Effect of DNA hairpin loops on the twist of planar DNA origami tiles

Zhe Li, Lei Wang, Hao Yan, Yan Liu

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D) DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved.

Original languageEnglish
Pages (from-to)1959-1965
Number of pages7
JournalLangmuir
Volume28
Issue number4
DOIs
Publication statusPublished - Jan 31 2012

Fingerprint

tiles
Tile
DNA
deoxyribonucleic acid
Conformations
curvature
oligonucleotides
genome
Oligonucleotides
nanotechnology
Nanotechnology
ribbons
Atomic force microscopy
Genes
atomic force microscopy
mechanical properties
computer programs
Mechanical properties

ASJC Scopus subject areas

  • Electrochemistry
  • Condensed Matter Physics
  • Surfaces and Interfaces
  • Materials Science(all)
  • Spectroscopy

Cite this

Effect of DNA hairpin loops on the twist of planar DNA origami tiles. / Li, Zhe; Wang, Lei; Yan, Hao; Liu, Yan.

In: Langmuir, Vol. 28, No. 4, 31.01.2012, p. 1959-1965.

Research output: Contribution to journalArticle

Li, Zhe ; Wang, Lei ; Yan, Hao ; Liu, Yan. / Effect of DNA hairpin loops on the twist of planar DNA origami tiles. In: Langmuir. 2012 ; Vol. 28, No. 4. pp. 1959-1965.
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