Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins

Abstract

DNA self-assembly has been employed non-conventionally to construct nanoscale structures and dynamic nanoscale machines. The technique of hybridization chain reactions by triggered selfassembly has been shown to form various interesting nanoscale structures ranging from simple linear DNA oligomers to dendritic DNA structures. Inspired by earlier triggered self-assembly works, we present a system for controlled self-assembly of linear cascade DNA hybridization chain reactions using nine distinct DNA hairpins. NUPACK is employed to assist in designing DNA sequences and Matlab has been used to simulate DNA hairpin interactions. Gel electrophoresis and ensemble fluorescence reaction kinetics data indicate strong evidence of linear cascade DNA hybridization chain reactions. The half-time completion of the proposed linear cascade reactions indicates a linear dependency on the number of hairpins.

Localized DNA Hybridization Chain Reactions on DNA Origami

“…The loop consists of two clamp domains (C i–1 and C i+1 ), a linker domain (L), and a sequestered domain (S i+1 ). The two clamp domains were used to prevent a hairpin from reclosing via a localized blunt-end displacement once it has been opened near both ends of the hairpin’s stem. , The purposes of the loop are (i) to encode the sequestered domain for the cascade reaction and (ii) to fasten the cargo (S i+1 ) from floating away to solution. Each hairpin has two toehold domains (S i and S i+1 ): S i is an external toehold domain and readily available for hybridization and S i+1 is an internal toehold domain and unavailable for hybridization.…”

Renewable Time‐Responsive DNA Circuits

“…Recent advances in DNA‐based computation have been proposed and experimented with DNA motifs that are localized on a surface. Recently our work has already produced empirical results that show computation on a DNA substrate using the DNA hairpin motif . It is conceivable that our time‐responsive design could also be localized on a substrate.…”

DNA Microsystems for Biodiagnosis

“…For instance, a double-stranded DNA duplex with an overhang at the 5 /3 end is used as the basis. Multiple individual bases are then programmed in a cascade reaction for achieving linear forward motions [118]. In general, the field of dynamic DNA nanotechnology aims to design systems that are often inspired by the behavior of molecular protein motors.…”

“…Furthermore, scalability is another current issue in the field, since it is necessary to implement practical functionalities in order to make the structures more advantageous [125]. Likewise, reliable sequence design and oligonucleotide synthesis are fundamental for the development of functional DNA structures [114,118].…”