Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields.
The assembly, structure, and stability of DNA nanocages with the shape of truncated octahedra have been studied. The cages are composed of 12 double-stranded B-DNA helices interrupted by single-stranded linkers of thymidines of varying length that constitute the truncated corners of the structure. The structures assemble with a high efficiency in a one-step procedure, compared to previously published structures of similar complexity. The structures of the cages were determined by small-angle X-ray scattering. With increasing linker length, there is a systematic increase of the cage size and decrease of the twist angle of the double helices with respect to the symmetry planes of the cage structure. In the present study, we demonstrate the length of the single-stranded linker regions, which impose a certain degree of flexibility to the structure, to be the important determinant for efficient assembly. The linker length can be decreased to three thymidines without affecting assembly yield or the overall structural characteristics of the DNA cages. A linker length of two thymidines represents a sharp cutoff abolishing cage assembly. This is supported by energy minimization calculations suggesting substantial hydrogen bond deformation in a cage with linkers of two thymidines.
Oliveira
Cristiano Luis Pinto
CL
Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark.
Juul
Sissel
S
Jørgensen
Hanne Laerke
HL
Knudsen
Bjarne
B
Tordrup
David
D
Oteri
Francesco
F
Falconi
Mattia
M
Koch
Jørn
J
Desideri
Alessandro
A
Pedersen
Jan Skov
JS
Andersen
Felicie Faucon
FF
Knudsen
Birgitta Ruth
BR
D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D006860:Hydrogen Bonding; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D053838:Scattering, Small Angle; D013816:Thermodynamics; D013936:Thymidine / Q000737:chemistry; D014961:X-Ray Diffraction
D004277:DNA, Single-Stranded; D013936:Thymidine