Tag Archives: DNA

Revisiting DNA origami

Creating a genetic program to crinkle DNA into the perfect shape can appear to be a scientific stunt. But DNA origami is more than a molecular magic trick. In this excerpt from a 2007 TED lecture, Paul Rothemund describes the science behind the work– how a chain– based on its sequence– becomes a two-dimensional shape.

But this work isn’t all fun and smiley-faces– as an article in today’s New York Times about tiny transistors points out:

I.B.M. is also exploring higher-risk ideas like “DNA origami,” a process developed by Paul W. K. Rothemund, a computer scientist at the California Institute of Technology.

The technique involves creating arbitrary two- and three-dimensional shapes by controlling the folding of a long single strand of viral DNA with multiple smaller “staple” strands. It is possible to form everything from nanometer-scale triangles and squares to more elaborate shapes like smiley faces and a rough map of North America. That could one day lead to an application in which such DNA shapes could be used to create a scaffolding just as wooden molds are now used to create concrete structures. The DNA shapes, for example, could be used to more precisely locate the gold nanoparticles that would then be used to grow nanowires. The DNA would be used only to align the circuits and would be destroyed by the high temperatures used by the chip-making processes.

The DNA transistor mold– what a cool nanoscale idea: build the shape, pour your circuit and destroy the mold when you’re done.

P.S.: my earlier origami post from May– in case you missed it.


June 8th birthday shout-out

birthday cake, copyright iStockphoto.com/MarcusPhoto1
birthday cake, copyright iStockphoto.com/MarcusPhoto1

I decided that in honor of my own birthday, I’d see which scientists also blew out candles on this spot on the calendar. (Okay, so I guess it’s a day late.)

My cosmic alignment is pretty distinguished. Francis Crick, co-discoverer of the DNA double helix was born on June 8, 1916. I also share a birthday with Giovanni Domenico Cassini, the Italian astronomer who co-discovered Jupiter’s Red Spot back in the 17th century. Yes, all those Cassini space missions are named for him.

But those aren’t the only distinguished scientist birthdays this week. For all of you June 11th babies, you share your day with Jacques Cousteau.

Update on June 10th- I initially missed a big scientist birthday this week. The biologist E. O. Wilson celebrates his 80th birthday today!


Science, Journalism and Inform-vs-Educate

Almost 6 years ago, I attended a conference of scientists and communicators about issues of communicating global warming to the general public.  At that point I was still wearing my graduate student hat and was still learning the ropes of science writing. The issues related to global warming and the public were different– this was before An Inconvenient Truth, and folks were genuinely worried that no one was believing the growing body of science showing that the Earth’s climate was indeed changing, and probably not for the better.

Though I learned a lot that week, the discussion that sticks most vividly in my mind doesn’t specifically relate to climate, but the role that journalists play in that process. When it came down to the question of whose job it was to educate the public about climate change, many of the experienced journalists in the room had a violent, seemingly knee-jerk reaction: “My job isn’t to educate. My job is to inform.”

My scientist-turning-journalist brain did a 180. Huh? I hadn’t come across this cultural tidbit before. I listened for a while and even chimed in at a couple of points. At the time– even though I disagreed– I thought maybe I was just naive and, perhaps, I might come to the same conclusion as these veterans once I had been a working science journalist for a while. But, no, I still disagree, but my understanding of the issues is now more nuanced.

In part, I think the problem is boiling it down to the words inform and educate. In many cases, part of the friction that can sometimes come when a scientist-educator talks to a journalist-informer. A couple of years ago, A Blog Around the Clock described that divide:

The scientists want to educate.

The journalists want to inform (if not outright entertain, or at least use entertaining hooks in order to inform).

There is a difference between the two goals. The former demands accuracy. The latter demands relevance. As long as both parties are aware of the existence of two disparate goals, there is a possibility of conversation that can lead to an article that satisfies both goals, thus both participants.

That defines the divide. Journalists have to find relevance and a connection that convinces their audience to read what they’ve written. Scientists sometimes want us to write about information that, while important to their grand vision, may not be relevant to the individual story that we’re trying to tell.

But the problem is that science journalists rarely ever have the opportunity to simply inform, even if that is their stated goal. Even if we have an easy news hook of extending human life, possible life on Mars, or the newest iPhone-type gadget strapped to your thumb, we constantly have to define, explain and educate the public about the nuts and bolts of what we’re writing about. Does a sports reporter have to explain a free throw, a home run, or an ace? Do political reporters have to give a two sentence description of how the Supreme Court works every time we have a new nominee? Generally not– but I can’t write a general news story and use the word protein, DNA or cell without somehow explaining what those words mean and why they’re important.

