Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins (original) (raw)
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2015
Theoretical models of localized DNA reactions on platforms indicate potential benefits to conventional DNA hybridization reactions. Recently locality has been proposed as a novel approach to speed up DNA hybridization reactions as well as to minimize incorrect binding among DNA sequences. Here we experimentally report evidence for a 169-fold speedup of localized DNA hybridization chain reactions in the system consisting of six DNA hairpin gates bound to a DNA track. Introduction DNA hybridization reactions have been wellstudied in the past decade and widely used to perform complex state changes and computation in DNA-based molecular computing.1–6 In most systems where DNA hybridization reactions are used for molecular computing, the reactants need to exist in low concentration (in the nano molar range) to avoid unwanted spurious bimolecular interactions. Hence diffusion of certain low concentration reactants generally plays an important factor in determination of the overall time fo...
DNA Hairpins: Fuel for Autonomous DNA Devices
Biophysical Journal, 2006
We present a study of the hybridization of complementary DNA hairpin loops, with particular reference to their use as fuel for autonomous DNA devices. The rate of spontaneous hybridization between complementary hairpins can be reduced by increasing the neck length or decreasing the loop length. Hairpins with larger loops rapidly form long-lived kissed complexes. Hairpin loops may be opened by strand displacement using an opening strand that contains the same sequence as half of the neck and a ''toehold'' complementary to a single-stranded domain adjacent to the neck. We find loop opening via an external toehold to be 10-100 times faster than via an internal toehold. We measure rates of loop opening by opening strands that are at least 1000 times faster than the spontaneous interaction between hairpins. We discuss suitable choices for loop, neck, and toehold length for hairpin loops to be used as fuel for autonomous DNA devices.
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The Journal of Physical Chemistry B, 2019
The construction of functionalizable branched DNA (bDNA) relies on the designing of oligonucleotides and exploitation of their complementary chemistries. The stability of these structures largely depend on the hybridization specificity of the contributing oligonucleotides. However, most of the bDNA structures are not found suitable for in vivo application due to poor yield owing to uncharacterized hybridization efficiency and instability in biological fluids. In this report, our group has explored a mechanistic way for studying the hybridization pathway of genomic sequence derived oligonucleotides which are self-assembled to fabricate robust bDNA structures. The effect of change in nucleotide sequence on bDNA stability was studied by taking oligonucleotides derived from primers of different genes. Additionally, the stability of the bDNA in solutions with different pH, salts and DNaseI which mimics physiological environment was reported. It was found that genomic sequence derived oligonucleotides selfassembled in a cooperative manner to yield the designed bDNAs which are stable in physiological environment.
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Proceedings of the National Academy of Sciences, 2008
A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the ''rungs'' of the ladder are used to bring together the individual rings of the mechanically interlocked structure, and the ''rails'' are available for hierarchical assembly, whose effectiveness has been demonstrated with proteins, complementary DNA, and gold nanoparticles. The ability of this template to form from linear monomers and simultaneously bind two proteins was demonstrated by chemical force microscopy, transmission electron microscopy, and confocal fluorescence microscopy. Finally, fluorescence resonance energy transfer between adjacent fluorophores confirmed the programmed spatial arrangement between two different nanomaterials. DNA templates that bring together multiple nanostructures with precise spatial control have applications in catalysis, biosensing, and nanomaterials design.
2012
Self-assembly of oligonucleotides with designed sequence, is very valuable method for building fairy long linear DNA constructs. Studies of sequence-specific interaction between different ligands and single DNA molecules are becoming increasingly important. An approach toward this end is assembling DNA molecules by oligonucleotides hybridization in solution. In this project we attempted to construct double strand DNA concatemer (>500 base pairs) from two specific sequencedesigned 50bp oligonucleotides by hybridization and ligation. Due to complementary base pairing process, two single stranded oligos can spontaneously attach together and form long comcatemeric dsDNA molecules. Various incubation conditions such as oligos concentration, heating and hybridization time, salt and PEG concentration were checked to optimize the building of longer DNA constructs. Also enzyme ligation was performed successfully to join the nicks in the concatemers. Gel electrophoresis was employed to ver...
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Nanoparticles coated with single stranded DNA have been shown to efficiently hybridize to targets of complementary DNA. This property might be used to implement programmable (or algorithmic) self-assembly to build nanoparticle structures. However, we argue that a DNA coated nanoparticle by itself cannot be used as a programmable self-assembly building block since it does not have directed bonds. A general scheme for assembling and purifying nanoparticle eight-mers with eight geometrically well-directed bonds is presented together ...
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Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature’s assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.