Electronic zippers control DNA strands

A research team from NPL and the University of Edinburgh have invented a new way to zip and unzip DNA strands using electrochemistry.

The DNA double helix has been one of the most recognisable structures in science ever since it was first described by Watson and Crick almost 60 years ago (paper published in Nature in 25 April 1953). The binding and unbinding mechanism of DNA strands is vital to natural biological processes and to the polymerase chain reactions used in biotechnology to copy DNA for sequencing and cloning.

The improved understanding of this process, and the discovery of new ways to control it, would accelerate the development of new technologies such as biosensors and DNA microarrays that could make medical diagnostics cheaper, faster and simpler to use.

The most common way of controlling the binding of DNA is by raising and lowering temperature in a process known as heat cycling. While this method is effective, it requires bulky equipment, which is often only suitable for use in laboratories. Medicine is moving towards personalised treatment and diagnostics which require portable devices to quickly carry out testing at the point of care, i.e. in hospitals rather than laboratories. The development of alternative methods to control the DNA binding process, for example with changes in acidity or the use of chemical agents, would be a significant step towards lab-on-a-chip devices that can rapidly detect disease.

However, until now, no method has been shown to enable fast, electrochemical control at constant temperatures without the need for dramatic changes in solution conditions or modifying the nucleotides, the building blocks of DNA.

A research team from NPL and the University of Edinburgh have invented a new way of controlling DNA using electrochemistry. The team used a class of molecules called DNA intercalators which bind differently to DNA, depending on whether they are in a reduced or oxidised state, altering its stability. These molecules are also electroactive, meaning that their chemical state can be controlled with an electric current.

A paper published in the Journal of the American Chemical Society explains how the process works. Electrodes apply a voltage across a sample containing double strands of DNA which are bonded to the electroactive chemicals. This reduces the chemicals (they gain electrons), decreasing the stability of the DNA and unzipping the double helix into single strands. Removing the voltage leads to the oxidisation of the chemicals and the DNA strands zip back up to re-form the familiar double helix structure. Put simply, with the flick of a switch, the oxidation state of the molecules can be changed and the DNA strands are zipped together or pulled apart.

Cancer checkpoint

Mitochondrial metabolic regulator SIRT4 guards against DNA damage

Healthy cells don’t just happen. As they grow and divide, they need checks and balances to ensure they function properly while adapting to changing conditions around them.

Researchers studying a set of proteins that regulate physiology, caloric restriction and aging have discovered another important role that one of them plays. SIRT4, one of seven sirtuin proteins, is known for controlling fuel usage from its post in the mitochondria, the cell’s energy source. It responds to stressful changes in the availability of nutrients for the cell.

New research reveals that SIRT4 is also extremely sensitive to a different form of stress: DNA damage. This unsuspected response by the metabolic checkpoint means SIRT4 doubles as a sentry guarding against cancer, which is spurred by genetic abnormalities.

Sirtuins have become familiar for their connection to longevity and to resveratrol, the red-wine compound that activates SIRT1, but less attention has been focused on SIRT3, SIRT 4 and SIRT5, all of which are found in mitochondria. Marcia Haigis, HMS associate professor of cell biology, led a team that has uncovered SIRT4 as an important player in the DNA damage response pathway, coordinating a sequence of events that normally result[s] in tumor suppression. They published their results April 4 in Cancer Cell.

“When we started studying SIRT4, we were focused only on its metabolic role, looking for functions related to diabetes and obesity,” said Haigis. “What we found, to our surprise, was that SIRT4 was responsive to DNA damage, so that led us to investigate the metabolic response to DNA damage and how SIRT4 controls the metabolic response to genotoxic stress.”

To see how SIRT4 normally functions, Haigis and her colleagues induced DNA damage by exposing cells in a lab dish to ultraviolet light. This damage triggered a halt in glutamine metabolism, limiting the amount of nutrients the cell could use as it goes through a cycle of division and growth.

