DNA Constructs Antenna for Solar Energy
Researchers at Chalmers Univ. of Technology have found an effective solution for collecting sunlight for artificial photosynthesis. By combining self-assembling DNA molecules with simple dye molecules, the researchers have created a system that resembles nature’s own antenna system.
Artificial photosynthesis is one of the hot trends in energy research. A large number of the worlds’ energy problems could be resolved if it were possible to recreate the ability plants have to transform solar energy into fuel. The Earth receives enough solar energy every hour to satisfy our energy needs for an entire year.
Read more: http://www.laboratoryequipment.com/news/2013/06/dna-constructs-antenna-solar-energy
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.
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.
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.”
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.
Harvard Researchers Create Self-Assembling Nano Bricks Made of DNA
Harvard’s Wyss Institute, which brought us 700-terabytes-per-gram-of-DNA data storage earlier in the year, has now produced DNA Lego bricks — three-dimensional DNA building blocks that self-assemble into more than 100 different, three-dimensional structures (pictured above).
These DNA Lego bricks are short strands of DNA that have been specially crafted to join with other DNA bricks at a 90-degree angle — just as if you had pushed two eight-stud Lego bricks on top of each other at 90 degrees.
By joining more and more of these DNA bricks together, a 3D structure emerges. In this case, the DNA Legos are built into 25-nanometer cubes, which consist of around 1,000 voxels, with each voxel consisting of DNA strands that are just 2.5nm. A voxel (volumetric pixels) is a term borrowed from graphics; it’s essential the 3D equivalent of a 2D pixel.
DNA could soon be used to reconstruct images of your face
Police may soon be able to get an accurate sketch of a suspect’s face merely by finding some DNA.
The DNA double helix that we’re all familiar with is a molecular ladder made of three key parts. The backbone of phosphates that tie everything together up and down, the sugar rings (“deoxyribose”) that serve as rungs, and the bases (A, C, G, T) that invisibly bond the two strands of the helix together, head to toe.
But that helix can be broken or mutated in nature, leading to mutations. And out of all the compounds in the world that could have evolved to carry our information, why just DNA and its cousin RNA? To answer that question, Vitor Pinheiro’s team created a completely new set of information molecules called XNA.
XNA replaces the deoxyribose sugar ring with other chemical rings like threose and cyclohexane. By evolving an enzyme that could read these funny bases, they were able to read DNA into XNA as well as the reverse. Plus it’s super-strong and resistant to breaking or cleaving.
Molecules like XNA could expand the information code for synthetic biology as well as help us answer the ultimate question about DNA: Why that, and not something else? Ed Yong has more great detail here.
Art of Science by Stephen Gaeta. In this project, Gaeta uses passages from significant historical science texts to form his images.
The Watson Table, named after James Watson and designed by Paul Loebach. This otherwise minimalist design has spiraling legs that are inspired by DNA structure.
Researchers Find Antibiotics Work by Attacking DNA
Penicillin and other antibiotics have revolutionized medicine, turning once-deadly diseases into easily treatable ailments. However, while antibiotics have been in use for more than 70 years, the exact mechanism by which they kill bacteria has remained a mystery.
Now a new study by MIT and Boston Univ. researchers reveals the killing mechanism behind all three major classes of antibiotics: the drugs produce destructive molecules that fatally damage bacterial DNA through a long chain of cellular events. Understanding the details of this mechanism could help scientists improve existing drugs, according to the researchers. Few new antibiotics have been developed in the past 40 years, and many strains of bacteria have become resistant to the drugs now available.
Read more: http://www.laboratoryequipment.com/news-Antibiotics-Work-by-Attacking-DNA-042012.aspx