DNA Double-Helix Structure (OpenStax Biology 2e)
DNA has a double-helix structure. The sugar and phosphate lie on the outside of the helix, forming the DNA’s backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. The helix’s two strands run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (Scientists call this an antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)– What is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands?
Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C, as the image below shows. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand copies itself, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.– What is a method widely used in molecular biology to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail?
DNA is a relatively rigid polymer, typically modelled as a worm-like chain. It has three significant degrees of freedom; bending, twisting, and compression, each of which cause certain limits on what is possible with DNA within a cell. Twisting-torsional stiffness is important for the circularisation of DNA and the orientation of DNA bound proteins relative to each other and bending-axial stiffness is important for DNA wrapping and circularisation and protein interactions. Compression-extension is relatively unimportant in the absence of high tension.
Clark, M., Douglas, M., Choi, J. Biology 2e. Houston, Texas: OpenStax. Access for free at: https://openstax.org/details/books/biology-2e
Date Published: April 7, 2016 Publisher: Public Library of Science Author(s): Young-Joo Kim, Do-Nyun Kim, Claudine Mayer. http://doi.org/10.1371/journal.pone.0153228 Abstract: In this article, we investigate the principal structural features of the DNA double helix and their effects on its elastic mechanical properties. We develop, in the pursuit of this purpose, a helical continuum model consisting of … Continue reading
Research Article: The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study
Date Published: February 12, 2019 Publisher: Public Library of Science Author(s): You Xu, Olof Gissberg, Y. Vladimir Pabon-Martinez, Jesper Wengel, Karin E. Lundin, C. I. Edvard Smith, Rula Zain, Lennart Nilsson, Alessandra Villa, Freddie Salsbury. http://doi.org/10.1371/journal.pone.0211651 Abstract: Locked nucleic acid (LNA) oligonucleotides bind DNA target sequences forming Watson-Crick and Hoogsteen base pairs, and are therefore … Continue reading
Date Published: April 3, 2017 Publisher: Public Library of Science Author(s): Viveca Lindahl, Alessandra Villa, Berk Hess, Alexander MacKerell Abstract: The flipping-out of a DNA base from the double-helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base … Continue reading
Date Published: January 20, 2004 Publisher: Public Library of Science Author(s): unknown Abstract: None Partial Text: One of the central problems for much of the 20th century was how to reconcile genetic stability with evolutionary change. Genomic fidelity was thought to arise from an inherent invariability in the DNA structure itself. Biologists now know that … Continue reading
Research Article: Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea
Date Published: September 29, 2016 Publisher: Public Library of Science Author(s): Lei Tian, Zhenfeng Zhang, Hanqian Wang, Mohan Zhao, Yuhui Dong, Yong Gong, Fenfei Leng. http://doi.org/10.1371/journal.pone.0163361 Abstract: T:G base pair arising from spontaneous deamination of 5mC or polymerase errors is a great challenge for DNA repair of hyperthermophilic archaea, especially Crenarchaea. Most strains in this … Continue reading