Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

Abstract

DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beam line NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences, as well as the impact of 5’- and 3’-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2- and 3-nt sticky ends all form crystals. X-ray diffraction data from the same beam line reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 Å and 4.2 Å respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5’-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1–2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1–2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends, as well as the use of 3’-sticky ends. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.

Supramolecular assembly of DNA-constructed vesicles

“…[5][6][7] Engineering short single-stranded overhangs, known as sticky ends, extend potential strategies for the assembly of DNA into nanostructures ranging from two-dimensional tiles, to three-dimensional DNA crystals, or nanocapsules. [8][9][10][11][12] Merging purely artificial DNA nucleotide surrogates with natural DNA nucleotides lead to DNA conjugates and the resulting functional supramolecular assemblies have recently gained much attention in the fields of nanotechnology and materials science. [13][14][15][16][17][18][19] Such functional supramolecular polymers feature properties beyond the classical role of DNA in biological systems, with applications in optoelectronic devices, drug delivery systems, and diagnostics to name a few.…”

Ribbon of DNA Lattice on Gold Nanoparticles for Selective Drug Delivery to Cancer Cells

“…Therepetitive unit within the RPs was designed to contain sequence elements capable of creating three in-unit duplexes (iuDP1,2,3) and two between-unit duplexes (buDP1,2). These pairing interactions were predicted to force each RP to form aribbon of DNAlattice (named RDL1 in Figure 1b).…”

“…[2] These two traits of DNAa llow for the design of user-defined 2D or 3D DNAa rchitectures that offer controllable flexibility and rigidity by rational combination of single-stranded and double-stranded DNAe lements. [3] The flexible single-stranded DNAelements in these structures are particularly attractive for functional realization as they permit the placement of functional DNAe lements,s uch as DNA aptamers and DNAzymes,i np redefined positions.…”

Bottom-Up Self-Assembly Based on DNA Nanotechnology

“…This work is considered to be a major breakthrough in the field of DNA nanotechnology. Since then, a lot of work has been carried out around the tensegrity triangle, such as controlling the crystal nucleation and growth process [ 38 ], improving the quality and stability of the single crystal [ 39 , 40 ], and completing dynamic changes [ 41 ].…”