While we released a preprint manuscript [2] on our findings shortly, it was late in a certain sense. ‘Same concept from Jiao et al. Science (Apr 2021). Powerful nevertheless.’, one peer who is engaged in related research commented on Twitter. At that point, my mood was a little complicated. I’m happy to see the outstanding achievement from our peers, giving the mutual validation of discoveries from nature and SynBio. But a bit disappointed when people believe that our research is based on another similar work.

At the end of 2021, I finished my postdoc work and relocated to Cambridge to join my family. When I was invited to write a blog about the story behind this article, my mind went back to Edinburgh to recall how we started this study.

The exploration of the programmability of crRNA-tracrRNA paring was based on engineering needs. When I arrived in Edinburgh in 2016, my mission was to develop a programmable cellular computing system. The programmable AND gate is a tempting goal. Particularly, the CRISPR/Cas9 system is initially a dual-RNA-guided system, and it’s not hard to imagine that we can make many orthogonal AND gate devices if the crRNA-tracrRNA pairing is programmable.

The idea above is not a castle in the sky. In the same year I started my PhD study, Ma et al. published an exciting paper about using sgRNAs to recruit fluorescent proteins for genomic loci labeling [3]. Their sgRNA optimization made a deep impression: the U-A pair was mutated to G-C in the sgRNA tetraloop stem to enhance the CRISPR function (also often seen in the stgRNA to create a PAM for CRISPR recording [4]). This design gave me the concept that the wild-type sequence of the crRNA-tracrRNA pairing is not strictly conserved and can be replaced and improved. I also adopted this strategy to design our CRISPRa system [5].

Additionally, I found that the programmability of crRNA and tracrRNA pairing regions has been indirectly supported by two previous research. In 2012, Jinek et al. showed that the Streptococcus pyogenes Cas9 is functional when bound to tracrRNA:crRNA of Listeria innocua, although the RNA pairing sequence differences are not within the core region [6]. In 2014, Briner et al. reported that replacing RNA base pairs inside the sgRNA tetraloop stem does not destroy the CRISPR function [7]. During our research, such clues continued to emerge. In 2019, Reis et al. reported nonrepetitive extra-long sgRNA arrays, which were obtained by large-scale reprogramming of sgRNA scaffold including the tetraloop stem [8]. In 2020, Harrington et al. reported scoutRNA and Cas12d. For the comparison of Cas12d to Cas9, compensatory mutations were made in the pairing regions of crRNA and tracrRNA [9].

For exploring the idea of reprogrammed crRNA-tracrRNA pairing, we first created a dual-RNA mediated CRISPRa system, leading to surprising results. SpCas9 is largely tolerant of sequence changes within the crRNA-tracrRNA pairings.

We immediately realized that any RNAs may become crRNA. Since the crRNA mainly consists of a spacer region paired with the target DNA and a repeat region paired with the tracrRNA. If these two parts are both variable, then a fixed conserved sequence is not required for a crRNA.

We randomly selected and tested several sites in the mRNA of RFP as the targets of tracrRNA to activate a reporter circuit with GFP as the output. When the green fluorescence signal induced by RFP mRNA showed an amazing linear relationship with the red fluorescence, ‘I can finally be awarded my PhD.’, I told my lab colleagues.

Over the next year, we conducted several experiments to study the sequence preference issue. Primarily, we tried to understand how to predict what sequence on a piece of RNA would be the most functional tracrRNA target. However, we found it isn’t easy to find a rule. Complete mRNAs and the mRNA fragments behaved differently for the same target sequence, indicating sequence context can strongly influence the availability of a target site. When this factor was incorporated into the sequence preference on dual-RNA paring of Cas9, it was hard to provide a simple strategy for the target site selection.

We planned to demonstrate the enormous potential of this discovery through several independent applications, of which I was most tempted is to hijack endogenous RNA for CRISPR gene regulation. For many years, my coveted synthetic biology tool has been a programmable ‘genetic network connector’ with a simple elegant mechanism. By simply changing the tracrRNA sequence, endogenous transcripts can be linked to the specified artificial gene circuit and can be further linked to the behavior of other genes in the genome. The reprogramming of genetic networks will then become easy and efficient to achieve. Finally, we make it happen. By hijacking endogenous small RNAs and mRNAs, we monitored how the bacterial genome responds to arsenic, lead, zinc, hydrogen peroxide, and other substances in the environment.

