RNA origami

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RNA origami mechanism. Rna origami adaption.png
RNA origami mechanism.

RNA origami is the nanoscale folding of RNA, enabling the RNA to create particular shapes to organize these molecules. [1] It is a new method that was developed by researchers from Aarhus University and California Institute of Technology. [2] RNA origami is synthesized by enzymes that fold RNA into particular shapes. The folding of the RNA occurs in living cells under natural conditions. RNA origami is represented as a DNA gene, which within cells can be transcribed into RNA by RNA polymerase. Many computer algorithms are present to help with RNA folding, but none can fully predict the folding of RNA of a singular sequence. [2]

Contents

Overview

RNA adapted motifs RNA Origami Motifs.png
RNA adapted motifs

In nucleic acids nanotechnology, artificial nucleic acids are designed to form molecular components that can self-assemble into stable structures for use ranging from targeted drug delivery to programmable biomaterials. [3] DNA nanotechnology uses DNA motifs to build target shapes and arrangements. It has been used in a variety of situations, including nanorobotics, algorithmic arrays, and sensor applications. The future of DNA nanotechnology is filled with possibilities for applications. [4]

The success of DNA nanotechnology has allowed designers to develop RNA nanotechnology as a growing discipline. RNA nanotechnology combines the simplistic design and manipulation characteristic of DNA, with the additional flexibility in structure and diversity in function similar to that of proteins. [5] RNA's versatility in structure and function, favorable in vivo attributes, and bottom-up self-assembly is an ideal avenue for developing biomaterial and nanoparticle drug delivery. Several techniques were developed to construct these RNA nanoparticles, including RNA cubic scaffold, [6] templated and non-templated assembly, and RNA origami.

The first work in RNA origami appeared in Science, published by Ebbe S. Andersen of Aarhus University. [7] Researchers at Aarhus University used various 3D models and computer software to design individual RNA origami. Once encoded as a synthetic DNA gene, adding RNA polymerase resulted in the formation of RNA origami. Observation of RNA was primarily done through atomic force microscopy, a technique that allows researchers to look at molecules a thousand times closer than would normally be possible with a conventional light microscope. They were able to form honeycomb shapes, but determined other shapes are also possible.

Cody Geary, a scholar in the field of RNA origami, described the uniqueness of the method of RNA origami. He stated that its folding recipe is encoded in the molecule itself, and determine by its sequence. The sequence gives the RNA origami both its final shape and movements of the structure as it folds. The primary challenge associated with RNA origami stems from the fact RNA folds on its own and can thus easily tangle itself. [2]

Computer-aided design

Computer-aided design of the RNA origami structure requires three main processes; creating the 3D model, writing the 2D structure, and designing the sequence. First, a 3D model is constructed using tertiary motifs from existing databases. This is necessary to ensure the created structure has feasible geometry and strain. The next process is creating the 2D structure describing the strand path and base pairs from the 3D model. This 2D blueprint introduces sequence constraints, creating primary, secondary, and tertiary motifs. The final step is designing sequences compatible with designed structure. Design algorithms can be used to create sequences that can fold into various structures. [8]

DNA and RNA origami double cross over building block comparison. The left panel is the blueprint design of a multi-stranded DX used commonly in DNA origami. The right panel is the design of the single stranded DX by inserting hairpins, kissing loops, and dovetail seam motif. Kissing loop.png
DNA and RNA origami double cross over building block comparison. The left panel is the blueprint design of a multi-stranded DX used commonly in DNA origami. The right panel is the design of the single stranded DX by inserting hairpins, kissing loops, and dovetail seam motif.

