Coupling Across a DNA Helical Turn Yields a Hybrid DNA/Organic Catenane Doubly Tailed with Functional Termini

Abstract

Catenanes constructed from organic building blocks have been used in the demonstration of molecular devices such as positional switches, unidirectional motors, and other nanoscale functional materials. 1 In the nucleic acid world, catenanes have long been known; they are found in nature and are common in structural DNA nanotechnology. 2 Designed, all-DNA catenanes have been used as topological labels. 3 Crosslinks with organic linkages have been utilized to probe the structures and properties of DNA duplexes, hairpins, and higher order structures, such as t-RNA and ribozymes, 4 as well as to build DNA nanostructures and nanodevices. 5 In this paper, we describe the synthesis of a macrocycle that is prepared by formation of an amide linkage across one full turn of DNA, forming a tailed DNA/organic catenane containing 5'-and 3'-termini that are available for further functionalization.In prior work, we showed that 2'-pendent amines and carboxylates could be linked to form nylon along the phosphodiester backbone contour. 6 Our inquiry here began when we asked whether longer linkers could be used to attach polymeric components parallel to the helix axis. This target requires bridging approximately 35Å across a nucleic acid turn, which had not been reported previously (Fig. 1A), although there is now a report by Gothelf et al. 7 Tetraethylene glycol was used as a spacer into a carboxylate-functionalized uridine and undecaethylene glycol was incorporated into an aminefunctionalized uridine. The linker distances have not been optimized, although studies with tetraethylene glycol as spacer for both amine and caboxylate were unsuccessful.Three 16-mer ODNs 1, 2 and 3 were synthesized, where two modified uridines were separated by 8, 9 and 10 unmodified nucleotides, respectively. Cross-turn coupling using a DNA hairpin template gave > 97% yields of ODN 1 and 2, as estimated by MALDI-TOF spectra and denaturing gel electrophoresis, whereas the coupling yield of 3 was about 62 % (Table 1, Supporting Information). For further characterization, the coupled product was subjected to complete nuclease digestion followed by analysis to detect linked nucleotides. The detection of a polyethylene glycol (PEG)-amide linked uridine dimer by LCMS corroborated the formation of coupled products (Supporting Information).These data established the formula of the reaction product but did not distinguish between a newly formed linkage parallel to the helix axis (i.e., across the turn) versus along the phosphodiester backbone contour. However, templation of the reaction by a circular DNA template (Fig. 1A) would yield an interlocked complex only if the coupling reaction occurred across the turn. ODNs 1 and 2 paired with a 78-mer DNA circular template were subjected to E-mail: E-mail: james.canary@nyu.edu; E-mail: ned.seeman@nyu.edu. Supporting Information. Full experimental details including: Syntheses of phosphoramidites, MALDI-TOF MS of ODNs, LCMS analysis of complete nuclease digestion, denaturing gel analyses of catenane synthesis, exonucle...

Site-specific inter-strand cross-links of DNA duplexes

“…The syntheses of $U_N^5,U_C^5$, and $U_C^{16}$ were reported previously. 26, 30 The synthesis of $U_N^{16}$ phosphoramidite followed a route similar to earlier compounds and is described in the supporting information. After incorporation into nucleic acid strands, the monomers were coupled via amide bond formation to produce ICLs.…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…95 The same group have used longer linkers (2 0 -S-CH 2 CH 2 (OCH 2 CH 2 ) 11 NH 2 and 2 0 -S-(CH 2 ) 3 (OCH 2 CH 2 ) 4 COOH) such that when the amide bond is formed it bridges one helical turn of DNA. 96 Using shorter (C4) linkers it was possible to link together neighbouring nucleotides in an oligonucleotides through an amide bond. 97 All four RNA analogues bearing 2 0 -selenomethyl modifications have been prepared using TOM chemistry, and are for use in phasing of X-ray crystal structures.…”

“…The structure of a DNA duplex fully modified by 4 0 -thio sugars was found to exist as an A-form duplex which may account for its enhancing properties. 119 A solution structure has been reported for a duplex containing the rarer cis-anti cyclobutane thymine dimer (96). 210 To study the dynamics of methylation by adenine methyltransferases a solution structure of a duplexes containing a fully, hemior un-methylated GATC recognition sequence with N6-methyladenine were solved.…”

Distance Dependent Interhelical Couplings of Organic Rods Incorporated in DNA 4-Helix Bundles

“…To the best of our knowledge the only example of a DNA-directed interhelical coupling relies on a short distance amide formation (36), and the only two examples of longer distance couplings within the same helix are from Seeman et al (27). and our labs (35).…”