Solution-Phase Synthesis of Branched DNA Hybrids via H-Phosphonate Dimers

Abstract

A method for the solution-phase synthesis of branched oligonucleotides with tetrahedral or pseudo-octahedral geometry is described that involves the coupling of 3'-H-phosphonates of protected dinucleoside phosphates and organic core molecules. The dimer building blocks are produced by a synthesis that requires no chromatographic purification and that produces the dimer H-phosphonates in up to 44% yield in less than three days of laboratory work. A total of seven different branched hybrids were prepared, including a new hybrid of the sequence (CG)(4)TBA, where TBA stands for tetrakis(p-hydroxybiphenyl)adamantane that assembles into a material from micromolar aqueous solution upon addition of MgCl(2).

Solution‐Phase Synthesis of Branched Oligonucleotides with up to 32 Nucleotides and the Reversible Formation of Materials

“…The intermediates of solution-phase syntheses are polar mixtures of diastereomers that readily lose their cyanoethyl protecting groups, all but precluding conventional chromatography on supports like silica. [39] At the beginning of our study, the favored assembly method was block condensation of the core with CG dimer "zipper" arms via H-phosphonate chemistry (Scheme 1a). [37,38] Finally, the purification of the final products can be challenging, as increasingly complex mixtures are being formed that have the ability to assemble into higher order structures, even in protected state.…”

“…Scheme 2. With the two cores in hand, we then synthesized DNA hybrids. [36,39] Preparation of dimer building block 11, [39] proceeded uneventfully. [36,39] Preparation of dimer building block 11, [39] proceeded uneventfully.…”

Encapsulating Active Pharmaceutical Ingredients in Self‐Assembling Adamantanes with Short DNA Zippers

“…Two different adamantane cores were used. The first is the tetrakis( p ‐hydroxybiphenyl)adamantane (TBA) core,27 with stiff spacers between the adamantane branching element and the DNA arms. The second core dubbed “TOA” features just the four hydroxy groups of adamantane tetraol as the attachment points for the DNA arms and was designed to form more hydrophilic lattices with smaller cavities 28.…”

“…The active pharmaceutical ingredients (APIs), fetal bovine serum (FBS) and water (Chromasolv for HPLC) were from Sigma Aldrich (Deisenhofen, Germany) or TCI Europe (Zwijndrecht, Belgium) and were used without further purification. The hybrids (CG) 4 TBA ( 1 ) and (CG) 4 TOA ( 2 ) were synthesized as described 27, 28. Thin layer chromatography (TLC) was performed with precoated silica gel sheets (SIL G/UV254 from Machery‐Nagel) with visualization by ultraviolet light (254 nm) or staining.…”

“…Because of multivalent interactions, dinucleotide arms of the sequence 5′‐CG‐3′ suffice to induce the formation of materials upon hybridization of hybrids with four, six or eight arms in aqueous buffer containing magnesium ions 24, 25. Efficient and scalable solution‐phase syntheses make these compounds available at a fraction of the cost of linear oligonucleotides 26, 27. Uptake of DNA staining agents demonstrated that the three‐dimensional networks can accommodate guest molecules in the solids formed upon hybridization,24, 27 but it was unclear whether drugs would be incorporated.…”