Blocking the cell cycle at this juncture is important. If cell growth after DNA damage goes unchecked, proliferation of impaired cells can lead to cancer. When SIRT4 works properly, this chain of events is broken before bad cells and their abnormal genes multiply. SIRT4 blocks glutamine metabolism, arrests the cell cycle and suppresses tumor formation.

The scientists tested this SIRT4 response in mice. Bred to lack the gene that encodes the SIRT4 protein but otherwise normal, the mice spontaneously developed lung cancer by 15 months.

“When SIRT4 is missing, you don’t have this metabolic checkpoint involving glutamine, which is important because glutamine is an amino acid required for proliferation in the cell,” Haigis said. “Without SIRT4, the cell keeps dividing even in the face of DNA damage, so the cell accumulates more damage.”

The scientists also analyzed data showing SIRT4 gene expression levels are low in several human cancers, including small-cell lung carcinoma, gastric cancer, bladder carcinoma, breast cancer and leukemia.

While they cannot say if SIRT4 loss alone will initiate cancer, its absence appears to create an environment in which tumor cells survive and grow.

“Our findings suggest that SIRT4 may be a potential target against tumors,” they conclude.

A healthy mitochondrion contains the metabolic regulator SIRT4, which responds to DNA damage and other stress. (Credit: National Institute on Aging)

Biological transistor enables computing within living cells

When Charles Babbage prototyped the first computing machine in the 19th century, he imagined using mechanical gears and latches to control information. ENIAC, the first modern computer developed in the 1940s, used vacuum tubes and electricity. Today, computers use transistors made from highly engineered semiconducting materials to carry out their logical operations.

And now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper to be published March 28 in Science, the team details a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor.”

“Transcriptors are the key component behind amplifying genetic logic — akin to the transistor and electronics,” said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper’s lead author.

The creation of the transcriptor allows engineers to compute inside living cells to record, for instance, when cells have been exposed to certain external stimuli or environmental factors, or even to turn on and off cell reproduction as needed.

“Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics,” said Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author.

The biological computer

In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.

“We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic,” said Endy.

Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell.

They refer to their transcriptor-based logic gates as “Boolean Integrase Logic,” or “BIL gates” for short.

Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.

Despite their outward differences, all modern computers, from ENIAC to Apple, share three basic functions: storing, transmitting and performing logical operations on information.

Last year, Endy and his team made news in delivering the other two core components of a fully functional genetic computer. The first was a type of rewritable digital data storage within DNA. They also developed a mechanism for transmitting genetic information from cell to cell, a sort of biological Internet.

It all adds up to creating a computer inside a living cell.

Boole’s gold

Digital logic is often referred to as “Boolean logic,” after George Boole, the mathematician who proposed the system in 1854. Today, Boolean logic typically takes the form of 1s and 0s within a computer. Answer true, gate open; answer false, gate closed. Open. Closed. On. Off. 1. 0. It’s that basic. But it turns out that with just these simple tools and ways of thinking you can accomplish quite a lot.

“AND” and “OR” are just two of the most basic Boolean logic gates. An “AND” gate, for instance, is “true” when both of its inputs are true — when “a” and “b” are true. An “OR” gate, on the other hand, is true when either or both of its inputs are true.

In a biological setting, the possibilities for logic are as limitless as in electronics, Bonnet explained. “You could test whether a given cell had been exposed to any number of external stimuli — the presence of glucose and caffeine, for instance. BIL gates would allow you to make that determination and to store that information so you could easily identify those which had been exposed and which had not,” he said.

By the same token, you could tell the cell to start or stop reproducing if certain factors were present. And, by coupling BIL gates with the team’s biological Internet, it is possible to communicate genetic information from cell to cell to orchestrate the behavior of a group of cells.

“The potential applications are limited only by the imagination of the researcher,” said co-author Monica Ortiz, a PhD candidate in bioengineering who demonstrated autonomous cell-to-cell communication of DNA encoding various BIL gates.

Building a transcriptor

To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes — the integrases mentioned earlier — that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.

“The choice of enzymes is important,” Bonnet said. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”

On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification.

With transcriptors, a very small change in the expression of an integrase can create a very large change in the expression of any two other genes.

