ICL. We here wish to report on the synthesis and incorporation of 2 0 -O-(3-(furan-2-yl)propyl)adenosine as a building block for crosslinking of DNA duplexes.From a synthetic point of view, 2 0 -modification was an obvious choice as nucleobase modification will in most cases be unfavourable for hybridization. Taking into account that 2,2 0 -anhydrointermediates are only feasible for pyrimidines, a 2 0 -amido modification of adenosine is difficult to achieve. Therefore, we decided to take advantage of our previously developed 2 0 -O-alkylation strategy ...