Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

Abstract

Uniform conjugates combining a DNA aptamer (either anti-MUC1 or ATP aptamer) and a synthetic polymer segment were synthesized by automated phosphoramidite chemistry. This multistep growth polymer chemistry enables the use of both natural (i.e. nucleoside phosphoramidites) and non-natural monomers (e.g. alkyl-and oligo(ethylene glycol)phosphoramidites). Thus, in the present work, six different aptamer-polymer conjugates were synthesized and characterized by ion-exchange HPLC, circular dichroism spectroscopy and electrospray mass spectrometry. All these methods evidenced the formation of uniform molecules with precisely-controlled chain-length and monomer sequences. Furthermore, aptamer folding was not affected by polymer bioconjugation. The method described herein is straightforward and allows covalent attachment of homopolymers and copolymers to biofunctional DNA aptamers.

Design, Synthesis and Actual Applications of the Polymers Containing Acidic P–OH Fragments: Part 1. Polyphosphodiesters

“…High efficiency of the phosphoramidite approach was demonstrated mainly by Lutz and coll. in the preparation of sequence-defined PCPAs of different structures [ 109 , 111 , 113 , 114 , 115 ]. In particular, a series of sequence-defined poly(phosphodiester)s were synthesized based on a cross-linked polystyrene bead with the use of three monomers 0 – 2 ( Scheme 29 a) prepared from the corresponding 1,3-diols [ 113 ].…”

“…A carefully developed strategy of the synthesis of ‘artificial’ NAs was further used in the preparation of aptamer- b -poly(phosphodiester) conjugates containing conventional nucleic acid fragments [ 115 ]. Interesting examples of the use of phopshoramidite chemistry was reported by Serpell et al who have synthesized two sequence-isomeric polymers from dodecane diol (C12) and hexa(ethylene glycol) (HEG)-containing substrates, namely, C12 10 - b -HEG 10 block and (C12–HEG) 10 alternating copolymers [ 120 ] ( Scheme 30 ).…”

Chemical conjugation of nucleic acid aptamers and synthetic polymers

“…92,93 In a recent work of our group, phosphoramidite synthesis was investigated for the first time as a straightforward method for the synthesis of APCs. 94 Uniform conjugates combining a DNA aptamer segment (either anti-MUC1-or ATP-aptamer) and a synthetic polymer segment were successfully synthesized by using both natural and non-natural monomers (e.g. alkyl-and oligo(ethylene glycol)phosphoramidites) (Figure 5).…”

Synthesis of Linear and Cyclic Discrete Oligomers with Defined Sequences via Efficient Anionic Coupling Reaction

“…Recently, there have been increasing efforts in the preparation of monodisperse, or uniform, sequence-defined polymers that has been one of the biggest challenges in polymer science. − Most of the reported methodologies for preparing uniform macromolecules with specific sequences rely on multistep iterative addition of corresponding monomer units one by one in desired orders. − A number of orthogonal and efficient organic reactions have been applied for constructing sequence-defined macromolecules, such as radical addition − and single unit monomer addition (SUMI), − multicomponent reactions, − Pd-catalyzed C–C coupling reactions, − Williamson etherification, ,− thiolactone chemistry, − triazine-based chemistry, , photo-ligation, ,, boronate chemistry, phosphoramidite chemistry, − and click reactions such as thiol-ene, ,,,− azide-alkyne, ,− Diels–Alder reaction, − and sulfur-fluoride exchange reaction, among others. These reactions furnish chain growth either in divergent style, such as unidirectional …”