A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy

Abstract

G-DNA is a polymorphic family of quadruple helical nucleic acid structures containing guanine tetrad motifs [G-quartets; Williamson, J.R., Raghuraman, M.K. and Cech, T.R. (1989) Cell 59, 871-880; Williamson, J.R. (1993) Proc. Natl. Acad. Sci. USA 90, 3124-3124]. Guanine rich oligonucleotides that are self-complimentary, as found in many telomeric G-strand repeat sequences, form G-DNA in the presence of monovalent and/or divalent metal cations. In this report we use the atomic force microscope (AFM) to explore the structural characteristics of long, linear polymers formed by the telomeric oligonucleotide d(GGGGTTGGGG) in the presence of specific metal cations. In the AFM these polymers, termed G-wires, appear as filaments whose height and length are determined by the metal ions present during the self-assembly process. The highly ordered, controllable self-assembly of G-wires could provide a basis for developing advanced biomaterials.

Auto-orientation of G-wire DNA on mica

“…The caged metal cations integrated into the G-wires may have some mobility [4]. In addition, the metal cations are sufficiently close to each other (about 0.3 nm) to support electron tunneling.…”

“…G-wire DNA molecules were prepared according to the technique developed by Marsh et al [4]. G-wires were grown from the G 4 T 2 G 4 monomer in a buffered solution of 50 mM NaCl, 10 mM MgCl 2 , 50 mM Tris-HCl pH 7.6 at 37 • C. One microliter aliquots of concentrated G-wire solution (original Tet1.5 oligonucleotide concentration: 0.12 g/l) were diluted in the either of the two following "imaging" buffers containing magnesium:…”

“…"G-wires" are formed by the self-assembly of G 4 T 2 G 4 (Tet1.5) monomers. In their seminal paper on G-wires, Marsh et al [4] first observed that the G-wires tended to orient in the absence of any external electric field, but the phenomena was not pursued. Though the auto-orienation was suggested to be the result of lattice alignment between the G-wires and mica, because the samples were imaged in air, the potential for drying artifacts could not be ruled out.…”

Scanning probe microscope visualization of t-loop assembly by TRF2 in cells

“…The average height of the tail-loop junction area is about 0.851 + 0.293 nm (Fig.3 A). Due to the height of triplex is two times that of duplex, so we conclude that the structure of junction area is triplex [21,22]. The height of some tail-loop junction is higher than above average height, it is 1.286 + 0.051 nm, suggesting tetra-stranded structure may exist the tail-loop junction models of triplex or two kinds of tetra-stranded were proposed (Fig.3 …”

Redox behaviour of G-quadruplexes

“…In addition, G-rich oligonucleotides are able to self-organize in quadruplex-based two-dimensional networks and long nanowires, relevant for nanotechnology applications [16][17][18][19][20][21].…”