DNA

Deoxyribonucleic acid (DNA) discovered by Watson and Crick, who received a Nobel Prize for their work in 1962, is the blueprint of life [86,87].

From: Biopolymer Composites in Electronics, 2017

Perspective of DNA Computing in Computer Science

Sachin Minocha, Suyel Namasudra, in Advances in Computers, 2023

4 Conclusions

DNA computing can be referred to as an emerging branch of computing that utilizes DNA, molecular biology hardware, and biochemistry instead of traditional electronic computing. It uses molecular reaction techniques that are executed on DNA molecules. DNA computing is mainly based on four nitrogen bases, i.e., guanine, thymine, adenine, and cytosine. DNA computing provides high computation power and storage capacity due to its structure. The key challenge for implementing DNA computing is the wet lab experiments in a controlled manner. In this chapter, many research challenges are discussed faced by the research community while implementing DNA computing. Moreover, many future work directions in DNA computing are also presented in this chapter. The ability of DNA computing to perform with quantum computing and nanotechnology has widened the scope of research in the DNA computing field. In the future, this work can be expanded in any of the domains mentioned in the future work directions, including DNACloud, quantum computing, DNA nanotechnology, security, and DNA computing-based compilers.

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FORENSIC SCIENCES | Hair

N. Watson, in Encyclopedia of Analytical Science (Second Edition), 2005

DNA Analysis

DNA fingerprinting was developed for individualization system in 1985. Analyses using DNA profiling with variable numbers of tandem repeat polymorphism has been carried out for identification of forensic samples such as bloodstains and sectional stains. Concerning forensic hairs, several DNA analyses of hair root sheath cells have been reported. However, DNA analysis of a hair shaft has not succeed to date, because DNA recovery from a hair shaft is in order of tens of picograms and only low molecular weight DNA (below 200 base pairs (bp)) is left in the hair shape. Recently, microsatellite DNA polymorphism has been detected by the polymerase chain reaction technique. This polymorphism can be applied to DNA analysis of hair shaft. If DNA analysis is combined with microscopic and instrumental analysis in forensic examination, hair individualization can be more accurate.

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Engineering biosynthetic cell encapsulation systems

J.J. Roberts, P.J. Martens, in Biosynthetic Polymers for Medical Applications, 2016

9.2.2.3 Deoxyribonucleic acid

Deoxyribonucleic acid (DNA) is composed of two polynucleotide chains held together by weak intermolecular forces. DNA has been probed for its ability to form hydrogels (Um et al., 2006). Hydrogels made from DNA can efficiently self-assemble into predictable networks under physiological conditions and can be biodegraded by nucleases. The mechanical properties of DNA hydrogels can be tuned by adjusting the concentration and type of DNA monomers. Their unique properties make DNA hydrogel networks ideal for specific biomedical applications, such as 3D cell culture, cell transplant therapy, controlled drug delivery and cell-free protein production (Zhu and Marchant, 2011). However, limited supply and purification cost are challenges that will need to be overcome for scale-up of DNA hydrogels.

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Perspective of DNA Computing in Computer Science

