{"id":202167,"date":"2017-06-29T10:47:00","date_gmt":"2017-06-29T14:47:00","guid":{"rendered":"http:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/the-architecture-of-structured-dna-nature-com\/"},"modified":"2017-06-29T10:47:00","modified_gmt":"2017-06-29T14:47:00","slug":"the-architecture-of-structured-dna-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/dna\/the-architecture-of-structured-dna-nature-com\/","title":{"rendered":"The architecture of structured DNA &#8211; Nature.com"},"content":{"rendered":"<p><p>        P. Rothemund et al.\/Caltech      <\/p>\n<p>          Van Gogh's The Starry Night recreated using DNA.        <\/p>\n<p>    Vincent van Gogh's The Starry Night is a classic of    post-Impressionist art. Its whimsical whorls have entranced art    lovers since the Dutch artist painted it in 1889. In 2016, Paul    Rothemund, a bioengineer at the California Institute of    Technology in Pasadena, recreated the work. But instead of    oils, Rothemund drew his copy in DNA.  <\/p>\n<p>    Drawn on a silicon chip, Rothemund's creation demonstrates the    growing power of a once-obscure branch of materials science:    DNA nanotechnology. The field emerged in the 1990s when    scientists began to dream up nanoscale machines. Today, more    than 300 research groups are trying to harness the base-pairing    properties of DNA, with the goal of manipulating the molecule    as if it were a building material, rather than a carrier of    genetic information.  <\/p>\n<p>        Once we realized you can use the information in DNA to        organize stuff, it started a cascade of activity.      <\/p>\n<p>    Once we started to realize that you can use the information in    DNA to organize stuff, it started a cascade of activity, says    Ned Seeman, a synthetic chemist at New York University who is    widely acknowledged to be the founder of DNA nanotechnology.  <\/p>\n<p>    DNA's dimensions make it ideal for building nanostructures: the    double helix is a flexible, configurable rod, 2 nanometres    wide, with a twist that repeats every 3.43.6 nm. Researchers    have exploited the well-characterized structure, and the ease    of synthesizing custom DNA, to build ever-more-elaborate    designs for applications from drug delivery and diagnostics to    nanofabrication. But challenges remain, and nanotechnologists    are rethinking the fundamentals of building with DNA.  <\/p>\n<p>    The collection of shapes assembled from DNA ranges from 2D    smiley-faced emojis to 3D geometrical objects and blocks of    alphabetic characters. But the underlying technology is based    on one simple rule: base-pair complementarity. Driven by    hydrogen bonds that pair the bases adenine and thymine, and    cytosine and guanine, complementary DNA strands will    spontaneously form a double helix. In nature, the two strands    are usually fully complementary. If strands are only partially    complementary, however, both can accept multiple DNA partners.    This concept, says Rothemund, is the foundation of DNA    nanotechnology.  <\/p>\n<p>    During cell division, DNA forms a four-armed intermediate    structure known as a Holliday junction. The structure is    unstable and disintegrates quickly into two double helices. In    the early 1980s, Seeman managed to stabilize it1 by pairing each    strand's sequence with another at the junction. He went on to    produce a junction with six strands, forming the first branched    DNA structure in 3D. A series of increasingly complex designs    followed: a stick cube in 1991, branched DNA crystals in 1998    and DNA tubes in 2005.  <\/p>\n<p>    In 2004, William Shih, a biochemist now at the Wyss Institute    for Biologically Inspired Engineering at Harvard University in    Boston, Massachusetts, took a different approach. He formed a    22-nm-wide octahedron from just a single strand of    DNA2. The 1,669-base    DNA strand was held in shape using five 40-base strands.  <\/p>\n<p>    Building on this idea, two years later, Rothemund used hundreds    of 26- to 32-base segments of DNA that he called staples to    guide the folding of a 7-kilobase 'scaffold' strand into a    variety of 2D shapes roughly 100 nm in diameter3. This was a    landmark achievement, says DNA scientist Peng Yin, also at the    Wyss Institute, because it greatly increased the complexity and    size of DNA nanostructures.  <\/p>\n<p>    Rothemund built his structures using the single-stranded DNA of    a virus as a scaffold  the DNA required was too long for    conventional oligonucleotide synthesis. He worked out how the    DNA could be folded and where the 200 or so staples would need    to attach to form shapes such as squares, triangles, stars and    smiley faces. By mixing the DNA with a 100 times more staples    than were needed, heating to 95 C and cooling to room    temperature over 2 hours, the shapes formed spontaneously on    the basis of the instructions programmed into their sequences.  <\/p>\n<p>    DNA 'origami' has come a long way since then. Initially, says    Shawn Douglas, a biophysicist at the University of California,    San Francisco, it could take an entire month to work out where    the folds and staples go for just one design. It was easy to    make mistakes, he says, and also hard to make modifications.    This challenge inspired Douglas to develop software to    accelerate origami design (see 'DNA    origami'). The first working version of caDNAno was built    in 2009, while Douglas was completing his PhD in Shih's group    at Harvard. The software cut origami design to one    day4. In the next 3    months, we made 30 shapes, says Douglas, including rectangular    blocks, crosses and genie bottles.  <\/p>\n<p>        Folding DNA typically begins with choosing a scaffold.        Single-stranded sequences of up to 200 bases can be        synthesized relatively easily, but beyond that, it is        simpler to use viral DNA.      <\/p>\n<p>        Once a shape has been chosen, the software tools caDNAno or        DAEDALUS can be used to help design the structure. caDNAno        can map a preselected sequence in the desired shape,        identify crossover points and generate the short strands of        DNA or 'staples' required to fold it. With DAEDALUS, only        the desired geometry is needed; the software generates the        scaffold and staple sequences. The blueprints can be        checked for accuracy using the tool CanDo, which predicts        the 3D structure.      <\/p>\n<p>        The strands are then mixed together in the right ratios        (with an excess of staples), heated and cooled. Well-formed        DNA nanostructures are seen on gel electrophoresis as sharp        bands that are distinct from the starting material. They        can be further characterized using electron microscopy or        atomic force microscopy. If no band is present, the DNA        either failed to fold or the yield was low. This could be        due to a design mistake, especially at crossover points. If        the design is correct, the folding conditions may need to        be optimized by tuning parameters such as the buffer,        temperature and reaction time.      <\/p>\n<p>        For researchers who don't want to create their own DNA        nanomaterials, Tilibit Nanosystems in Garching, Germany,        supplies made-to-order structures and prefabricated        structures and kits.      <\/p>\n<p>    A couple of years later, another team, led by biophysicist Mark    Bathe at the Massachusetts Institute of Technology in    Cambridge, developed an ancillary tool called    CanDo5 to check the DNA    origami blueprint from caDNAno. It will tell you what it    thinks the structure looks like in 3D, says Bathe. Bathe's    group has since developed a tool called DAEDALUS that tells    users all the sequences, including the scaffold, they need just    by entering a desired geometry6.  <\/p>\n<p>    Another way to build with DNA is using DNA bricks. In 2012,    while a postdoctoral fellow in Shih's lab, Yonggang Ke, a    biochemist now at Georgia Institute of Technology and Emory    University in Atlanta, developed a technique in which every    brick in a DNA nanostructure has a unique sequence of 32 or 42    bases. A quarter of each sequence is complementary to another    quarter on a different brick. By connecting and extending the    bricks, researchers can assemble a canvas like building a brick    wall. Each brick can bind to two at the top and two at the    bottom, Yin explains.  <\/p>\n<p>    For a flat, 2D canvas, the bricks contain 10.5 bases per    quarter, which allows them to connect to each other in a single    plane; any 2D pattern can be prepared by simply picking the    correct bricks. To add a third dimension, Ke shortened the    bricks to eight bases per quarter, which forced them to connect    perpendicularly. The researchers produced 102 distinct    structures, including hearts, spheres and the Roman    alphabet7. In that first    paper, we produced more 3D structures than the whole field    combined, says Yin.  <\/p>\n<p>    One use for these novel DNA shapes is to carry materials such    as drug molecules, metal nanoparticles and proteins.    