In another separate application, we developed an in vitro RNA sensor. Initially, this sub-project aimed to design an RNA sensor array with reprogrammed tracrRNAs for multi-channel bacterial 16S rRNA detection. However, the COVID-19 outbreak prompted us to switch to creating an in vitro sensor for viral RNA. This device was first named CRISPR-operated nuclear acid amputation notification (CONAN), as a tribute to the pioneers of CRISPR RNA sensors. However, when we found that CONAN was already being used, we finally named it an Atypical gRNA-activated Transcription Halting Alarm (AGATHA) system, as a tribute to another of my favorite detective literature masters, Agatha Christie.

All in all, I’m glad that this work has finally been officially published. Thanks to all co-authors for their contributions and to friends for their support. I hope this research will inspire more great ideas for programming biology.

Our paper:

Liu, Y., Pinto, F., Wan, X. et al. Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors. Nat Commun 13, 1937 (2022). https://doi.org/10.1038/s41467-022-29604-x

References

1. Jiao, C. et al. Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science 372, 941-948, (2021).

2. Liu, Y. et al. Reprogrammed tracrRNAs enable repurposing RNAs as crRNAs and detecting RNAs. bioRxiv, (2021).

3. Ma, H. H. et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34, 528-530, (2016).

4. Perli, S. D., Cui, C. H. & Lu, T. K. Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353, (2016).

5. Liu, Y., Wan, X. Y. & Wang, B. J. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat commun 10, (2019).

6. Jinek, M. et al. A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 337, 816-821, (2012).

7. Briner, A. E. et al. Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality. Mol Cell 56, 333-339, (2014).

8. Reis, A. C. et al. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nat Biotechnol 37, 1294–1301, (2019).

9. Harrington, L. B. et al. A scoutRNA Is Required for Some Type V CRISPR-Cas Systems. Mol Cell 79, 416-424, (2020).

Intein-assisted Bisection Mapping (IBM) Credit: Baojun Wang

A new method of breaking and fixing proteins could speed the development of sophisticated computer-like circuits in cells that will pave the way to new biotechnology and medical advances.

The advance will make it easier to engineer cells that are programmed to behave as diagnostics or biological sensors—patrolling the body to detect disease or identifying toxins in the environment.

It could also provide a faster, cheaper and easier method of assembling large ‘designer’ proteins with many applications, such as antibodies or those used in vaccines or cell-based therapies.

The technique expands the synthetic biology toolkit, allowing proteins to be programmed to control the behavior of complex systems inside cells, creating defined pathways and signaling systems.

A key feature of more complex genetic circuits, that mimic those found in electronics, is the ability to build logical behavior—such as converting two signals into a response.

A team led by researchers at the University of Edinburgh developed a method to program proteins with this dual logic function, paving the way to the precision-level control needed in biocomputational circuits.

In cells one of the simplest logic behaviors is an AND gate function—this involves an input, the presence of two different molecules, which produce an output, activating or suppressing a gene.

This requires programming proteins, which regulate genes and control the cell’s functions. Breaking a protein-coding gene into two inactivates it and allows each to be tailored to receive different signals.

When both signals are received the genes are activated and two protein sub-units are produced which bind together, forming the original protein which activates or suppresses the gene of interest.

However a key limitation in building logic circuits in cells is that breaking protein-coding genes at random points can damage their function and prevent the protein from being reassembled later.

To tackle this the team harnessed moveable genetic parts, known as transposons, to find break points that protect the protein’s function and allow the two subunits to be joined together later.

Transposons, also known as jumping genes, are common in the genome and move around controlling how genes are used.

By harnessing the ingenuity of nature’s existing genetic toolbox, transposons allow scientists to test all the potential break points in a protein’s genetic sequence to find the sweet spot.

