Novel RNA nanodevices in living cells can sense and ...

Novel RNA nanodevices in living cells cansense and analyze multiple complex signals26 July 2017

Ribonucleic acid (RNA) is used to create logic circuitscapable of performing various computations. In newexperiments, Green and his colleagues haveincorporated RNA logic gates into living bacterial cells,which act like tiny computers. Credit: Jason Drees forthe Biodesign Institute

The interdisciplinary nexus of biology andengineering, known as synthetic biology, isgrowing at a rapid pace, opening new vistas thatcould scarcely be imagined a short time ago.

In new research, Alex Green, a professor at ASU'sBiodesign Institute, demonstrates how living cellscan be induced to carry out computations in themanner of tiny robots or computers.

The results of the new study have significantimplications for intelligent drug design and smartdrug delivery, green energy production, low-costdiagnostic technologies and even the developmentof futuristic nanomachines capable of huntingdown cancer cells or switching off aberrant genes.

"We're using very predictable and programmableRNA-RNA interactions to define what these circuitscan do," says Green. "That means we can usecomputer software to design RNA sequences that

behave the way we want them to in a cell. It makesthe design process a lot faster."

The study appears in the advance online edition ofthe journal Nature.

Designer RNA

The approach described uses circuits composed ofribonucleic acid or RNA. These circuit designs,which resemble conventional electronic circuits, self-assemble in bacterial cells, allowing them to senseincoming messages and respond to them byproducing a particular computational output, (in thiscase, a protein).

In the new study, specialized circuits known aslogic gates were designed in the lab, thenincorporated into living cells. The tiny circuitswitches are tripped when messages (in the form ofRNA fragments) attach themselves to theircomplementary RNA sequences in the cellularcircuit, activating the logic gate and producing adesired output.

The RNA switches can be combined in variousways to produce more complex logic gates capableof evaluating and responding to multiple inputs, justas a simple computer may take several variablesand perform sequential operations like addition andsubtraction in order to reach a final result.

The new study dramatically improves the ease withwhich cellular computing may be carried out. TheRNA-only approach to producing cellularnanodevices is a significant advance, as earlierefforts required the use of complex intermediaries,like proteins. Now, the necessary ribocomputingparts can be readily designed on computer. Thesimple base-pairing properties of RNA's fournucleotide letters (A, C, G and U) ensure thepredictable self-assembly and functioning of theseparts within a living cell.

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Green's work in this area began at the WyssInstitute at Harvard, where he helped develop thecentral component used in the cellular circuits,known as an RNA toehold switch. The work wascarried out while Green was a post-doc workingwith nanotechnology expert Peng Yin, along withthe synthetic biologists James Collins and PamelaSilver, who are all co-authors on the new paper."The first experiments were in 2012," Green says."Basically, the toehold switches performed so wellthat we wanted to find a way to best exploit themfor cellular applications."

After arriving at ASU, Green's first grad studentDuo Ma worked on experiments at the BiodesignInstitute, while another postdoc, Jongmin Kimcontinued similar work at the Wyss Institute. Bothare also co-authors of the new study.

Nature's Pentium chip

The possibility of using DNA and RNA, themolecules of life, to perform computer-likecomputations was first demonstrated in 1994 byLeonard Adleman of the University of SouthernCalifornia. Since then, rapid progress hasadvanced the field considerably, and recently, suchmolecular computing has been accomplished withinliving cells. (Bacterial cells are usually employed forthis purpose as they are simpler and easier tomanipulate.)

The technique described in the new paper takesadvantage of the fact that RNA, unlike DNA, issingle stranded when it is produced in cells. Thisallows researchers to design RNA circuits that canbe activated when a complementary RNA strandbinds with an exposed RNA sequence in thedesigned circuit. This binding of complementarystrands is regular and predictable, with Anucleotides always pairing with U and C alwayspairing with G.

With all the processing elements of the circuit madeusing RNA, which can take on an astronomicalnumber of potential sequences, the real power ofthe newly described method lies in its ability toperform many operations at the same time. Thiscapacity for parallel processing permits faster andmore sophisticated computation while making

efficient use of the limited resources of the cell.

Similar to how computer scientists use logical languageto have their programs make accurate AND, OR andNOT decisions towards a final goal, "RibocomputingDevices" (stylized here in yellow) developed by a team atthe Wyss Institute can now be used by syntheticbiologists to sense and interpret multiple signals in cellsand logically instruct their ribosomes (stylized in blue andgreen) to produce different proteins. Credit: WyssInstitute at Harvard University

Logical results

In the new study, logic gates known as AND, ORand NOT were designed. An AND gate producesan output in the cell only when two RNA messagesA AND B are present. An OR gate responds toeither A OR B, while a NOT gate will block output ifa given RNA input is present. Combining thesegates can produce complex logic capable ofresponding to multiple inputs.

Using RNA toehold switches, the researchersproduced the first ribocomputing devices capable offour-input AND, six-input OR and a 12-input deviceable to carry out a complex combination of AND,OR and NOT logic known as disjunctive normalform expression. When the logic gate encountersthe correct RNA binding sequences leading toactivation, a toehold switch opens and the processof translation to protein takes place. All of thesecircuit-sensing and output functions can beintegrated in the same molecule, making the

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systems compact and easier to implement in a cell.

The research represents the next phase of ongoingwork using the highly versatile RNA toeholdswitches. In earlier work, Green and his colleaguesdemonstrated that an inexpensive, paper-basedarray of RNA toehold switches could act as a highlyaccurate platform for diagnosing the Zika virus.Detection of viral RNA by the array activated thetoehold switches, triggering production of a protein,which registered as a color change on the array.

The basic principle of using RNA-based devices toregulate protein production can be applied tovirtually any RNA input, ushering in a newgeneration of accurate, low-cost diagnostics for abroad range of diseases. The cell-free approach isparticularly well suited for emerging threats andduring disease outbreaks in the developing world,where medical resources and personnel may belimited.

The computer within

According to Green, the next stage of research willfocus on the use of the RNA toehold technology toproduce so-called neural networks within livingcells—circuits capable of analyzing a range ofexcitatory and inhibitory inputs, averaging them andproducing an output once a particular threshold ofactivity is reached, much the way a neuronaverages incoming signals from other neurons.Ultimately, researchers hope to induce cells tocommunicate with one another via programmablemolecular signals, forming a truly interactive, brain-like network.

"Because we're using RNA, a universal molecule oflife, we know these interactions can also work inother cells, so our method provides a generalstrategy that could be ported to other organisms,"Green says, alluding to a future in which humancells become fully programmable entities withextensive biological capabilities.

More information: Alexander A. Green et al,Complex cellular logic computation usingribocomputing devices, Nature (2017). DOI:10.1038/nature23271

Provided by Arizona State University

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APA citation: Novel RNA nanodevices in living cells can sense and analyze multiple complex signals(2017, July 26) retrieved 7 January 2022 from https://phys.org/news/2017-07-rna-nano-devices-cells-multiple-complex.html

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