Jiechao Gao, Tiange Xie, in Advances in Computers, 2023

8 Conclusions

DNA computing has a variety of applications in cryptography. Cryptography has evolved from the use of codebooks to the use of DNA computing techniques. The reliability and performance of DNA encryption algorithms apply to the layered security routines of today's network architectures. Some DNA algorithms can overcome exhaustive or statistical, differential attacks. The DNA computational techniques most commonly used in encryption and steganography schemes include OTP, DNA arithmetic operations (AND, OR, XOR, XNOR), PCR, DNA sequencing, and 3D DNA matrices. Most encryption schemes follow a similar strategy of converting data to ASCII values and further converting them to binary equivalents. These binary pairs are mapped to each of the four DNA bases and stored in a randomly generated DNA sequence. Steganography schemes propose to embed the data into a dummy DNA sequence that is sent to the recipient through any network or medium. DNA computation-based steganography schemes need to achieve higher data hiding ability and minimal cracking probability. When comparing different steganographic schemes, encrypting the data before hiding provides an additional level of security to the whole process. The massive parallelism and storage capabilities of DNA are useful for authentication, encryption processes, and digital signatures. Cryptography techniques based on DNA computing still need extensive research. There are many issues to be addressed such as accuracy of the process, the time consumption of individual procedures, feasible implementation of all mentioned techniques, and biological axioms. The application of DNA computing in cryptography is not limited to encryption of text/messages but extends to providing reliable security mechanisms for image encryption, cloud computing environments, big data, and deep learning. The use of DNA computing in cryptography has significant potential for the development of secure, reliable, and feasible cryptographic algorithms and systems. The concept of DNA computing in cryptography can be extended to secure cloud computing environments, and wireless sensor networks (WSNs). For cloud computing, encryption schemes based on DNA computing can be developed to ensure data confidentiality, security, and client authentication. For WSNs, efficient, attack-resistant schemes that use DNA bases to hide data can be improved. Data can be first converted to ASCII values and then to their binary equivalents. With DNA encoding, binary pairs can be mapped to DNA bases and then encrypted with a key. DNA computing techniques can also be merged with existing encryption algorithms such as AES to enhance the complexity of the resulting cryptosystem.

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Toxicology of textile dyes

P. Gregory, in Environmental Aspects of Textile Dyeing, 2007

3.4.2 Classes of carcinogens based on chemical structure

DNA is nucleophilic. Therefore, the active species of most carcinogens, known as the ultimate carcinogen, is an electrophile, E. In most cases, the electrophile is either a nitrenium ion R2N+ or a carbonium ion R3C+. These ultimate carcinogens attack a nucleophilic site in DNA, which may be a carbon, nitrogen or oxygen atom, to form a covalent chemical bond (equation 3.1).

[3.1]E+DNAEDNA

As well as chemical reaction, intercalation is another way for molecules to interact with DNA. In this interaction, a flat portion of the molecule inserts itself into the DNA helix (Gregory, 1991).

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Synthesis of nanostructured materials by green methods

Muhammad Aamir, ... Javeed Akhtar, in Green Sustainable Process for Chemical and Environmental Engineering and Science, 2023

2.10 DNA template synthesis

Deoxyribonucleic acid (DNA) contains double-stranded helical structures with the ability of programmability. DNA also shows a strong affinity for various metals like gold, silver, palladium, etc. The features make DNA an excellent template for nanostructured materials synthesis with variable shapes and sizes.

DNA conformations contain a negatively charged phosphate backbone. This property provides a platform to fabricate low-dimensional nanostructured materials. DNA develops electrostatic interaction between metal cations and the phosphate backbone.

The metal nanoparticles are presynthesized by a chemical reduction method, and capping of these nanostructured materials by DNA is performed by a ligand exchange reaction. Using this methodology, various shapes and morphologies, including linear, ribbon-like, and branched, of DNA-gold nanoparticles assemble by metallization (Warner and Hutchison, 2003).

Apart from the metallization through electrostatic interaction between metal ions and DNA, the metal-DNA complex can be prepared and in situ metal ion reduction on DNA results in the formation of nanoparticles. This process takes place in two steps. One is the mixing of metal precursors with DNA followed by incubation to ensure the metal-DNA complex formations. In the second step, reducing agents such as ascorbic acid or sodium borohydride are introduced to form metal nanoparticles onto the DNA. Using this methodology, spherical, wire-like, rod-like, and ring-like nanomorphologies have been synthesized. The DNA templates were used to synthesize the silver nanowires by mixing DNA and silver nitrate followed by ultraviolet irradiation exposure for 3 h (Majumdar et al., 2013).

In the synthesis of metallic nanostructured materials, the development of controlled morphology has been used in various applications including electronics and optics. The plasmonic coupling between metallic nanoparticles leads to enhancement of electric fields. This enhancement depends on the interparticle distances. For example, the modified thio-DNA strands have been used for gold/silver nanoparticles as the mercapto group had shown strong interaction between metal nanoparticles and DNA strands (Mucic et al., 1998).