Previously researchers needed to rely on complex computer programs or laborious laboratory work to make educated guesses or test potential break points that will not destroy the protein.

The technique also offers researchers better control of the on-off switch in genetic circuits, as the reassembled proteins do not risk becoming partially active in the ‘off’ state, a common problem.

The advance builds on the team’s earlier work, creating a library of protein glues, known as split inteins, which act as ‘molecular velcro’ to seamlessly join protein sub-units together.

The process, known as protein splicing, allows very large proteins to be assembled from smaller units without disrupting the protein’s function.

Inteins are also part of nature’s toolbox, common in many forms of life, and form part of the protein production machinery in cells. They fine tune and modify proteins after they have been built.

The combined power of transposons and split inteins paves the way for scientists to more easily program proteins with the logic functions needed to build more complex genetic circuits.

The technique could also be used to design and mass produce very large proteins that have useful properties for medicine or industry, but are currently difficult or expensive to manufacture.

The study, published in Nature Communications, was funded by a UKRI Future Leaders Fellowship, awarded to Dr. Wang, and Leverhulme Trust. It involved researchers from Microsoft Research Cambridge, University of Turku and Zhejiang University.

“We developed a new powerful method for engineering functional split proteins by combining the advantages of two revolutionary biological tools, the transposon and split intein, to rapidly locate all suitable breaking and recombining sites of a target protein. This tool will help unlock many applications by splitting proteins in biotechnology and medicine such as design of biocomputing programs in cells, reduction of a protein’s harmful basal expression and engineered proteins that are responsive to new controllable signals.”

In the past year, things have been complicated for me. I had my first baby last November. It is joyful and exciting to see how the little thing grow up so fast and try his best to interact with everyone and explore everything, but raising a child, particularly at early stage and during this pandemic when things are not going well, has posed big challenges to my emotions and physical health, as well as to my career. I wouldn’t have reached this far without any support, and I am very grateful that I have an excellent supervisor, a great team, a cheerful husband and a loving mother. Here, I would like to thank everyone that has been always supportive during this difficult time!

Many research studies come from small inspirations and ours is no exception. It started two and a half years ago when we were preparing another manuscript (on whole-cell biosensors and cascaded amplifiers) for Nature Chemical Biology[1]. This is where the inspiration and motivation for the DNA sponge project came from.

When we were studying the impact of cascaded amplifiers on biosensors’ performance, we also tested whether they could cause notable burdens on the host cells. We observed that for one cascaded amplifier (HrpRS-RinA-ECF11), having the three-layered amplifiers in a single low-copy number plasmid negatively affected growth. Surprisingly, we found that moving the last amplifier’s output promoter to a high-copy number plasmid not only improved the sensor’s output readout, but also recovered the host cell growth (Supplementary Fig. 9b1). This was contradictory to our general knowledge, in which high-copy number plasmids should impose higher burden on the host cells than low-copy number plasmids, if there are burdensome elements. This raised the questions of ‘how it happened’ and ‘what was the regulation mechanism behind it’. Moreover, we found that such effect did not occur for a different cascaded amplifier circuit with the same elements, but where the last two amplifiers were swapped (HrpRS- ECF11-RinA; Supplementary Fig. 9a1). This led us to believe that the change in burden was specifically related to the last amplifier, and that the regulation mechanism must be hidden somewhere between the last amplifier’s activator (i.e., ECF11) and the high-copy number reporter plasmid used. So, what was it?

My supervisor, Dr Baojun Wang, often says that inspirations always come from learning other people’s work.

It is true! Particularly in this case, we found potential answers in another paper published in Nature, where “DNA sponges” were used to improve the function of a repressilator[2]. In that work, the authors used the promoters responding to repressors TetR, LacI and cI as the “DNA sponges” to decoy away the excess repressors, enabling the precise and long-term operation of their synthetic clock. From there, we realized that in our cascaded amplifier, the ECF11’s cognate promoter Pecf11 not only played a role in activating the reporter GFP expression when bound with ECF11, but also “sponged” the ECF11 during the process. Besides, we found the ECF11 itself was very toxic to the host cells (Supplementary Fig. 31). Together with another paper’s suggestions that the toxicity of ECF could derive from RNA polymerase (RNAP) competition for native RNAP with host sigma factors and/or from aberrant gene expression[3], we then hypothesized that the recovery of cell growth might be due to ECF11 sponging. This would prevent most of the ECF11 from interfering with the host’s native transcription system and harming the cells. Encouraged by Baojun, we decided to study the DNA sponge and validate our hypothesis.