The double crossover (DX)

To produce a desired shape, the RNA origami method uses double-crossovers (DX) to arrange the RNA helices in parallel to each other to form a building block. While DNA origami requires the construction of DNA molecules from multiple strands, researchers were able to devise a method in making DX molecules from only one strand for RNA. This was done through adding hairpin motifs to the edges and kissing-loop complexes on internal helices. The addition of more DNA molecules on top of one another creates a junction known as the dovetail seam. This dovetail seam has base pairs that cross between adjacent junctions; thus, the structural seam along the junction becomes sequence-specific. An important aspect of these folding interactions is its folding; the order that interactions form can potentially create a situation in which one interaction blocks another, creating a knot. Because the kissing-loop interactions and dovetail interactions are a half-turn or shorter, they do not create these topological issues. [8]

Comparison with DNA origami

RNA and DNA nanostructures are used for the organization and coordination of important molecular processes. However, there exist several distinct differences between the fundamental structure and applications between the two. Although inspired by the DNA origami techniques established by Paul Rothemund, [9] the process for RNA origami is vastly different. RNA origami is a much newer process than DNA origami; DNA origami has been studied for approximately a decade now, while the study of RNA origami has only recently begun.

In contrast to DNA origami, which involves chemically synthesizing the DNA strands and arranging the strands to form any shape desired with the aid of "staple strands", RNA origami is made by enzymes and subsequently folds into pre-rendered shapes. RNA is able to fold into unique ways in complex structures due to a number of secondary structural motifs, such as conserved motifs and short structural elements. A major determinant for RNA topology is the secondary-structure interaction, which include motifs such as pseudoknots and kissing loops, adjacent helices stacking on one another, hairpin loops with bulge content, and coaxial stacks. This is largely a result of four different nucleotides: adenine (A), cytosine (C), guanine (G) and uracil (U), and ability to form non-canonical base pairs.

There also exist more complex and longer-range RNA tertiary interactions. DNA are unable to forms these tertiary motifs and thereby cannot match the functional capacity of RNA in performing more versatile tasks. RNA molecules that are correctly folded can serve as enzymes, due to positioning metal ions at their active sites; this gives the molecules a diverse array of catalytic abilities. [10] Because of this relationship to enzymes, RNA structures can potentially be grown within living cells and used to organize cellular enzymes into distinct groups.

Additionally, the DNA origami's molecular breakup is not easily incorporated into the genetic material of an organism. However, RNA origami is capable of being written directly as a DNA gene and transcribed using RNA polymerase. Therefore, while DNA origami requires expensive culturing outside of a cell, RNA origami can be produced in mass, cheap quantities directly within cells just by growing bacteria. [11] The feasibility and cost effectiveness of manufacturing RNA in living cells and combined with the extra functionality of RNA structure is promising for the development of RNA origami.

Applications

RNA origami is a new concept and has great potential for applications in nanomedicine and synthetic biology. The method was developed to allow new creations of large RNA nanostructures that create defined scaffolds for combining RNA based functionalities. Because of the infancy of RNA origami, many of its potential applications are still in the process of discovery. Its structures are able to provide a stable basis to allow functionality for RNA components. These structures include riboswitches, ribozymes, interaction sites, and aptamers. Aptamer structures allow the binding of small molecules which gives possibilities for construction of future RNA based nanodevices. RNA origami is further useful in areas such as cell recognition and binding for diagnosis. Additionally, targeted delivery and blood-brain barrier passing have been studied. [6] Perhaps the most important future application for RNA origami is building scaffolds to arrange other microscopic proteins and allow them to work with one another. [8]

Related Research Articles

<span class="mw-page-title-main">DNA</span> Molecule that carries genetic information

Deoxyribonucleic acid is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

<span class="mw-page-title-main">Protein biosynthesis</span> Assembly of proteins inside biological cells

Protein biosynthesis is a core biological process, occurring inside cells, balancing the loss of cellular proteins through the production of new proteins. Proteins perform a number of critical functions as enzymes, structural proteins or hormones. Protein synthesis is a very similar process for both prokaryotes and eukaryotes but there are some distinct differences.

<span class="mw-page-title-main">Macromolecule</span> Very large molecule, such as a protein

A macromolecule is a very large molecule important to biological processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The most common macromolecules in biochemistry are biopolymers and large non-polymeric molecules such as lipids, nanogels and macrocycles. Synthetic fibers and experimental materials such as carbon nanotubes are also examples of macromolecules.

In biochemistry, the native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. The native state of a biomolecule may possess all four levels of biomolecular structure, with the secondary through quaternary structure being formed from weak interactions along the covalently-bonded backbone. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure.

