CRISPR-Based Tool Expands DNA-Hydrogel Versatility
CRISPR-Based Tool Expands DNA-Hydrogel Versatility

CRISPR-Based Tool Expands DNA-Hydrogel Versatility

DNA-responsive polymer gels used for releasing drugs, encapsulating cells, and much more now have greater adaptability thanks to the Cas12a nuclease.

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Ruth Williams

Ruth is a freelance journalist and regular correspondent for The Scientist, writing news for the website and monthly Modus Operandi articles for the magazine. Before freelancing, Ruth was a...

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Dec 1, 2019

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DNA is more than just a genetic molecule. Its physical structure and predictable behavior also make it a versatile biological building material. Indeed, DNA has been used to create nanoscale robots, patterns, and 3-D structures for various purposes, and it has been incorporated into hydrophilic polymer gels (hydrogels) for a variety of innovative applications, including biosensing, drug delivery, and more. 

But such gels have limited versatility, says Max English, a graduate student in the laboratory of MIT bioengineer Jim Collins. Often, DNA-containing gels are designed with strands that are complementary to the intended DNA activators. This means that “whenever you want to design a material that responds to a different [DNA] cue, you have to redesign the material in its entirety,” English explains. 

SEQUENCE-DIRECTED GEL DEGRADATION: One potential application for DNA-containing hydrogels is to encapsulate cells or particles to be released in response to a particular DNA stimulus. The hydrogel, which contains single-stranded DNA molecules cross-linked at bridges, is degraded via the collateral cleavage action of Cas12a when the enzyme is triggered by a guide RNA (gRNA) that corresponds to the double-stranded DNA stimulus. The payload is then released. WEB | PDF
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To avoid such overhauls, English and colleagues created a system for making  DNA-containing gels that are capable of responding to nearly any DNA cue simply by providing the CRISPR system’s Cas12a nuclease and a guide RNA (gRNA) that matches the desired DNA trigger. The team exploited a feature of Cas12a called collateral cleavage, in which the enzyme, after cutting its target double-stranded (ds) DNA, nonspecifically chops up surrounding single-stranded (ss) DNAs. The hydrogels are thus fabricated with ssDNAs that are cleaved by Cas12a when, and only when, a given gRNA and dsDNA combination is present. 

Using this principle, the team created DNA-containing hydrogels that, in response to a dsDNA cue provided by the researchers, could either release DNA-bound compounds or fully degrade. Such degradation could be used for applications such as liberating encapsulated contents like cells or nanoparticles, initiating flow of a buffer through a microfluidic device, or opening an electrical circuit. These last two examples could potentially be used in diagnostic devices, says Collins, with a change in buffer flow or electrical output signaling the presence of a DNA sequence of interest in a patient sample. 

“They showed some really novel applications of responsive hydrogels,” says Rebecca Schulman, a chemical and biomolecular engineer at Johns Hopkins University who did not participate in the study, in an email to The Scientist.

“Their approach is totally customizable . . .  [and] is really cleverly designed,” adds bio-engineer Dan Luo of Cornell University who was not involved in the research. “It’s a real integration of molecular biology and materials science.” (Science, 365:780–85, 2019)


Hydrogel ActivationHow it worksSensitivityVersatility
Via complementary strandsA gel that contains cross-linked DNA strands can be dissolved or expanded when a complementary DNA strand binds and either displaces or extends the crosslinks.Low, because each molecule of activating DNA targets just one cross-linked strandLimited. Each gel must be redesigned to match each input DNA.
Via CRISPR-based system
The Cas12a nuclease cuts ssDNAs within hydrogels when given a particular dsDNA cue along with a matching gRNA.
High, because Cas12 cuts multiple ssDNAs within the gel for each dsDNA molecule.
High. Each gel can be specifically activated by nearly any gRNA/dsDNA combination.
 

Ruth Williams is a freelance journalist based in Connecticut. Email her at ruth@wordsbyruth.com or find her on Twitter @rooph.