Oligonucleotide design
This protocol is extracted from research article:
Nano-bio-computing lipid nanotablet
Sci Adv, Feb 22, 2019; DOI: 10.1126/sciadv.aau2124

Nanoparticles were functionalized with single-stranded DNA strands that contain thiol modifications at their 3′ or 5′ ends. DomainDesign (44, 45) was used to generate a set of orthogonal 10-nucleotide (nt) toeholds, 10-nt supporting domains, 14-nt binding domains, and 34-nt linker domains. These sequences were then verified using NUPACK (46) and further optimized if any undesirable interaction was detected during experiments. The thiolated DNA strands include (i) biotinylated linker DNA strands used for the tethering of nanoparticles to streptavidin-modified SLB surfaces and (ii) ligand DNA strands directly involved in the nanoparticle computing process. A linker strand with 5′-thiol modification contains (i) an A15 domain after a 5′-thiol group, (ii) six ethylene glycol (EG) units (a PEG moiety), and (iii) a linker domain followed by biotin modification. A linker strand with 3′-thiol modification (with biotin modification at 5′ end) contains (i) a linker domain, (ii) a PEG moiety, and (iii) an A15 domain followed by 3′-thiol modification. Ligand DNA strands were categorized into two types: “normal” single-stranded DNA strands that do not form hairpin loops and hairpin-type DNA ligands used in Assembly AND gate. The normal ligand type was further classified into two groups: one with 3′-thiol modification and another with 5′-thiol modification. A ligand with 5′-thiol modification contains (i) an A15 domain after 5′-thiol, (ii) a PEG moiety, (iii) a supporting domain, and (iv) a binding domain. A ligand with 3′-thiol modification contains (i) a binding domain, (ii) a supporting domain, (iii) a PEG moiety, and (iv) an A15 domain followed by 3′-thiol modification. Unless otherwise noted, receptor and floaters were functionalized with 3′ thiol ligands and 5′ thiol ligands. Hairpin-type DNA ligands were thiolated at 5′ end. Supporting domains were introduced to better expose binding domains to solution, thereby promoting the hybridization of the binding domains with input strands. The A15 domain and PEG moiety in each strand are essential parts of the design, as these two components enhance DNA hybridization on nanoparticle surfaces and decouple functional units (binding domains) from a core structure (nanoparticle) by providing optimal DNA density, reducing nonspecific interactions, and stretching out the binding domain. Sequences of thiolated strands are listed in table S2.

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