China
Africa
Explore chapters and articles related to this topic
Principles and Techniques for Deoxyribonucleic Acid (DNA) Manipulation
Published in Hajiya Mairo Inuwa, Ifeoma Maureen Ezeonu, Charles Oluwaseun Adetunji, Emmanuel Olufemi Ekundayo, Abubakar Gidado, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Medical Biotechnology, Biopharmaceutics, Forensic Science and Bioinformatics, 2022
Nwadiuto (Diuto) Esiobu, Ifeoma M. Ezeonu, Francisca Nwaokorie
In the second step, small RNA primers, synthesized by a special RNA polymerase called Primase, attach to the template strands to kick off the action of the replicating enzyme, DNA polymerase III. DNA polymerase III catalyzes the formation of a phosphodiester bond between the 5′ phosphate group of an incoming nucleotide and the 3′-hydroxyl group of an existing nucleotide, but is unable to start a chain; hence, the need for a primer to provide the 3′-hydroxyl group. When the enzyme is activated, it binds to the unzipped DNA template strand and subsequently “walks” through it, adding new complementary nucleotide bases (A, G, C and T), as specified by the template and extending the growing DNA chain in the 5′ to 3′ direction. The replication of the two strands involves the same proteins. However, since the two strands are oriented differently, as described above, and since the replicating enzyme operates in only one particular direction (5′ → 3′), the precise mechanism of replication of the two strands differs slightly.
Nanostructured Cellular Biomolecules and Their Transformation in Context of Bionanotechnology
Published in Anil Kumar Anal, Bionanotechnology, 2018
The replication of DNA has three distinct stages that include initiation, elongation, and termination. Initially, helicase enzyme untwists the helical structure, breaks the hydrogen bond between base pairs, separates double strand into single DNA strand, and creates fork-like structures known as replication fork at the site known as origin of replication. Primer, a short double-stranded piece of nucleic acid synthesized by RNA polymerase, binds to the site of action. DNA polymerase III synthesizes a new DNA from deoxyribonucleotide triphosphates with the release of pyrophosphate; the cleavage of pyrophosphate by a pyrophosphatase provides the energy required for DNA biosynthesis. The addition of new nucleotide always takes place at the 3−OH group of the deoxyribose sugar; therefore, all biologically synthesized nucleic acids grow in the 5′ → 3′ direction. As DNA strands are antiparallel in 3′ → 5′ strand, synthesis occurs backward and discontinuously forming Okazaki fragments, which are later joined by DNA ligase. Thus, the formed strand is known as lagging strand, whereas the strand synthesized continuously in forward direction is known as the leading strand. Addition of nucleotides occurs at a fast pace, around 750 bases per second at each fork. As replication proceeds, the duplicated strand loops down. When the fork forms a full circle and meets at its ends, ligases move along the lagging strand to link the fragments and separate the circular daughter molecules. DNA polymerase I removes the primers and replaces with the DNA. The replication of DNA is a semiconservative process, that is, one strand of each of the two new daughter molecules of DNA is an old strand and the other one is a newly synthesized one (Ullmann 2007).
Subsets of adjacent nodes (SOAN): a fast method for computing suboptimal paths in protein dynamic networks
Published in Molecular Physics, 2021
Thomas Dodd, Xin-Qiu Yao, Donald Hamelberg, Ivaylo Ivanov
Recent advances in computer architecture have made the simulation of large macromolecular complexes computationally feasible. However, conventional suboptimal paths analysis may be ill-suited to handle networks derived from large systems since the runtime is expected to increase significantly with the increased number of edges. In this work, we propose a neighbours-based approach for rapidly computing suboptimal paths between two protein residues in a dynamic network. Our protocol is written in the Python programming language and takes advantage of well-established Python packages, including NumPy and NetworkX [25–29]. To establish the utility and computational efficiency of our approach, we provide benchmark calculation on four biological systems of increasing size: (i) acid-β-glucosidase (GlcCerase) comprised of ∼500 residues, (ii) the E. coli replication machinery DNA polymerase III (Pol III) comprised of ∼2000 residues, (iii) the human transcription factor IIH (TFIIH) comprised of ∼4000 residues and (iv) the human pre-initiation complex (PIC) comprised of ∼10,000 residues. Additionally, we compare the computational efficiency and accuracy of our approach with widely used network analysis methods: CNAPATH in the Bio3D R package [30–32], the Weighted Implementation of Suboptimal Paths (WISP) [33], and NetworkView [24].