DNA Computing Using Carbon Nanotube-DNA Hybrid Nanostructure

DNA Computing Using Carbon Nanotube-DNA Hybrid Nanostructure

Swati Sinha (University of Calcutta, India & West Bengal University of Technology, India), Jaya Bandyopadhyay (West Bengal University of Technology, India) and Debashis De (West Bengal University of Technology, India & University of Western Australia, Australia)
DOI: 10.4018/978-1-5225-0058-2.ch030
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Abstract

DNA computing is a branch of biomolecular computing using the physical and chemical properties of deoxyribonucleic acid or DNA. It is a fast-developing interdisciplinary research area consisting of nano-biotechnology, computer science and biochemistry. DNA computing is widely used now-a-days for logic design, biomarker, cryptography, disease detection etc. In recent years, carbon nanotube or CNT research has reached a new peak with its various applications including nano-biocomputing. DNA plays a pivotal role in biology and CNT is considered as a wonder material of this century in nanoscience. This chapter combines these two promising research areas including CNT and DNA to form CNT-DNA based nanostructured system and its applications in diverse fields like electronics, biomedical engineering, drug delivery, gene therapy, biosensor technology etc. CNT-DNA hybrid and its various suitable combinations open up a new dimension called CNT-DNA computing.
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Introduction

In 1994 Leonard Adleman of University of Southern California put his first step in the field of DNA computing (Liu, 2000) by solving the Hamiltonian path problem (Adelman, 1994). CNTs are extremely sensitive for molecular detection (Valentini, 2004) for their large aspect ratio. Needle-like tip of the tube and surface property of CNT enable it to penetrate the plasma membrane (Chen,1994) of cell and help to act as a delivery system (Khaled, 2005; Singh et al, 2006; Singh 2014; Gentschev, 2000, 2001)) of different types of therapeutic molecules (Bianco, 2004), DNA, siRNA to the target cells (Fortina, 2005). In nanomedicine, synergistic approach of CNT-DNA (Khusenov, 2014) has opened up a new avenue (Tardani, 2014) for the treatment of different diseases (Frusawa, 2015) including cancer detection (Elhissi, 2011; Jabir, 2012) and treatment (Ali-Boucetta, 2013; Liu, 2011; Liu, 2012). Furthermore, in targeted gene therapy, controlled release of designed genes or DNA (Rajaee, 2014; Kolosnjaj, 2007; Corredor, 2013) to the diseased cells can be achieved due to the remarkable optical and electrical properties of CNT (Cheung, 2010). Owing to the strong base pairing rule the base sequence of single-strand (ssDNA) DNA (Chaves,2014) attached over CNT can recognize their complementary sequence and bind together to form the helical structure of double-strand (dsDNA) DNA (Wu, 2015). In 1982, Nadrian C. Seeman first established an idea of DNA nanotechnology (Seeman, 1982, 2004). This technology provides us an unprecedented opportunity to fight against various diseases by designed nucleic acid sequences. Apart from the diverse applications in biomedicine, CNT-DNA nano-hybrid structure finds its use in CNT-DNA computing also. In Biology, genetic information are passed from generation to generation through DNA in living cells while in DNA computing, DNA is considered to be a non-biological engineering nanomaterial (Amir, 2014). Nowadays DNA computers (Borush, 2015) are widely used for simulation procedure. Computer data storage capacity can be increased using human DNA (Alaudeen, 2015). For ternary computing, DNA as a functional material using of three-valued oligonucleotide inputs is introduced recently (Orbach, 2015).

Key Terms in this Chapter

Nano-Bio-Robot: A nano-bio-robot is a small (measured in nanometers, where 1 nm = 10 -9 meter) machine made up of biological molecule like DNA and non-biological molecule to perform a specific job.

Deoxyribose: Deoxyribose is a monosaccharide pentose sugar having five carbon atoms and is derived from sugar ribose by loss of an oxygen atom at C 2 position.

CNT-DNA FET: FET or Field Effect Transistor is designed using ssDNA and CNT and is used as a biosensor.

