DNA Display I. Sequence-Encoded Routing of DNA Populations

Abstract

Recently reported technologies for DNA-directed organic synthesis and for DNA computing rely on routing DNA populations through complex networks. The reduction of these ideas to practice has been limited by a lack of practical experimental tools. Here we describe a modular design for DNA routing genes, and routing machinery made from oligonucleotides and commercially available chromatography resins. The routing machinery partitions nanomole quantities of DNA into physically distinct subpools based on sequence. Partitioning steps can be iterated indefinitely, with worst-case yields of 85% per step. These techniques facilitate DNA-programmed chemical synthesis, and thus enable a materials biology that could revolutionize drug discovery.

Nucleic Acid-programmed Assemblies: Translating Instruction into Function in Chemical Biology

“…Both DNA and PNA platforms have been used successfully to encode small molecule libraries with the first libraries reported in 2004. [25][26][27][28][29][30] PNA encoded synthesis (PES) is facilitated by the fact that it can be carried out using conventional solid phase synthesis. [31] Starting with a resin loaded with a bifunctional linker (such as lysine) bearing orthogonal protecting groups, the synthesis of the small molecule can be carried out alongside the PNA synthesis ( Fig.…”

Chemistry on Nucleic Acid Templates

“…This splits the library in subpopulations, which are eluted on a cationic resin, exposed to unique reaction conditions, and then repooled before another round DNA-programmed splitand-pool synthesis (Fig. 10) [124]. Following this protocol, Harbury and co-workers routed a 5'-amino functionalized 340mer single-stranded DNA through a series of ten anticodon columns, each recognizing a 20-base sequence on the DNA.…”

“…DNA Hybridization is not relevant during bond-formation, making a vast chemical repertoire available for the synthesis of encoded libraries [11]. DNA-Displayed libraries have been constructed using peptide-coupling reactions, nucleophilic displacement reactions involving amines and thiols, reductive aminations, electrophilic aromatic substitutions, periodate oxidations, and phosphine-based reductions [11] [125] [127], without detectable sign of DNA or peptide side-chain modification, as evident from MS, Edman degradation, and binding characteristics to the 3-E7 antibody [124].…”

Replicator Dynamics in Protocells

“…Recent advances in DNA chemistry demonstrate the possibility to "translate" the information stored in a nucleic acid sequence directly into non-polymeric compounds without the help of sophisticated enzymes (Calderone & Liu, 2004;Gartner & Liu, 2001;Halpin & Harbury, 2004). Such mechanisms might provide a physico-chemical basis for the direct influence of the genome on the lipid aggregate which is implicitly postulated by the function G( x, c a ) above.…”