China
Africa
Explore chapters and articles related to this topic
Genes and genomics
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2018
In all living organisms, DNA usually exists as a pair of molecules that are held tightly together in the shape of a double helix. These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. In general, a base linked to a sugar is called a nucleoside, and a base linked to a sugar and one or more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide. The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phospho-diester bonds between the third and fifth carbon atoms of adjacent sugar rings (Figure 2.5). These asymmetric bonds mean a strand of DNA has a direction. In a double helix, the direction of the nucleotides in one strand is opposite to their direction in the other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of DNA strands are referred to as the 5’ (five prime) and 3’ (three prime) ends, with the 5’ end being that with a terminal phosphate group and the 3’ end that with a terminal hydroxyl group. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA.
Nanostructured Cellular Biomolecules and Their Transformation in Context of Bionanotechnology
Published in Anil Kumar Anal, Bionanotechnology, 2018
Transcription is the process by which genetic information is transferred from DNA to mRNA synthesized from ribonucleoside triphosphates utilizing the energy released by the removal of pyrophosphate. The site for initiation of transcription process is known as promoters, whereas in bacteria it is known as operon from which several genes are cotranscribed from same promoters. DNA is double stranded in antiparallel orientation, that is, top strand runs from 5′ → 3′ direction, whereas the bottom strand runs from the 3′ → 5′ direction. During the transcription process, RNA synthesis proceeds in 5′ → 3′ direction such that the bottom strand is known as a template strand as it acts as a template for RNA synthesis, whereas the top strand is known as the coding strand as its sequence corresponds to the DNA version of the mRNA. Top strand is also called sense strand as mRNA with this sequence will make the correct protein, whereas the bottom strand is known as the antisense strand. The transcription process initiates with the unwinding of DNA helix and synthesis of short chain RNA primer, process being catalyzed by RNA polymerase. The chain length elongates with the addition of ribonucleotides triphosphates forming phosphodiester linkage. The transcription process terminates as it reaches to a specific gene sequence known as termination sequence or binding of a specific protein rho that causes disassembly of template, enzyme, and synthesized mRNA (Moran et al. 2012).
DNA Nanostructures
Published in Yubing Xie, The Nanobiotechnology Handbook, 2012
Single-stranded (ss) DNA is the raw material used for construction of DNA nanostructures. It consists of DNA bases attached to 2-deoxyribose sugar units; these units are linked together through phosphodiester bonds between the 3' and 5' carbons on neighboring sugars. Thus, oligonucleotides have a 3' end and a 5' end. In duplex DNA (Figure 1.1), the strand directions run antiparallel—that is, the 3' end of one oligonucleotide lies next to the 5' end of the complementary oligonucleotide. The oligonucleotides are held together by a combination of hydrogen bonding between the complementary DNA bases and base-stacking interactions that help to hide the hydrophobic DNA bases from exposure to water. In normal B-form DNA, the helix repeat length is 10.4 bases, which corresponds to about 3.5 nm per turn of the helix. Thus, a duplex segment 70 nm in length would require 20 turns of the duplex or 208 base pairs. Getting this DNA presents a practical problem, for if the oligos are constructed synthetically, the longer the sequence, the worse the yield.
A hydroxyquinoline-appended ruthenium(II)-polypyridyl complex that induces and stabilizes G-quadruplex DNA
Published in Journal of Coordination Chemistry, 2019
Xuexue Xu, Shuang Wang, Yaxuan Mi, Huaqian Zhao, Zebao Zheng, Xiaolong Zhao
A hydroxyquinoline-appended ruthenium(II) complex has been prepared and interacted with G-quadruplex DNA. Compelling evidence provided by CD spectroscopy indicated that the complex is capable of inducing the formation of antiparallel G-quadruplex DNA in Tris–HCl buffer and the transition of G-quadruplex DNA structure from parallel configuration to antiparallel conformation in Tris–KCl buffer. The gradual disappearance of PCR product in PCR stop assay and the emergence of blue solution in color reaction experiment under the influence of the complex also confirmed the formation of G-quadruplex. As revealed by FRET measurements, the complex not only behaved as a promising G-quadruplex DNA stabilizer that can increase the Tm value of G quadruplex by 3.0–21.0 °C, but also exhibited high selectivity for quadruplex versus duplex DNA with Tm value unchangeable in the presence of 50-fold ct-DNA. The complex was found to interact with G-quadruplex DNA tightly with Kb = 2.56 × 106 M−1, and showed 3.1 and 4.2-fold luminescence increments after binding saturately to G-quadruplex DNA in Tris–NaCl and Tris–KCl buffer, respectively. The 1:1 binding stoichiometry of the complex for G-quadruplex DNA was determined by Job plot and molecular docking.
Liquid crystals as signal transducers for sensing of analytes using aptamer as a recognition probe
Published in Liquid Crystals Reviews, 2021
Manisha Devi, Ipsita Pani, Santanu Kumar Pal
Conjugated β-lactoglobulin-23 (β-LG) aptamer at 3′ with C16 dialkyl tails or through spacer C12/T10 can be used to decorate the aqueous-LC interface [74]. Aptamer-amphiphile without spacer was found to be the best in terms of binding affinity and form antiparallel G-quadruplex secondary structure in the presence of β-LG. A very interesting concept for the detection of tumour markers (carcinoembryonic antigen (CEA), alpha-fetoprotein (AFP), and prostate-specific antigen (PSA)) in blood was reported using aptamer-decorated LC-aqueous interface assisted with target-induced dissociation (TID) of aptamer [75]. The authors used magnetic beads coated with streptavidin which were further coated with biotin-labelled aptamer (Apt1-MBs) for capturing the proteins. In the presence of signal DNA duplex (Apt2 and signal ssDNA), magnetic beads form the sandwich complex of Apt1-protein-Apt2 and release the signal DNA from the signal DNA duplex which hybridized with the specific DNA-OTAB-laden LC-aqueous interface. Furthermore, they employed this principle for the simultaneous detection of CEA, AFP, and PSA by using 3D printed optical cells. Very recently, Hu et al. used aptamer-decorated OTAB LC-aqueous interface for the detection of bleomycin (BLM, antibiotic used to treat cancer) and bleomycin hydrolase (BLMH, enhance the activity of BLM) [76]. Recently, Wang et al. developed a LC-based diagnostic kit for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [77]. RNA of SARS-CoV-2 hybridized with ssDNA decorated on the CTAB-laden LC-aqueous interface. The change in the LC orientation after hybridization was easily observed using smartphones. Based on these reports, we can conclude that LC-based aptasensors can act as a robust platform for other biomolecules. We have summarized the detection of various biomolecules using aptamers at LC interfaces in Figure 10 and Table 1.