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Optimizing DNA strand lengths for assisted self-assembly

The specific binding of complementary DNA sequences has provided a set of easily programmed molecular interactions to build a wide range of nanostructures, molecular devices, and materials. One of the practical issues in designing DNA strands to serve as “glue” is to make the strands long enough to bind strongly to their complementary sequences, but not so long as to have other possible interactions that compete with the desired interaction. From North Carolina State University “Researchers Find ‘Goldilocks’ Of DNA Self-Assembly“:

Researchers from North Carolina State University have found a way to optimize the development of DNA self-assembling materials, which hold promise for technologies ranging from drug delivery to molecular sensors. The key to the advance is the discovery of the “Goldilocks” length for DNA strands used in self-assembly — not too long, not too short, but just right.

DNA strands contain genetic coding that will form bonds with another strand that contains a unique sequence of complementary genes. By coating a material with a specific DNA layer, that material will then seek out and bond with its complementary counterpart. This concept, known as DNA-assisted self-assembly, creates significant opportunities in the biomedical and materials science fields, because it may allow the creation of self-assembling materials with a variety of applications.

But, while DNA self-assembly technology is not a new concept, it has historically faced some significant stumbling blocks. One of these obstacles has been that DNA segments that are too short often failed to self-assemble, while segments that are too long often led to the creation of deformed materials. This hurdle can lead to basic manufacturing problems, as well as significant changes in the properties of the material itself.

A team of researchers from NC State and the University of Melbourne have proposed a solution to this problem, using computer simulations of DNA strands to identify the optimal length of a DNA strand for self-assembly – and explaining the scientific principles behind it (see video below).

“Strands that are too short or long form self-protected motifs,” says Dr. Yara Yingling, an assistant professor of materials science and engineering at NC State and co-author of a paper describing the research. That means that the strands bond to each other, rather than to “partner” materials.

“The optimal lengths are not long enough to intertwine with each other, and are not short enough to fold over on themselves,” Yingling explains. That leaves them exposed, and available to bond with the materials in another layer – the perfect situation for DNA self-assembly.

Thanks to Philippe Van Nedervelde, Foresight Executive Director, Europe.

4 Responses to “Optimizing DNA strand lengths for assisted self-assembly”

  1. flashgordon Says:

    once again, late and needing somebody else to tell you!

  2. Un nuevo sensor biológico detecta y analiza secuencias de ADN « RDi Press Says:

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  3. Nanoman Says:

    Flashgordon, Foresight is a great organization and their news releases are valued and appreciated greatly. Instead of being so “negative” on this, why not congratulate them? Also: What is your take on the development time and applications of mechanosynthetic chemistry? Who do you think will be the first nation to develop real molecular manufacturing systems and what are some of the uses you expect to see? Stronger fiber materials? Powerful memory storage? Medical devices?

    Also: What are some alternatives to diamondoid for nanomechanical devices? Silicates? Glass? Metals?

  4. flashgordon Says:

    I congratulate them on announcing the cellular automata solution to parallel processing; something that hasn’t been announced anywhere else in the world!

    As for the rest of your questions . . . mechanochemistry was first accomplished back in like 97 I do believe! Zyvez has been moving fifty atoms(as of the last report I’ve heard; see this website!) per second; i don’t know if that was actual mechanochemistry. Their timeline is sometime around moore’s law – 2020; almost certainly before 2030, the world won’t be the same(if we’re still here; china is itching to take out Taiwon, and North Korea wants to take out South Korea and Zyvex is intimately tied up with them; seems to me that North Korea is waiting for China to perfect their anti-aircraft carrier technology to start war with South Korea with China keeping America at bay; i’ve heard that china could have their anti-aircraft carrier weapons system perfected in three years . . . ;)

    But, there’s other ‘nanotechnologies’; dna-nanotechnologies; right now, we can self-organize pretty well; now, we have some hints of being able to do some mechanochemistry with it as well. There was also an Israel group which figured out how to make ‘stiff’ carbon structures of any shape(only spheroids have so far been reported). The race to a nanomanufacturing that can cure the sick, kind of sweep away the economic system is heating up for sure! I would think within five years, dna-nanotech can do a lot. Question is how much and can it ‘bootstrap’ itself to a more robust nanomanufacturing system before Zyvex gets going?

    Applications are harder to predict; new scientific instruments and some medical abilities for sure.

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