A nanoruler is a tool or a method used within the subfield of "nanometrology" to achieve precise control and measurements at the nanoscale. Measurements of extremely tiny proportions require more complicated procedures, such as manipulating the properties of light (plasmonic) or DNA to determine distances. At the nanoscale, materials and devices exhibit unique properties that can significantly influence their behavior. In fields like electronics, medicine, and biotechnology, where advancements come from manipulating matter at the atomic and molecular levels, nanoscale measurements become essential.

Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic. This is similar to the action of other biological enzymes, such as proteins or ribozymes . However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s, there is only little evidence for naturally occurring deoxyribozymes. Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.

<span class="mw-page-title-main">DNA origami</span> Folding of DNA to create two- and three-dimensional shapes at the nanoscale

DNA origami is the nanoscale folding of DNA to create arbitrary two- and three-dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material, through design of its base sequences. DNA is a well-understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own.

<span class="mw-page-title-main">Holliday junction</span> Branched nucleic acid structure

A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after Robin Holliday, the molecular biologist who proposed its existence in 1964.

<span class="mw-page-title-main">Biomolecular structure</span> 3D conformation of a biological sequence, like DNA, RNA, proteins

Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary. The scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecule's various hydrogen bonds. This leads to several recognizable domains of protein structure and nucleic acid structure, including such secondary-structure features as alpha helixes and beta sheets for proteins, and hairpin loops, bulges, and internal loops for nucleic acids. The terms primary, secondary, tertiary, and quaternary structure were introduced by Kaj Ulrik Linderstrøm-Lang in his 1951 Lane Medical Lectures at Stanford University.

<span class="mw-page-title-main">Nucleic acid design</span>

Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing. It is necessary because there are many possible sequences of nucleic acid strands that will fold into a given secondary structure, but many of these sequences will have undesired additional interactions which must be avoided. In addition, there are many tertiary structure considerations which affect the choice of a secondary structure for a given design.

<span class="mw-page-title-main">Molecular models of DNA</span>

Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.

<span class="mw-page-title-main">Nucleic acid tertiary structure</span> Three-dimensional shape of a nucleic acid polymer

Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structural motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.

<span class="mw-page-title-main">Nucleic acid structure</span> Biomolecular structure of nucleic acids such as DNA and RNA

Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.

<span class="mw-page-title-main">DNA nanotechnology</span> The design and manufacture of artificial nucleic acid structures for technological uses

DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, and functional devices such as molecular machines and DNA computers. The field is beginning to be used as a tool to solve basic science problems in structural biology and biophysics, including applications in X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins to determine structures. Potential applications in molecular scale electronics and nanomedicine are also being investigated.

<span class="mw-page-title-main">Nucleic acid secondary structure</span>

Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.

Numerous key discoveries in biology have emerged from studies of RNA, including seminal work in the fields of biochemistry, genetics, microbiology, molecular biology, molecular evolution and structural biology. As of 2010, 30 scientists have been awarded Nobel Prizes for experimental work that includes studies of RNA. Specific discoveries of high biological significance are discussed in this article.

<span class="mw-page-title-main">Nucleic acid quaternary structure</span>

Nucleic acidquaternary structure refers to the interactions between separate nucleic acid molecules, or between nucleic acid molecules and proteins. The concept is analogous to protein quaternary structure, but as the analogy is not perfect, the term is used to refer to a number of different concepts in nucleic acids and is less commonly encountered. Similarly other biomolecules such as proteins, nucleic acids have four levels of structural arrangement: primary, secondary, tertiary, and quaternary structure. Primary structure is the linear sequence of nucleotides, secondary structure involves small local folding motifs, and tertiary structure is the 3D folded shape of nucleic acid molecule. In general, quaternary structure refers to 3D interactions between multiple subunits. In the case of nucleic acids, quaternary structure refers to interactions between multiple nucleic acid molecules or between nucleic acids and proteins. Nucleic acid quaternary structure is important for understanding DNA, RNA, and gene expression because quaternary structure can impact function. For example, when DNA is packed into heterochromatin, therefore exhibiting a type of quaternary structure, gene transcription will be inhibited.

