Hybridization Chain Reaction

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Roshan's picture
Hybridization Chain Reaction

I heard of a new technique called: Hybridization Chain Reaction based on chain reaction of recognition and hybridization events between two sets of DNA hairpin molecules. which offers an enzyme-free alternative to PCR.for the rapid detection of specific DNA sequences.

Does anyone know about this technique and kits that are available in the market?

omid's picture
Roshan wrote:I heard of a new

Roshan wrote:

I heard of a new technique called: Hybridization Chain Reaction based on chain reaction of recognition and hybridization events between two sets of DNA hairpin molecules. which offers an enzyme-free alternative to PCR.for the rapid detection of specific DNA sequences.

Does anyone know about this technique and kits that are available in the market?

In the polymerase chain reaction (PCR), recognition is provided by cequence-specific-hybridization of short oligonucleotides to a larger target, whereas signal amplification requires the use of a polymerase coupled with with extremely driven melting and rehybridization. The key to HCR ( Hybridization Chain Reaction ) is the storage of potential energy in two hairpin species. When a single-stranded DNA initiator is added to this previously stable mixture, it open the hairpin of one species, exposing a new
single stranded region that opens the hairpin of other species. This process, in turn, exposes a single-stranded region identical to the original initiator.

I don't think this method is commercialized but anyone is welcome to provide more information.

life analyzer
life analyzer's picture
I am also very insterested in

I am also very insterested in this technique, but it seems hard to get detailed information about the designing. Does anybody know how to design those two hairpin sequence and that initiator? How many bases for the loop, stem, and the initiator are the best way to make an efficient system? I would appreciate it if somebody can provide more informations about the design. Thanks.

Tony Rook
Tony Rook's picture
Here are some references and

Here are some references and abstracts concerning HCR:

Triggered amplification by hybridization chain reaction
Robert M. Dirks, and Niles A. Pierce
Departments of Chemistry and Applied and Computational Mathematics and Bioengineering, California Institute of Technology, Pasadena, CA 91125
PNAS | October 26, 2004 | vol. 101 | no. 43 | 15275-15278

We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in solution until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers. The average molecular weight of the HCR products varies inversely with initiator concentration. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.


Chain Reaction Systems Based on Loop Dissociation of DNA
Keiichiro Takahashi, Satsuki Yaegashi,
Atsushi Kameda and Masami Hagiya

In the field of DNA computing, more and more efforts are made for constructing molecular
machines made of DNA that work in vitro or in vivo. States of some of those machines are
represented by their conformations, such as hairpin and bulge loops, and state transitions are
realized by conformational changes, in which such loops are opened. The ultimate goal of this
study is to implement not only independent molecular machines, but also networks of interacting
machines, called chain reaction systems, where a conformational change of one machine triggers
a conformational change of another machine in a cascaded manner. A chain reaction system
would result in a much larger computational power than a single machine in the number of
states and in the complexity of computation. As a simple example, we propose a generalpurpose
molecular system consisting of logical gates and sensors. As a more complex example,
we present a new idea of constructing a DNA automaton by a chain reaction system, which can
have an arbitrary number of states.


Dirks, Robert Michael (2005-05-11)
Analysis, design, and construction of nucleic acid devices. http://resolver.caltech.edu/CaltechETD:etd-05242005-133116
PhD Dissertation

Nucleic acids present great promise as building blocks for nanoscale devices. To achieve this potential, methods for the analysis and design of DNA and RNA need to be improved. In this thesis, traditional algorithms for analyzing nucleic acids at equilibrium are extended to handle a class of pseudoknots, with examples provided relevant to biologists and bioengineers. With these analytical tools in hand, nucleic acid sequences are designed to maximize the equilibrium probability of a desired fold. Upon analysis, it is concluded that both affinity and specificity are important when choosing a sequence; this conclusion holds for a wide range of target structures and is robust to random perturbations to the energy model. Applying the intuition gained from these studies, a process called hybridization chain reaction (HCR) is invented, and sequences are chosen that experimentally verify this phenomenon. In HCR, a small number of DNA or RNA molecules trigger a system wide configurational change, allowing the amplification and detection of specific, nucleic acid sequences. As an extension, HCR is combined with a pre-existing aptamer domain to successfully construct an ATP sensor, and the groundwork is laid for the future development of sensors for other small molecules. In addition, recent studies on multi-stranded algorithms and improvements to HCR are included in the appendices. Not only will these advancements increase our understanding of biological RNAs, but they will also provide valuable tools for the future development of nucleic acid nanotechnologies.


DNA Hairpins: Fuel for Autonomous DNA Devices
Simon J. Green, Daniel Lubrich and Andrew J. Turberfield
Biophysical Journal 91:2966-2975 (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 10100 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