9 DNA and RNA nanotechnology

AbstractMolecular computers have existed on our planet for more than 3.5 billion years. Molecular computing devices, composed of biological substances such as nucleic acids, are responsible for the logical processing of a variety of inputs, creating viable outputs that are key components of the cellular machinery of all living organisms. We have begun to adopt some of the structural and functional knowledge of the cellular apparatus in order to fabricate nucleic-acid-based molecular computers in vitro and in vivo. Nucleic acid computing is directly dependent on advances in DNA and RNA nanotechnology. The field is still emerging and a number of challenges persist. Perhaps the most salient among these is how to translate a variety of nucleic-acid-based logic gates, developed by numerous research laboratories, into the realm of silicon-based computing. This mini-review provides some basic information on the advances in nucleic-acid-based computing and its potential to serve as an alternative that can revolutionize silicon-based technology.

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Unified Nanotechnology Format: One Way to Store Them All

Molecules ◽

10.3390/molecules27010063 ◽

2021 ◽

Vol 27 (1) ◽

pp. 63

Author(s):

David Kuťák ◽

Erik Poppleton ◽

Haichao Miao ◽

Petr Šulc ◽

Ivan Barišić

Keyword(s):

Free Form ◽

File Format ◽

Dna Structures ◽

Rna Nanotechnology ◽

Dna And Rna ◽

File Formats ◽

Computer Based ◽

Wet Lab ◽

The Many ◽

Future Work

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

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9 DNA and RNA nanotechnology

Biomimetics ◽

10.1515/9783110281194.191 ◽

2013 ◽

Keyword(s):

Rna Nanotechnology ◽

Dna And Rna

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High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140130 ◽

1995 ◽

Vol 53 ◽

pp. 752-753

Author(s):

B.A. Hamkalo ◽

S. Narayanswami ◽

A.P. Kausch

Keyword(s):

Nucleic Acid ◽

Interphase Nucleus ◽

Genome Mapping ◽

Precise Location ◽

Electron Microscope Level ◽

Rna Sequences ◽

Fundamental Interest ◽

Whole Cells ◽

Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

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Scanning tunneling microscopy (STM) of DNA and RNA

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152148 ◽

1989 ◽

Vol 47 ◽

pp. 34-35

Author(s):

Patricia G. Arscott ◽

Gil Lee ◽

Victor A. Bloomfield ◽

D. Fennell Evans

Keyword(s):

Molecular Structures ◽

Inorganic Materials ◽

Resolving Power ◽

Scanning Tunneling ◽

Tunneling Microscopy ◽

Form And Function ◽

Dna And Rna ◽

Calf Thymus ◽

And Function ◽

The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

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