Small ideas are like snowballs that can get bigger if they keep rolling.

By reading more publications about DNA sponges or decoy DNAs, we became more and more interested in how they reshaped gene circuits’ responses, buffered gene expression noise and even contributed to gene therapy. By gathering all these ideas, we thought we could study the DNA sponge phenomenon more deeply, not only in relation to its impact on cellular burden, but also to get a more complete picture on how it could regulate the performance of gene circuits (Fig. 1). As a result, we started the study from simple to complex gene circuits and from single to multi-layered sponges. We were very excited to find out that DNA sponge could actually regulate gene circuits in a systematic manner, including decreasing basal leakage, improving output readout and induction fold, shifting responding input range and mitigating toxicity caused by the burdensome proteins. More interestingly, a single sponge could do most of these jobs at the same time without causing further burden to the cells!

We are pleased to have our work published in Nature Communications, and I am grateful that we have grasped the small inspiration from the very beginning and expanded it to the present stage. Although all the work was done in Escherichia coli, DNA sponges may also be applied to other prokaryotic and eukaryotic organisms. We expect this simple yet versatile tool will benefit many bioengineering researchers with their gene circuits optimization tasks as well as providing a way to mitigate the toxicity of burdensome regulatory proteins for a variety of applications in biosensing, biotherapy and biomanufacturing.

Our paper:

Wan, X., Pinto, F., Yu, L. & Wang, B. Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity. Nat Commun 11, 5961 (2020).

Reference

1. Wan, X., Volpetti, F., Petrova, E., French, C., Maerkl, S. J. & Wang, B. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat. Chem. Biol. 15, 540–548 (2019).
2. Potvin-Trottier, L., Lord, N. D., Vinnicombe, G. & Paulsson, J. Synchronous long-term oscillations in a synthetic gene circuit. Nature 538, 514–517 (2016).
3. Rhodius, V. A., Segall-Shapiro, T. H., Sharon, B. D., Ghodasara, A., Orlova, E., Tabakh, H., Burkhardt, D. H., Clancy, K., Peterson, T. C., Gross, C. a & Voigt, C. a. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol. Syst. Biol. 9, 702 (2013).

The technique involves the use of proteins, known as split inteins, that act like ‘molecular velcro’ and could provide a faster, cheaper and easier method of building large ‘designer’ proteins with many applications.

The advance could speed the early stages of vaccine development, which often involves building and testing many proteins to investigate those most effective at boosting the immune system.

Mimic Nature’s Proteins

Researchers could also use the technique to design and mass produce proteins found in nature, that have useful properties but are currently difficult or expensive to manufacture.

For instance, strong yet lightweight fabrics could be modelled on spider silk proteins. Glue for underwater repairs in the shipping industry could be based on the sticky fibres mussels use to attach themselves to the surface of rocks.

Protein Library

The team at the University of Edinburgh have created a library of 15 intein proteins that act as glues to seamlessly join protein strands together end to end.

The process, known as protein splicing, allows very large proteins to be assembled from smaller units without disrupting the protein’s function.

Inteins are common in many forms of life and form part of the protein production machinery found in cells. They normally fine tune and modify proteins after they have been built.

The team developed a high throughput screening platform, to assess the activity of inteins and identify those that could be used simultaneously to fuse many smaller protein strands, both inside and outside of cells.

After inteins have built a permanent bridge between small protein sub-units they seamlessly cut themselves out leaving no trace of their presence.

One-Pot Reaction

Conventional methods of building large proteins are challenging and often result in poor protein quality and low yields.

