On the planet of biomolecules, none is extra iconic, nor extra versatile than DNA. Nature makes use of the well-known double-helix to retailer the blueprints of all residing kinds, drawing on a four-letter alphabet of nucleotides.
Researchers within the discipline of DNA nanotechnology have been impressed by the seemingly inexhaustible number of residing kinds nature has usual from this genetic uncooked materials. The sector seeks to emulate nature’s inventive enterprise and even prolong the chances of DNA structure past what nature has created.
In a brand new examine, Hao Yan and his colleagues Nicholas Stephanopoulos and Petr Sulc, discover a fundamental constructing block used within the fabrication of many DNA nanoforms. Often called a Holliday junction, this nexus of two segments of double stranded DNA has been used to kind elaborate, self-assembling crystal lattices on the nanometer scale, (or roughly 1/75,000th the width of a human hair).
“The unique imaginative and prescient of structural DNA nanotechnology was to rationally design self-assembling 3D crystals with DNA junctions,” Yan stated. “A basic structural motif used for this goal was based mostly on the Holliday junction moiety.”
The buildings take their title from molecular biologist Robin Holliday, who first proposed their existence in 1964. Holliday junctions play a necessary position in nature, the place they’re concerned in a course of often called homologous recombination, a driving drive in producing novel genetic variation in residing issues.
Because the inception of DNA nanotechnology, the sphere has made outstanding strides, utilizing DNA elements to design tiny buildings of intricate magnificence in addition to nanoscale units whose functions contact on fields as diverse as photonics, laptop storage, biosensing and tissue regeneration.
Professor Yan has been on the forefront of the sphere’s speedy transformations, designing a myriad of helpful nanoarchitectural kinds, from cartwheeling nanorobots and DNA spiders to cancer-fighting seek-and-destroy units.
The brand new examine makes use of crystallography strategies to explain the traits of 36 fundamental variants of the Holliday junction. The outcomes present that the effectiveness of a given Holliday junction for the development of crystalline nanoarchitectures is sensitively dependent not solely on the association of the 4 nucleotide pairs forming the junction, but in addition on sequences forming the junction’s 4 protruding arms. Some DNA sequences act to boost the crystallization course of of those kinds, whereas 6 of the 36 Holliday junction variants had been deemed “deadly” on account of their failure to kind crystals.
Professor Yan directs the Biodesign Heart for Molecular Design and Biomimetics (BCMDB) and holds the Milton D. Glick Distinguished Professorship in ASU’s Faculty of Molecular Sciences (SMS). Stephanopoulos and Sulc are additionally college members in BCMDB and SMS.
The analysis findings, which symbolize the primary systematic examine of Holliday junctions, not too long ago appeared within the journal Nature Communications.
DNA proves to be an excellent materials with which to design and fabricate nanoscale buildings. The constant and predictable nature of base pairing amongst DNA’s 4 nucleotides ensures that correctly engineered kinds will reliably self-assemble into desired buildings. To this finish, varied elaborate nanoforms have been constructed utilizing basic DNA constructing blocks, one of the standard and helpful being the Holliday junction. DNA crystals composed of repeating structural models are key elements for nanotechnology functions, permitting for versatile and scalable design options.
Holliday junctions are noticed in nature as an middleman stage in the course of the means of cell meiosis. The results of this transformation is an change of genes between maternal and paternal chromosomes. This course of, often called homologous recombination, happens in 4 levels. (See illustration.)
First, a pair of double-stranded DNA helices sit alongside one another. An enzyme often called an endonuclease then causes a single-stranded break in every of the 2 double strands. The subsequent step, often called strand invasion, happens when the free ends of every single-stranded break be a part of collectively, inflicting the initially separate double strands to be intertwined.
This cross-shaped construction, which joins the 2 separate double strands of DNA collectively, is the Holliday junction. In organic processes, the junction is then “resolved” when one other enzyme cuts the Holliday junction in certainly one of two methods, each leading to two separate DNA strands, which differ from the unique strands as a result of the Holliday junction has launched new DNA segments into the 2 DNA double strands.
This type of DNA recombination is a common organic occasion of nice significance. It concurrently acts to protect genome integrity by means of mechanisms of DNA restore whereas producing novel variability, with out which, organisms would quickly attain an evolutionary lifeless finish. The important thing construction within the shuffling of the DNA deck throughout cell division is the Holliday junction.
It was later famous that the Holliday junction motif may very well be used as a robust constructing block for a multiplicity of synthetic DNA buildings. Though the Holliday junctions occurring throughout cell division can slide alongside the DNA size, in a course of often called department migration, the junctions used for developing DNA nanostructures are immobilized as a result of the sequences flanking them are usually not complementary.
“The primary motionless Holliday junction was described in 1982, and this sequence has since been used completely in self-assembling DNA crystals,” stated Chad Simmons, first creator of the paper and the lead scientist making use of X-ray crystallography for this examine. “Our work sought to vary this paradigm by probing the 35 different potential motionless junctions. Because of this, we had been in a position to establish a number of sequences that yielded superior efficiency in comparison with their predecessors by way of their potential to robustly crystallize and diffract to excessive decision, and which allowed the flexibility to manage the symmetry of the lattice association. This required an exhaustive effort that yielded 134 new crystal buildings, and we’re very excited to share a complete toolbox of sequence combos to direct the design and development of future self-assembling DNA crystal methods.”
The brand new analysis demonstrates that almost all Holliday junction variants produce self-assembling crystals, although 6 deadly junction preparations had been incompatible with crystal formation. The frequent function in these failed junctions was their lack of two vital binding websites for ions that are important for crystal formation.
“This examine was fascinating as a result of it confirmed how delicate variations in Holliday junction geometries — which may very well be understood on the single-nucleotide stage — may have dramatic results on crystal meeting and symmetry. That is actually “molecular science,” permitting us to ultimately engineer interactions on the molecular stage that may give rise to thrilling nanomaterials with unprecedented management,”stated Stephanopolous.
“One of many challenges of this analysis was to find out why some Holliday junctions may produce crystals, however others don’t. Empirically, we may examine the crystal buildings of these junctions that crystallize, however to grasp the conduct of the deadly junction preparations that don’t, computational chemistry was wanted,” stated Sulc. “To this finish, we teamed up with Dr. Miroslav Krepl and Prof. Jiri Sponer from the Czech Academy of Sciences, who simulated all Holliday junctions at atomistic decision, and gained the vital perception that the deadly junctions weren’t in a position to bind ions that stabilize conformation. This effort offered a wonderful instance of the place laptop modeling and experiments can collectively clarify complicated phenomena.”
The brand new analysis offers worthwhile clues for the design and improvement of novel kinds to be added to the ever-growing plethora of nanostructures and nanodevices serving a broad vary of functions in electronics, imaging, laptop science and medication.