Positioning these useful materials on the DNA is generally    easiest before it is coaxed into a structure. The cargo is    typically carried on the staple strands, and because each    structure can include some 200 staples, says Rothemund, they    offer plenty of opportunities to precisely place the molecular    cargo.  <\/p>\n<p>    DNA molecules are charged, which means that nanostructures can    be arranged electrostatically by etching a pattern of    negatively charged binding sites on a flat surface using an    electron beam. You can get them exactly where you want,    oriented how you want, says Rothemund. This is just what his    team demonstrated when it recreated The Starry Night    from a dense array of photonic crystal cavities     micrometre-sized devices in which light can resonate  that    contained meticulously placed DNA nanostructures carrying    dyes8.  <\/p>\n<p>    Another idea is to cast nanoparticles using DNA nanostructures    as the mould. This requires fairly large and stiff DNA    nanostructures with internal cavities. In collaboration with    Bathe's team, Yin's group built such structures using DNA    bricks. The teams then introduced silver nanoparticle seeds    into the cavities, and allowed them to develop in the presence    of soluble silver, like rock sugar growing in supersaturated    solution. The seeds developed to fill the cavities, producing    cubic, spherical, triangular and Y-shaped    nanoparticles9.  <\/p>\n<p>        P. Rothemund\/Caltech      <\/p>\n<p>          Smiley-faced emojis are one of the many shapes assembled          from DNA.        <\/p>\n<p>    Chad Mirkin, a chemist at Northwestern University in Evanston,    Illinois, is pursuing yet another nano-strategy, which he calls    programmable atom equivalents. These nanoparticle cores can    range from metals and polymers to proteins. Hundreds of    partially double-stranded DNA molecules are attached to the    core's surface to form a dense DNA shell. The single-stranded    free ends are complementary to the free ends of other 'atom    equivalents'. When those structures are mixed together, they    link up and extend into a crystal lattice that positions the    desired atoms precisely in space. This is an incredibly    reliable method, says Mirkin.  <\/p>\n<p>    Remarkably, the crystal's structure and properties can be    controlled by varying the sizes and shapes of the nanoparticle    cores, as well as the length of the DNA strands  no small    achievement, given that crystallization processes are    notoriously tricky. We are trading ill-defined materials    chemistry for well-defined and programmable DNA interactions to    form high-quality crystals, and we can guide it down a path,    says Mirkin, whose research group has churned out more than 40    crystal symmetries, 6 of which have never been observed in    nature.  <\/p>\n<p>    One popular adornment to nanostructured DNA is light-emitting    materials called fluorophores. GATTAquant DNA Nanotechnologies    in Braunschweig, Germany, for instance, makes nanorulers from    DNA origami structures and fluorescent molecules to validate    super-resolution microscopes. Super-resolution microscopy    allows researchers to take images beyond the resolution limit    set by the diffraction of light, but there is no standard to    measure the resolution of the system, says Max Scheible, head    of research and development at GATTAquant. DNA nanotechnology    really enabled this.  <\/p>\n<p>    GATTAquant attaches fluorescent molecules at precise distances    on an origami structure and mounts them on glass slides. These    nanoscale rulers allow researchers to verify the resolution of    sub-diffraction-limit microscopes.  <\/p>\n<p>    The co-founders of Ultivue, a start-up company in Cambridge,    Massachusetts, are hoping to use nanostructures to make an    impact in cancer research. In cancer tissues, biomarkers such    as the proteins BRCA1 and HER2 can herald the onset or    progression of disease, and can potentially aid diagnosis,    prognosis and treatment. Until now, most biomarkers have been    studied in isolation. What's missing is a fingerprint of    biomarkers as they are seen in cancerous tissue, says Mael    Manesse, lead researcher at Ultivue.  <\/p>\n<p>    At Ultivue's headquarters, Manesse demonstrates the company's    technology. Lit on the computer monitor are cells from a thin    slice of lung tissue that Manesse has positioned under a    microscope. When he switches the microscope's light to red, the    cells disappear. In their place is a smattering of bright    spots, indicating CD3  a biomarker for immune cells called T    cells. These proteins are marked with Ultivue's DNA-based    imaging probe: a short 'docking' strand attached through an    antibody, and its complementary 'imaging' strand carrying a    fluorescent dye. Each biomarker of interest has its own docking    strand; the complementary imaging strands can be added, imaged    and removed one at a time. The images are then superimposed to    obtain a composite picture of the tissue. This allows almost    unlimited numbers of biomarkers to be studied, but the tissue    sample remains preserved, says Manesse.  <\/p>\n<p>    DNA nanostructures can also be used to build sensors, drugs and    vaccines for therapeutic or diagnostic applications. For    example, researchers have made a synthetic vaccine by anchoring    the antigen streptavidin and oligonucleotides with an    immune-response-boosting, repeating cytosineguanine motif on    tetrahedral DNA nanostructures10. In mouse    studies, the vaccine produced higher levels of antibodies    against streptavidin than a mixture of just streptavidin and    oligonucleotides.  <\/p>\n<p>    Eventually, Shih hopes to make drug nanofactories: DNA origami    nanocapsules that can produce drugs on demand inside the body    using building blocks from the cell. It is very exploratory at    this point, he says. In theory, the nanocapsules would hold    RNA polymerase  an enzyme that makes RNA  and DNA templates.    Once triggered, it would begin manufacturing and releasing its    payload, like a virus using cellular materials to replicate    itself.  <\/p>\n<p>    Although well into its third decade, DNA nanotechnology still    faces a number of challenges. One key obstacle, says    biophysicist Hendrik Dietz at the Technical University of    Munich, Germany, is production yield: researchers have yet to    break into gram-scale synthesis. DNA origami can make a very    big difference in health, Dietz says. But the problem is we    can't even make quantities that are big enough to use.  <\/p>\n<p>    Another hurdle is the limited variety of materials that can be    attached to DNA. Researchers are working to expand origami    designs to use materials other than DNA. Earlier this year, for    example, Dietz reported the preparation of DNA structures that    fold using protein staples11, and Douglas    is updating caDNAno to include RNA and protein building blocks.  <\/p>\n<p>    Perhaps the biggest limitation is the lack of control over the    self-assembly process. As structures get larger, the chances of    misfolding increase. We need new strategies to suppress    self-assembly errors, says Shih.  <\/p>\n<p>    One possibility, Rothemund suggests, would be to move away from    the standard in vitro method of mixing, heating and    cooling, and allow cells to build the structures instead. Last    year, bioengineer Christopher Voigt at the Massachusetts    Institute of Technology engineered the bacterium Escherichia    coli to produce a simple, branched, four-part junction from    single-stranded DNA12. But for    more-complex origami nanostructures, Rothemund says, a shift to    RNA may be necessary. Unlike DNA, single-stranded RNA can hold    its shape without staples. Building with RNA is largely    uncharted territory, but Rothemund is excited to explore it.    It is like building with wood, but now you can't use nails or    notches or glue, he says. We still need to learn a lot of    things.  <\/p>\n<p><!-- Auto Generated --><\/p>\n<p>Read the rest here:<br \/>\n<a target=\"_blank\" href=\"http:\/\/www.nature.com\/nature\/journal\/v546\/n7660\/full\/546687a.html\" title=\"The architecture of structured DNA - Nature.com\">The architecture of structured DNA - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> P. Rothemund et al.\/Caltech Van Gogh's The Starry Night recreated using DNA. Vincent van Gogh's The Starry Night is a classic of post-Impressionist art <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/dna\/the-architecture-of-structured-dna-nature-com\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[26],"tags":[],"class_list":["post-202167","post","type-post","status-publish","format-standard","hentry","category-dna"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/202167"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=202167"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/202167\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=202167"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=202167"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=202167"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}