Current techniques involve encoding the instructions to make proteins into the DNA of living cells, such as bacteria. But the complex instructions to make larger proteins often overloads cells.

The technique would allow scientists to split the instructions to make a protein across different cells. Once the protein sub-units have been produced the cells can be broken up, and the inteins present will assemble them into the larger protein in a one-pot reaction.

Genetic Controls and Switches

Harnessing the power of nature is also the basis of the rapidly expanding field of synthetic biology which merges biology and engineering principles for useful industrial and medical purposes.

Inteins could be used to build tailored regulatory proteins that provide sophisticated genetic controls and switches that would allow living systems to be reprogrammed or new biological systems to be built.

The study, published in Nature Communications, was funded by a UKRI Future Leaders Fellowship, awarded to Dr Wang, the Biotechnology and Biological Sciences Research Council and Leverhulme Trust.

“Inteins are remarkable tools from nature to achieve seamless protein ligation. In this study, we developed to date the largest library of non cross-reacting split inteins, and demonstrated their vast potential to be scalable tools for gene circuit design, protein engineering and biomaterial manufacturing.”
Dr Baojun Wang
School of Biological Sciences, University of Edinburgh

The powerful method could enable bacteria to be used as cheap and environmentally friendly living factories that make a range of useful products.

It will allow researchers to target genes that are normally difficult to activate, including those involved in infections, or with industrial applications.

The advance could also make it easier to study how harmful strains of bacteria thrive and cause infections, researchers say.

Scientists at the University of Edinburgh invented the new technique—known as programmable gene activation—which enables them to control a wider range of genes and increase product yields.

Until now, a lack of techniques that work well in bacteria has hindered research and limited their ability to be used to make useful products.

Using the new method, levels of gene activation are around 100 times higher than existing techniques, the team says. Current methods also mainly target basic genes involved in bacterial survival.

The team’s technique is adapted from an approach that uses scissor-like molecules—called CRISPR molecules—to make precise changes to the genetic code. They adapted the technology by attaching small guide molecules and proteins that target and switch on genes.

Their technique was developed for a widely studied species called Escherichia coli and a soil bacterium with potential industry applications. The method is also likely to work in many other species of bacteria, researchers say.

The team also developed a reusable scanning platform that makes it faster and cheaper to find the best ways of activating multiple genes in a pattern that produces high yields of useful substances.

The study, published in the journal Nature Communications, was funded by the Biotechnology and Biological Sciences Research Council, UK Research and Innovation, Leverhulme Trust and Wellcome.

Dr. Baojun Wang, of the University of Edinburgh’s School of Biological Sciences, who led the study, said: “This new method has the potential to be a powerful tool for programing bacteria, with diverse applications for research and industry. It could help save a lot of time and money.”

More information

Yang Liu et al. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria, Nature Communications (2019). DOI: 10.1038/s41467-019-11479-0

Journal information: Nature Communications

According to the researchers, there is an urgent need to provide simple, affordable, on-site solutions for contaminated water sources. In source-limited countries, such as Bangladesh, there is a lack of sufficiently skilled personnel and healthcare facilities to test water for contamination.

To tackle this, researchers say new devices could replace existing tests. Current tests are difficult to use, need specialist laboratory equipment and can produce toxic chemicals.

The sensor device, developed at the university in Scotland’s capital, however, generates easy-to-interpret patterns, similar to volume bars, which display the level of contamination.

The team tested the arsenic sensors using environment samples from affected wells in Bangladesh, which suffers from some of the world’s highest levels of arsenic-contaminated ground water.

“We tested out sensors with samples from wells in a village in Bangladesh,” said Dr Baojun Wang, from the School of Biological Sciences at the university. “The arsenic level reported by the sensors was consistent with lab-based standard tests, demonstrating the devices potential as a simple low-cost-use monitoring tool.”

It is estimated around 20 million people in Bangladesh – most in rural poor areas – drink contaminated water. Long-term exposure to unsafe levels of arsenic leads to skin lesions and cancers and is linked to 20 per cent of all deaths in the worst-affected regions.

