Abstract
We have fabricated a DNA-based nanofiber created by self-assembly of guanine quadruplex (Hoogsteen base pairing) and double-stranded DNA (Watson-Crick base pairing). When duplexes containing a long stretch of contiguous guanines and single-stranded overhangs are incubated in potassium-containing buffer, the preformed duplexes create high molecular weight species that contain quadruplexes. In addition to observation of these larger species by gel electrophoresis, solutions were analyzed by atomic force microscopy to reveal nanofibers. Analysis of the atomic force microscopy images indicates that fibers form with lengths ranging from 250 to 2,000 nm and heights from 0.45 to 4.0 nm. This work is a first step toward the creation of new structurally heterogeneous (quadruplex/duplex), yet controllable, DNA-based materials exhibiting novel properties suitable for a diverse array of nanotechnology applications.
Highlights
Programmable self-assembly from deoxyribonucleic acid (DNA) building blocks has led to a myriad of nanoscale structures, including 3D architectures [1,2,3,4,5,6,7,8]
We report the assembly of synapsable DNA-based nanofibers that constitute a novel DNA molecular manufacturing element
Tetramethylammonium chloride (TMACl), ammonium persulfate, mercaptoethanol, MgCl2, KCl, tris(hydroxymethyl) aminomethane (Tris), boric acid, and N-methylmesoporphyrin IX were biochemical grade or equivalent reagents purchased from commercial suppliers
Summary
Programmable self-assembly from deoxyribonucleic acid (DNA) building blocks has led to a myriad of nanoscale structures, including 3D architectures [1,2,3,4,5,6,7,8]. In DNA-based wires, tiles (double or triple crossover) [8,9,10,11], and DNA origami structures, canonical Watson-Crick base pairing drives and stabilizes formation of the desired structure. Non-canonical base pairing schemes are not typically exploited to create novel DNA-based materials [12], even though such interactions are in the lexicon of nucleic acid selfinteractions observed in biological systems [13,14,15,16,17,18,19,20,21,22,23]. Watson-Crick self-recognition was combined with non-canonical base pairing to create ‘synapsable’ DNA [24]. Each DNA strand in the unit created originally by Sen's group contains an internal run of eight guanines, which creates a
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