To understand the importance of amplification, consider that the transistor was first conceived as a way to replace expensive, inefficient and unreliable vacuum tubes in the amplification of telephone signals for transcontinental phone calls. Electrical signals traveling along wires get weaker the farther they travel, but if you put an amplifier every so often along the way, you can relay the signal across a great distance. The same would hold in biological systems as signals get transmitted among a group of cells.

“It is a concept similar to transistor radios,” said Pakpoom Subsoontorn, a PhD candidate in bioengineering and co-author of the study who developed theoretical models to predict the behavior of BIL gates. “Relatively weak radio waves traveling through the air can get amplified into sound.”

Public-domain biotechnology

To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools.

“Most of biotechnology has not yet been imagined, let alone made true. By freely sharing important basic tools everyone can work better together,” Bonnet said.

The Father of All Men Is 340,000 Years Old

A change in the way we understand the root of the tree where Y chromosome originated from has left geneticists amazed

Albert Perry carried a secret in his DNA: a Y chromosome so distinctive that it reveals new information about the origin of our species. It shows that the last common male ancestor down the paternal line of our species is over twice as old as we thought.

One possible explanation is that hundreds of thousands of years ago, modern and archaic humans in central Africa interbred, adding to known examples of interbreeding – with Neanderthals in the Middle East, and with the enigmatic Denisovans somewhere in southeast Asia.

Perry, recently deceased, was an African-American who lived in South Carolina. A few years ago, one of his female relatives submitted a sample of his DNA to a company called Family Tree DNA for genealogical analysis.

Geneticists can use such samples to work out how we are related to one another. Hundreds of thousands of people have now had their DNA tested. The data from these tests had shown that all men gained their Y chromosome from a common male ancestor. This genetic “Adam” lived between 60,000 and 140,000 years ago.

All men except Perry, that is. When Family Tree DNA’s technicians tried to place Perry on the Y-chromosome family tree, they just couldn’t. His Y chromosome was like no other so far analysed.

—

“The Y-chromosome tree is much older than we thought,” says Chris Tyler-Smith at the Wellcome Trust Sanger Institute in Hinxton, UK, who was not involved in the study. He says further work will be needed to confirm exactly how much older.

“It’s a cool discovery,” says Jon Wilkins of the Ronin Institute in Montclair, New Jersey. “We geneticists have been looking at Y chromosomes about as long as we’ve been looking at anything. Changing where the root of the Y-chromosome tree is at this point is extremely surprising.”

(via NewScientist)

Something the to go with the line “Your genes have combined beautifully”:

3D Printed DNA Strand Gift

Half a Million DVDs of Data Stored in Gram of DNA

Paleontologists routinely resurrect and sequence DNA from woolly mammoths and other long-extinct species. Future paleontologists, or librarians, may do much the same to pull up Shakespeare’s sonnets, listen to Martin Luther King Jr.’s “I have a dream” speech, or view photos. Researchers in the United Kingdom report today that they’ve encoded these works and others in DNA and later sequenced the genetic material to reconstruct the written, audio, and visual information.

The new work isn’t the first example of large-scale storage of digital information in DNA. Last year, researchers led by bioengineers Sriram Kosuri and George Church of Harvard Medical School reported that they stored a copy of one of Church’s books in DNA, among other things, at a density of about 700 terabits per gram, more than six orders of magnitude more dense than conventional data storage on a computer hard disk. Now, researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, U.K., report online today in Nature that they’ve improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.

To do so, the team first translated written words or other data into a standard binary code of 0s and 1s, and then converted this to a trinary code of 0s, 1s, and 2s—a step needed to help prevent the introduction of errors. The researchers then rewrote that data as strings of DNA’s chemical bases: As, Gs, Cs, and Ts. At the storage density achieved, a single gram of DNA would hold 2.2 million gigabits of information, or about what you can store in 468,000 DVDs. What’s more, the researchers also added an error correction scheme, encoding the information multiple times, among other tricks, to ensure that it could be read back with 100% accuracy.