Developing the biosensor using the tests from the wells in Bangladesh, the researchers manipulated the genetic code of the bacteria Escherichia coli (E. coli), and then added genetic components to act as amplifiers when arsenic is detected.

Water samples were fed into a plastic device containing bacteria suspended in a gel. This produced fluorescent proteins that were visible in the presence of arsenic.

Arsenic is one of the most common elements on Earth and is present as arsenic salts in all water. The World Health Organization (WHO) sets the safe level for arsenic in drinking water at 10 parts par billion.

However, many places in the Himalayas and South-East Asia have 10 times that amount of arsenic levels in their drinking water.

The contamination of water by heavy metals is a worldwide health issue, with Unicef reporting that arsenic-contaminated drinking water is consumed by more than 140 million people worldwide.

The University of Edinburgh researchers believe that their approach could also be used to detect other environmental toxins, diagnose diseases and locate landmines.

The study was published in Nature Chemical Biology.

Wan X, Volpetti F, Petrova E, French C, Maerkel S and Wang B*, “Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals”, Nature Chemical Biology, 2019, 15(5):540–548 https://doi.org/10.1038/s41589-019-0244-3

Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals.

Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli).

The bio-amplifiers in the sensors enable us to detect even minute amounts of dangerous toxins, which would be of huge benefit to water quality controllers
– Dr Baojun Wang

The team say this ‘bio-amplifier’ might be used in microscopic cellular sensors , which scientists have already developed, that could detect minute traces of chemicals and toxins, to make them more sensitive. Ultimately, this could lead to new types of sensors to detect harmful toxins or diseases in our bodies and in the environment before they do any damage.

In laboratory tests, the team’s bio-amplifier was able to significantly boost the detection limit and sensitivity of a sensor designed to detect the toxin arsenic. The device is also modular, which means that the devices can be easily introduced in different genetic networks, and can potentially be used to increase the sensitivity and accuracy of a broad range of other genetic sensors to detect pathogens and toxins.

The results of the study are published in the journal Nucleic Acids Research.

Dr Baojun Wang, who is now based at the University of Edinburgh, but carried out the study while in the Division of Cell and Molecular Biology at Imperial, said: “One potential use of this technology would be to deploy microscopic sensors equipped with our bio-amplifier component into a water network. Swarms of the sensors could then detect harmful or dangerous toxins that might be hazardous to our health. The bio-amplifiers in the sensors enable us to detect even minute amounts of dangerous toxins, which would be of huge benefit to water quality controllers.”

Scientists have previously known that cells have their own inbuilt amplifiers to first detect and then boost biological signals, which are crucial for survival and reproduction. They have been attempting to understand how they work in more detail so as to remodel them for other applications. However the challenge for scientists has been engineering a device that can predictably amplify signals without distortion or feedback.

In the study, scientists first re-engineered genes involved in a special cell network called hrp (hypersensitive response and pathogenicity), which have naturally occurring amplifying proteins that function just like an electronic amplifier. They then cloned these amplifying components and inserted them into the harmless gut bacteria E. coli, fitting it with a synthetic arsenic input sensor and a fluorescent green protein gene as the output.

They also engineered the amplifier so that the input and output signals could be turned up and down just like an electronic amplifier, which is an important step forward for Dr Wang: “For me the most exciting part of our device is that it is tunable. We can predictably turn the amplifier up or down without distorting the signal, just like you turn a light dimmer switch up or down to make a room darker or brighter. This is really valuable because you can control the amplitude of an input signal to your desired level to match genes that have vastly different input-output strengths. This means that you could couple many modules together, using our tunable amplifiers, to build a large biological system with advanced function.”

The next stage of research will see the scientists test out this tunable amplifier in different biotechnological applications. Dr Wang added: “We would now like further test our design to tune the expression of genes in different metabolic pathways, such as the anti-cancer drug taxol synthesis pathway, that respond to different environmental and chemical cues within and outside microbial cell factories. We are planning to examine whether our design can control and balance our cells’ metabolism as well as produce high yields of valuable chemicals.”

