Related Research Articles
DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, and applications of DNA computing. Although the field originally started with the demonstration of a computing application by Len Adleman in 1994, it has now been expanded to several other avenues such as the development of storage technologies, nanoscale imaging modalities, synthetic controllers and reaction networks, etc.
John Joseph Hopfield is an American physicist and emeritus professor of Princeton University, most widely known for his study of associative neural networks in 1982. He is known for the development of the Hopfield network. Previous to its invention, research in artificial intelligence (AI) was in a decay period or AI winter, Hopfield work revitalized large scale interest in this field.
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.
Paul Wilhelm Karl Rothemund is a research professor at the Computation and Neural Systems department at Caltech. He has become known in the fields of DNA nanotechnology and synthetic biology for his pioneering work with DNA origami. He shared both categories of the 2006 Feynman Prize in Nanotechnology with Erik Winfree for their work in creating DNA nanotubes, algorithmic molecular self-assembly of DNA tile structures, and their theoretical work on DNA computing. Rothemund is also a 2007 recipient of the MacArthur Fellowship.
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.
A molecular logic gate is a molecule that performs a logical operation based on at least one physical or chemical inputs and a single output. The field has advanced from simple logic systems based on a single chemical or physical input to molecules capable of combinatorial and sequential operations such as arithmetic operations. Molecular logic gates work with input signals based on chemical processes and with output signals based on spectroscopic phenomena.
Roger David Kornberg is an American biochemist and professor of structural biology at Stanford University School of Medicine. Kornberg was awarded the Nobel Prize in Chemistry in 2006 for his studies of the process by which genetic information from DNA is copied to RNA, "the molecular basis of eukaryotic transcription."
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.
Maxine Frank Singer was an American molecular biologist and science administrator. She was known for her contributions to solving the genetic code, her role in the ethical and regulatory debates on recombinant DNA techniques, and her leadership of Carnegie Institution of Washington.
Multiple displacement amplification (MDA) is a DNA amplification technique. This method can rapidly amplify minute amounts of DNA samples to a reasonable quantity for genomic analysis. The reaction starts by annealing random hexamer primers to the template: DNA synthesis is carried out by a high fidelity enzyme, preferentially Φ29 DNA polymerase. Compared with conventional PCR amplification techniques, MDA does not employ sequence-specific primers but amplifies all DNA, generates larger-sized products with a lower error frequency, and works at a constant temperature. MDA has been actively used in whole genome amplification (WGA) and is a promising method for application to single cell genome sequencing and sequencing-based genetic studies.
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.
Erik Winfree is an American applied computer scientist, bioengineer, and professor at California Institute of Technology. He is a leading researcher into DNA computing and DNA nanotechnology.
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.
Nadrian C. "Ned" Seeman was an American nanotechnologist and crystallographer known for inventing the field of DNA nanotechnology.
Richard Alan Andersen is an American neuroscientist. He is the James G. Boswell Professor of Neuroscience at the California Institute of Technology in Pasadena, California. His research focuses on visual physiology with an emphasis on translational research to humans in the field of neuroprosthetics, brain-computer interfaces, and cortical repair.
Michael Lee Roukes is an American experimental physicist, nanoscientist, and the Frank J. Roshek Professor of Physics, Applied Physics, and Bioengineering at the California Institute of Technology (Caltech).
The Computation and Neural Systems (CNS) program was established at the California Institute of Technology in 1986 with the goal of training PhD students interested in exploring the relationship between the structure of neuron-like circuits/networks and the computations performed in such systems, whether natural or synthetic. The program was designed to foster the exchange of ideas and collaboration among engineers, neuroscientists, and theoreticians.
Barbara J. Wold is the Bren Professor of Molecular Biology, the principal investigator of the Wold Lab at the California Institute of Technology (Caltech) and the principal investigator of the Functional Genomics Resource Center at the Beckman Institute at Caltech. Wold was director of the Beckman Institute at Caltech from 2001 to 2011.