Pyrimidines: A class of nitrogenous aromatic organic compounds consisting of one heterocyclic ring. Thymine (T) and cytosine (C) are pyrimidines present in DNA and in RNA uracil (U) replaces T. In DNA molecule, purine binds with its complementary pyrimidine with hydrogen bonds.

CNT: CNT is the third allotrope of carbon along with graphite and diamond. They belong to the fullerenes and are formed by mono-layer sheet of carbon which is pie-stacked and sp 2 bonded, called graphene which is folded to form a tubular structure measured in nanometer scale.

Guanine: Guanine is a derivative of purine. It is a nucleobase found in both DNA and RNA and pairs with cytosine by three hydrogen bases. It contains a fused pyrimidine-imidazole ring with conjugated double bonds and has empirical formula C 5 H 5 N 5 O.

DNA: DNA or Deoxyribonucleic acid is a self-replicating material and it passes genetic information from generation to generation in living cells. It is the principal constituent of chromosomes consisting of a double-helix of two antiparallel strands of nucleotides formed by complementary base pairing between purine and pyrimidine.

DNA LOGIC: Designing of AND, OR, NOT etc. logic using basic DNA nanostructure.

Biosensor: A biosensor is an analytical instrument combining a biological component and a physico-chemical detector and is used to detect or sense an analyte.

Cytosine: Among the DNA and RNA nucleobases, cytosine is a derived from pyrimidine having a heterocyclic aromatic ring with two substituents - an amine group and a keto group. Cytosine binds with guanine by three hydrogen bonds.

Nucleotide: A nucleotide is a monomeric unit of DNA and RNA and is composed of a nucleoside and one or more phosphate groups.

Graphene: Graphene is an allotrope of carbon forming an atomic-scale two-dimensional hexagonal lattice in which one atom forms each vertex. Graphene is the structural constituent of other allotropes like CNT, graphite, charcoal and fullerenes.

SWCNT: Single-walled carbon nanotube (SWCNT) has a diameter of about 0.4-2.0 nanometer and the tube length may be of several hundred nanometers to several micrometers and is made up of a single layer of cylindrical sheet of graphene.

Computer Simulation: Computer simulation utilizes an abstract model to simulate the system. It is a simulation which runs on computer to reproduce the behavior of a system.

Purines: Purines are nitrogenous organic aromatic compounds with two fused heterocyclic rings. Adenine (A) and guanine (G) are two purines found in DNA and RNA.

Adenine: Adenine is a purine derivative nucleobase found in both DNA and RNA as a structural component. It is used as a functional component in synthesis of protein and as a chemical constituent part of adenosine triphosphate (ATP), nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD) during cellular respiration. Adenine pairs with thymine with the help of two hydrogen bonds.

Nucleoside: A nucleoside is formed of a nitrogenous base and a five-carbon sugar (ribose or deoxyribose) linked by a beta-glycosidic linkage.

Thymine: Thymine was first isolated by Albrecht Kossel and Albert Neumann in 1893 from calves' thymus glands. It is a nucleobase found only in DNA and is a pyrimidine derivative. In RNA, thymine is replaced by uracil. Thymine forms base pair with its complementary adenine molecule by two hydrogen bonds.

Uracil: The term “uracil” was first coined by German chemist Robert Behrend in 1885 during uric acid derivative synthesis. In RNA, uracil is found as one of the four nucleobases and binds with adenine by two hydrogen bonds. It is a pyrimidine derivative. In DNA molecule, thymine is present instead of uracil.

MWCNT: Multi-walled carbon nanotube (MWCNT) has a diameter of 2-100 nm and formed of several rolled layers of concentric tubes of graphene sheets.

DNA Computing: DNA computing is a branch of computing using physical, biochemical and mechanical properties of DNA and molecular biology hardware. DNA computing is now-a-days regarded as biomolecular computing which recently encompasses interdisciplinary area.

DNA Cryptography: Encryption and decryption using structural properties of DNA nanostructure.

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