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Commercialization of bionanocomposites

Vani Angra, ... Reena Gupta, in Bionanocomposites in Tissue Engineering and Regenerative Medicine, 2021

31.2.4 Deoxyribonucleic acid (DNA)

DNA is not only important in carrying genetic information, but it also serves an important block for the synthesis of bionanocomposites. The important features of DNA that are exploited for this purpose include single- and double-stranded nature and high-density charge of the polyphosphate backbone. The single- and double-stranded DNA are used for solubilizing the single-walled carbon nanotubes of DNA carbon nanocomposites [15]. They have wide applications in the pharmaceutical and biomedical industries. The main purpose of using DNA for this purpose is to carry out biodiagnostics and nonviral gene delivery [16].

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Strategy and Drug Research

E.E. Swayze, ... C.F. Bennett, in Comprehensive Medicinal Chemistry II, 2007

2.26.2.3.5 Other structures

DNA can form higher-order structures, such as the G quartets present as telomeres at the ends of genes. These G quartet DNAs are very stable, and are recognized specifically by cellular proteins. Hence, artificial G quartet structures have been prepared and demonstrated to have anticancer activity.

DNA : RNA duplexes formed during transcription are potential targets for drug discovery. These structures are present during transcription, and may be long-lived. For example, the transcription of human immunodeficiency virus (HIV) RNA has stall sites where DNA : RNA structures are formed as sites for recruitment of additional protein factors. DNA : RNA duplexes also are formed during trailing strand DNA synthesis (Okazaki fragment) and subsequently cleaved.

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Chemically Modified Electrodes

Grant A. Edwards, ... Marc D. Porter, in Handbook of Electrochemistry, 2007

8.3.8 DNA modified electrodes

Deoxyribonucleic acid (DNA) is increasingly used for molecular recognition purposes (132–134). Electrodes modified with DNA, therefore, are useful in the construction of electroanalytical sensors. Analytes, including carcinogens, drugs, and mutagenic pollutants with high binding affinities for DNA, will be important in testing water, food, soil, and plant samples. Electroactive molecules may be detected directly upon binding to DNA bound at the electrode surface. Indirect detection of electroinactive molecules may be accomplished by monitoring changes in the signal attributed to the bound DNA (134). Sensors can also be used to detect gene sequences (134) such as mutations associated with human diseases. Further information on DNA modified electrodes, including fabrication (i.e., immobilization of DNA using many of the techniques discussed above) and application can be found in references (134–142).

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Biosensors based on two-dimensional materials

Marco Filice, ... Francisco Gamiz, in 2D Materials for Nanophotonics, 2021

7.2.2 Deoxyribonucleic acid bioreceptors

DNA is a molecule composed of two chains that coil around each other to form a double helix carrying 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. The two DNA strands are also known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases [cytosine (C), guanine (G), adenine (A), or thymine (T)], a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar–phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to Chargaff’s rules of complementary bases (adenine pairs with thymine and cytosine pairs with guanine), with hydrogen bonds to make double-stranded DNA or dsDNA. When DNA is heated, the hydrogen bonds holding the base pairs together dissolve and the DNA separates into two single strands during a process known as DNA melting, thus forming single-stranded DNA or ssDNA. The temperature at which the DNA strands separate is called the melting temperature. When DNA is cooled, complementary bases realign and bind through hydrogen bonding. When single strands of DNA of different species are put together, they try to join together to form hybrid double helices. This process is called DNA–DNA hybridization. These hybrid segments of DNA can be used to determine the evolutionary relatedness of organisms by examining how similar or dissimilar the DNA base pair sequences are. The technique of DNA hybridization is based on two principles: the first, that double strands of DNA are held together by hydrogen bonds between complementary base pairs, and the second is that the more closely related two species are, the greater will be the number of complementary base pairs in the hybrid DNA. In other words, the degree of hybridization is proportional to the degree of similarity between the molecules of DNA from the two species. The hybridization of DNA strands produces physical changes of the molecule (changes in the charge, optical absorption, etc.), which are more important as the degree of hybridization increases.

DNA has a broad range of physical, chemical, and biological properties making this biomolecule highly suitable for biosensor technologies. Among the most critical properties of DNA for a biosensor is its flexibility, easy synthesis, facile chemistry to attach to diverse platforms, simple regeneration, and high specificity due to unique sequences of nucleotides.

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