Toehold mediated strand displacement (TMSD) is an enzyme-free molecular tool to exchange one strand of DNA or RNA (output) with another strand (input). It is based on the hybridization of two complementary strands of DNA or RNA via Watson-Crick base pairing (A-T/U and C-G) and makes use of a process called branch migration. Although branch migration has been known to the scientific community since the 1970s, TMSD has not been introduced to the field of DNA nanotechnology until 2000 when Yurke et al. was the first who took advantage of TMSD. He used the technique to open and close a set of DNA tweezers made of two DNA helices using an auxiliary strand of DNA as fuel. Since its first use, the technique has been modified for the construction of autonomous molecular motors, catalytic amplifiers, reprogrammable DNA nanostructures and molecular logic gates. It has also been used in conjunction with RNA for the production of kinetically-controlled ribosensors. TMSD starts with a double-stranded DNA complex composed of the original strand and the protector strand. The original strand has an overhanging region the so-called “toehold” which is complementary to a third strand of DNA referred to as the “invading strand”. The invading strand is a sequence of single-stranded DNA (ssDNA) which is complementary to the original strand. The toehold regions initiate the process of TMSD by allowing the complementary invading strand to hybridize with the original strand, creating a DNA complex composed of three strands of DNA. This initial endothermic step is rate limiting and can be tuned by varying the strength (length and sequence composition e.g. G-C or A-T rich strands) of the toehold region. The ability to tune the rate of strand displacement over a range of 6 orders of magnitude generates the backbone of this technique and allows the kinetic control of DNA or RNA devices. After the binding of the invading strand and the original strand occurred, branch migration of the invading domain then allows the displacement of the initial hybridized strand (protector strand). The protector strand can possess its own unique toehold and can, therefore, turn into an invading strand itself, starting a strand-displacement cascade. The whole process is energetically favored and although a reverse reaction can occur its rate is up to 6 orders of magnitude slower. Additional control over the system of toehold mediated strand displacement can be introduced by toehold sequestering.
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.
References
- ↑ "Lulu Qian | Caltech Directory". directory.caltech.edu. Retrieved 2023-03-05.
- ↑ "Introducing ISNSCE Vice President Lulu Qian". ISNSCE. 2021-12-11. Retrieved 2023-03-05.
- ↑ "Programming DNA for Molecular Robots: An Interview with Lulu Qian – Pasadena Now". www.pasadenanow.com. Retrieved 2023-03-05.
- ↑ Qian, Lulu; Winfree, Erik (2011-06-03). "Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades". Science. 332 (6034): 1196–1201. Bibcode:2011Sci...332.1196Q. doi:10.1126/science.1200520. ISSN 0036-8075. PMID 21636773. S2CID 10053541.
- ↑ "Lulu Qian's CV" (PDF).
- ↑ Major, Mario L. (2017-09-16). "Scientists Build DNA Robots That Could One Day Deliver Medicine Inside Your Body". interestingengineering.com. Retrieved 2023-03-04.
- ↑ "Caltech researchers build largest biochemical circuit out of small synthetic DNA molecules". EurekAlert!. Retrieved 2023-03-04.
- 1 2 Andy Extance2017-12-07T14:30:00+00:00. "DNA origami makes it big". Chemistry World. Retrieved 2023-03-04.
{{cite web}}: CS1 maint: numeric names: authors list (link) - 1 2 Qian, Lulu; Winfree, Erik; Bruck, Jehoshua (July 2011). "Neural network computation with DNA strand displacement cascades". Nature. 475 (7356): 368–372. doi:10.1038/nature10262. ISSN 1476-4687. PMID 21776082. S2CID 1735584.
- ↑ Mehar, Pranjal (2018-07-10). "Scientists created AI from DNA". Tech Explorist. Retrieved 2023-03-04.
- ↑ "Foresight Institute Awards 2019 Feynman Prizes in Nanotechnology to Qian, Galli; awards presented by Nobelist, Sir Fraser Stoddart". PRWeb. Retrieved 2023-03-04.
- ↑ "Two Professors Receive Caltech's Highest Honors for Teaching and Mentorship". California Institute of Technology. 2023-02-21. Retrieved 2023-03-04.
| Authority control databases: Academics |
|---|