<span class="mw-page-title-main">Spherical nucleic acid</span>

Spherical nucleic acids (SNAs) are nanostructures that consist of a densely packed, highly oriented arrangement of linear nucleic acids in a three-dimensional, spherical geometry. This novel three-dimensional architecture is responsible for many of the SNA's novel chemical, biological, and physical properties that make it useful in biomedicine and materials synthesis. SNAs were first introduced in 1996 by Chad Mirkin’s group at Northwestern University.

TectoRNAs are modular RNA units able to self-assemble into larger nanostructures in a programmable fashion. They are generated by rational design through an approach called RNA architectonics, which make use of RNA structural modules identified in natural RNA molecules to form pre-defined 3D structures spontaneously.

This glossary of cellular and molecular biology is a list of definitions of terms and concepts commonly used in the study of cell biology, molecular biology, and related disciplines, including genetics, biochemistry, and microbiology. It is split across two articles:

References

  1. ↑ "Programmed to Fold: RNA Origami | Caltech". The California Institute of Technology. Retrieved 2017-10-09.
  2. 1 2 3 "Scientists Fold RNA Origami from a Single Strand - Science Newsline". www.sciencenewsline.com. Retrieved 2017-11-20.
  3. ↑ Nucleic Acid Nanotechnology | SpringerLink (PDF). Nucleic Acids and Molecular Biology. Vol. 29. 2014. doi:10.1007/978-3-642-38815-6. ISBN   978-3-642-38814-9. S2CID   44920215.
  4. ↑ Seeman, Nadrian C. (2005). "Structural DNA Nanotechnology: An Overview". Nano Biotechnology Protocols. Methods in Molecular Biology. Vol. 303. pp. 143–166. doi:10.1385/1-59259-901-X:143. ISBN   978-1-59259-901-1. ISSN   1064-3745. PMC   3478330 . PMID   15923682.
  5. ↑ Guo, Peixuan (December 2010). "The Emerging Field of RNA Nanotechnology". Nature Nanotechnology. 5 (12): 833–842. Bibcode:2010NatNa...5..833G. doi:10.1038/nnano.2010.231. ISSN   1748-3387. PMC   3149862 . PMID   21102465.
  6. 1 2 Afonin, Kirill A; Bindewald, Eckart; Yaghoubian, Alan J.; Voss, Neil; Jacovetty, Erica; Shapiro, Bruce A.; Jaeger, Luc (September 2010). "In vitro Assembly of Cubic RNA-Based Scaffolds Designed in silico". Nature Nanotechnology. 5 (9): 676–682. Bibcode:2010NatNa...5..676A. doi:10.1038/nnano.2010.160. ISSN   1748-3387. PMC   2934861 . PMID   20802494.
  7. ↑ Geary, Cody; Rothemund, Paul W. K.; Andersen, Ebbe S. (2014-08-15). "A single-stranded architecture for cotranscriptional folding of RNA nanostructures" (PDF). Science. 345 (6198): 799–804. Bibcode:2014Sci...345..799G. doi:10.1126/science.1253920. ISSN   0036-8075. PMID   25124436. S2CID   5903435.
  8. 1 2 3 4 Sparvath, Steffen L.; Geary, Cody W.; Andersen, Ebbe S. (2017). 3D DNA Nanostructure. Methods in Molecular Biology. Vol. 1500. Humana Press, New York, NY. pp. 51–80. doi:10.1007/978-1-4939-6454-3_5. ISBN   9781493964529. PMID   27813001.
  9. ↑ Rothemund, Paul W. K. (2006-03-16). "Folding DNA to create nanoscale shapes and patterns" (PDF). Nature. 440 (7082): 297–302. Bibcode:2006Natur.440..297R. doi:10.1038/nature04586. ISSN   0028-0836. PMID   16541064. S2CID   4316391.
  10. ↑ Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter (2002). "The RNA World and the Origins of Life". Garland Science.{{cite journal}}: Cite journal requires |journal= (help)
  11. ↑ "Scientists fold RNA origami from a single strand". ScienceDaily. Retrieved 2017-10-09.
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