So, I’ve always considered that part of my role is to educate. Part of that is  my scientific training. Part of that is that I worked in a hands-on science museum and watched kids explore the joy of science. The reason that I do what I do is to make science fun, interesting, useful and relevant to broader society. But to do that, I provide context and connections, the education within the relevant plot points that justify “why now?”

So, I will always embrace education in my work. But I also recognize that I’ve often done my job best when the educator is wearing an invisibility cloak.


Molecule of the Week: RNA

messenger RNA credit: Wikimedia Commons
messenger RNA credit: Wikimedia Commons

You have it, I have it. Many viruses are based on it. It’s RNA, which stands for ribonucleic acid. It’s DNA’s chemical cousin with just a few slight differences.

While DNA serves as life’s genetic blueprint. RNA is more of a multitasker. DNA stores information in a kind of vault, and the cell makes RNA-based copies that ferry that information to other parts of the cell to provide the program for making proteins, the true cellular workhorses.  RNA’s reactivity also makes it a little like proteins– it’s been shown to actually do chemical reactions.

So, why does RNA make the cut this week? Researchers have found a new way to put RNA together, which may help scientists figure out how life begins. (See the New York Times story here).

Because RNA has many talents, some scientists had proposed an RNA world, the idea that all life was originally based on RNA, that DNA and proteins developed later. But there was a problem. The segments that make up RNA (and DNA) are made from three building blocks. Researchers couldn’t figure out how two of those building blocks could have fit together on their own– there was no way for the reaction to happen without external help.

However, scientists have now realized that maybe they were trying to put the wrong pieces together. Instead of fitting together the three components (a ribose sugar, a base, and a phosphate group), they’ve found a new way to assemble the molecule, by breaking it up into different starting pieces.


Think of it like building with Legos. You build each piece on brick by brick. But in this case, two of the pieces just won’t fit together. Instead scientists broke the Lego pieces into smaller parts and found a way to make them all come together to make the right molecule.

It’s a great example of scientists taking a step back and thinking about an old problem in a new way.


The Art and Math of the Fold

Last night I realized how long it’s been since I last folded a paper crane. The  documentary, Between the Folds, allows origami to explode into this beautiful world of artistic creations and amazing patterns and complexity driven by algorithms– sequences of mathematical instructions– ranging from simple to astronomically complex.

The funny thing is that on its surface, origami is simple– folding a piece of paper, no cutting and no glue. But there’s a beautiful tension throughout the nearly hour-long film between complexity– making a piece of paper as realistic and as complicated as possible– and simplicity, refining the art to be simple, cleaner and also more abstract.

In the trailer, one artist talks about the art of the origami process, the ballet of creating. The film shows him in a pas de deux with paper, with the beautiful score of Gil Talmi in the background. Vanessa Gould has created a beautiful, stunning film.

Beyond the beauty of the art itself, the scientific connections are wonderful. Teachers in Israel are using origami to inspire kids to learn math. In the film, mathematician Tom Hull shows how origami describes advanced mathematical concepts. MIT professor Erik Demaine and his sculptor father Marty (who collaborate), are perhaps the ultimate symbol of this blending of the artistic with the scientific (Erik also talked after the screening at CUNY Science & the Arts in Manhattan). In the Demaine family it appears that art and science are simply a matter of viewing the same coin from the opposite side. They create origami that then lets them test unusual math. It sounds like a wonderful symbiotic relationship.

The beauty of origami also has a practical package. Car airbags rely on the algorithms to fold efficiently into flat spaces. And origami has all sorts of biological implications. Proteins– the workhorses of living cells– are long strings that fold in specific shapes in order to work properly. Genetic material folds into complex shapes to fit inside the nucleus– the command center– of a cell. (I interviewed Paul Rothemund who designs DNA origami a few years ago. The magazine killed the story, but I still find the work fascinating).

And just for fun– Jeannine Mosely gave a lesson in origami: folding 6 cards into a cube (and even learning how to lock cubes with our neighbors). Here’s one I just put together at home with my outdated business cards.

cube made from my old business cards
cube made from my old business cards

Lots of fun. My sister bought me an origami set for Christmas last year. I think it’s time to break it out.


genetic (material) gyrations

Micrograph of Euplotes crassus, Image courtesy of L. Klobutcher
Micrograph of Euplotes crassus, Image courtesy of L. Klobutcher

RNA researchers rejoice! It’s been a good week for DNA’s often-underappreciated cousin. Most people are worried about the genetic material that stays safely tucked in the nucleus of cells, but RNA is definitely the genetic workhorse. Without these molecules, our genetic programs would be useless artifacts locked in the cell nucleus like some sort of museum object. DNA is the storage vehicle, but RNA is the messenger. RNA is cellular middle management, broadcasting the executive order from the nucleus’s control center, passing on the program to proteins, and even getting involved in regulating all those processes from time to time.

Continue reading genetic (material) gyrations