This research was funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and The Royal Society, and was carried out in collaboration with Professor Martin Buck and Professor Mauricio Barahona, both based at Imperial College London.

REFERENCE: Baojun Wang, Mauricio Barahona and Martin Buck. ‘Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks’. Nucleic Acids Research. July 2014. DOI: 10.1093/nar/gku593

Scientists have successfully demonstrated that they can build some of the basic components for digital devices out of bacteria and DNA, which could pave the way for a new generation of biological computing devices, in research published today in the journal Nature Communications.

The researchers, from Imperial College London, have demonstrated that they can build logic gates, which are used for processing information in devices such as computers and microprocessors, out of harmless gut bacteria and DNA. These are the most advanced biological logic gates ever created by scientists.

Professor Richard Kitney, co-author of the paper from the Centre for Synthetic Biology and Innovation and the Department of Bioengineering at Imperial College London, says:

“Logic gates are the fundamental building blocks in silicon circuitry that our entire digital age is based on. Without them, we could not process digital information. Now that we have demonstrated that we can replicate these parts using bacteria and DNA, we hope that our work could lead to a new generation of biological processors, whose applications in information processing could be as important as their electronic equivalents.”

Although still a long way off, the team suggest that these biological logic gates could one day form the building blocks in microscopic biological computers. Devices may include sensors that swim inside arteries, detecting the build up of harmful plaque and rapidly delivering medications to the affected zone. Other applications may include sensors that detect and destroy cancer cells inside the body and pollution monitors that can be deployed in the environment, detecting and neutralising dangerous toxins such as arsenic.

The team say that the advantage of their biological logic gates over previous attempts is that they behave like their electronic counterparts. Previous research only proved that biological gates could be made. The new biological gates are also modular, which means that they can be fitted together to make different types of logic gates, paving the way for more complex biological processors to be built in the future.

In the new study, the researchers demonstrated how these biological logic gates worked. In one experiment, they showed how biological logic gates can replicate the way that electronic logic gates process information by either switching “on” or “off”.

The scientists constructed a type of logic gate called an “AND Gate” from bacteria called Escherichia coli (E.Coli), which is normally found in the lower intestine. The team altered the E.Coli with modified DNA, which reprogrammed it to perform the same switching on and off process as its electronic equivalent when stimulated by chemicals.

The researchers were also able to demonstrate that the biological logic gates could be connected together to form more complex components in a similar way that electronic components are made. In another experiment, the researchers created a “NOT gate” and combined it with the AND gate to produce the more complex “NAND gate”.

The next stage of the research will see the team trying to develop more complex circuitry that comprises multiple logic gates. One of challenges faced by the team is finding a way to link multiple biological logic gates together similar to the way in which electronic logic gates are linked together to enable complex processing to be carried out.

Professor Martin Buck, co-author of the paper from the Department of Life Sciences at Imperial College London, adds: “We believe that the next stage of our research could lead to a totally new type of circuitry for processing information. In the future, we may see complex biological circuitry processing information using chemicals, much in the same way that our body uses them to process and store information.”

Professor Paul Freemont, Co-director for the Centre for Synthetic Biology and Innovation at Imperial College London, adds: “Even though this research is still in its early stages, it is already showing how collaborations between disciplines can bear fruit. I look forward to the next stage of this research, which could take information processing to a whole new ‘biological’ level.”

This research was part funded by the Engineering and Physcial Sciences Research Council.

Notes to Editors:

1.”Engineering modular orthogonal genetic logic gates for robust digital-like synthetic biology”, 18 October 2011, Nature Communications journal.

The full listing of authors and their affiliations for this paper is as follows:

Baojan Wang (1), Richard Kitney (1), Nicolas Joly (2) (*) and Martin Buck (2)

(1) Centre for Synthetic Biology and Innovation and Department of Bioengineering, Imperial College, London SW7 2AZ, UK (2) Division of Biology, Faculty of Natural Sciences, Imperial College, London SW7 2AZ, UK (*)Present address: Institute Jacques Monod, CNRS UMR 7592 , Universite Paris Diderot, Paris 75205, France.