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DNA Structure DNA Structure By Ronald Vale A Narrative produced by The Explorer’s Guide to Biology 2 The Explorer’s Guide to Biology https://explorebiology.org/ The Structure of DNA Ronald Vale, University of California, San Francisco Ronald (Ron) Vale Ronald (Ron) Vale is a professor at the University of California, San Francisco, and an investigator with the Howard Hughes Medical Institute. Ron received his PhD in Neuroscience from Stanford University in 1985. His honors include the Lasker Award in Basic Medical Research, the Shaw Prize in Life Sciences, and the Canada Gairdner Award; he was elected to the US National Academy of Sciences and the National Academy of Medicine. Ron believes in the free dissemination of scientific knowledge throughout the world. He is the founder of iBiology, a nonprofit orga- nization that produces free videos of talks by leading scientists, and the founder and executive producer of The Explorer’s Guide to Biology. Version Date: September, 2019 3 The Structure of DNA Summary The DNA double helix, one of the most influential discoveries in the history of science, revealed how information is stored and replicated in living organisms. Francis Crick and Jim Watson did not exagger- ate when they proclaimed that they had found “the secret of life” at the Eagle Pub in 1953. The double helix has since become the foundation of modern biology and its most iconic image. However, DNA is much more than a molecule to be memorized; it is a portal for understanding science and scientific strategy. In this Narrative, we will unravel the DNA helix in our minds and go back to a time when the structure was unknown and DNA was not even known to be the molecule of heredity. What did it take to catapult DNA into the modern era? What seems obvious now was not then. The quest to understand DNA was marked by mistakes by brilliant people, insights by underdogs, clues that lay forsaken, and flashes of brilliance. The path to the double helix also reveals the complementary roles of modeling (Watson and Crick) and experimentation (Rosalind Franklin, Maurice Wilkins, and Florence Bell, an unsung heroine whose early discoveries on DNA are featured here). Springing forward to modern times, we will explore how contemporary bio-engineers use DNA as a building material to create nanoscale devices. The DNA double helix continues to be a source of enormous creativity and inspiration. Learning Overview Big Concepts Complementarity between molecules governs many interactions and reactions in biology; the chemical complementarity between bases (guanine interacting with cytosine, and adenine with thymine) holds two DNA strands together in a double helix and provides simple rules for its replication. Terms and Concepts Used Adenosine triphosphate, alpha-helix, amino acid, angstrom, antibody, atomic force microscopy, base, bacterial strain, bacteriophage, Central Dogma, chromosome, CRISPR gene editing, diploid, DNA cloning, electron microscopy, gamete, genome, gene, germ cell, haploid, hemoglobin, insulin, keratin, meiosis, messenger RNA, mutation, polynucleotide, polypeptide, polysaccharide, protein, reverse transcription, ribosome, RNA, sickle cell anemia, T cell, transcription factor, van der Waals radius, virulence, virus, white blood cell, X-ray, X-ray crystallography Terms and Concepts Explained Codon, DNA aptamer, DNA chemical structure, DNA origami, DNA polymerase, DNA primase, helicase, hydrogen bond, major and minor groove, nucleoside, nucleotide, Okazaki fragment, phosphodiester bond, purine, pyrimidine, semi-conservative replication, start and stop codon, topoisomerase 4 The Structure of DNA Introduction The model for the DNA double helix in 1953 by Jim Watson and Francis Crick marked the start of a new era of molecular genetics and personalized medicine. The model provided a surprisingly simple and clear answer to the fundamental question of how the information for life is stored and replicates. The elucidation of the DNA double helix is a marvelous story of scientific detective work. It also illustrates how the two general scientific approaches of (1) experimental data gathering and (2) model building complement one another to advance our understanding of living organisms. Part I: Journey to Discovery: The DNA Double Helix Gregor Mendel’s experiments with peas in the mid-19th century revealed that different traits are conferred by discrete heritable entities that later were called genes. By the early 20th century, evidence suggested that genes reside on chromosomes, which are fibrous nuclear elements com- posed of DNA and protein. DNA (deoyxribose nucleic acid), discovered in 1869 by Friedrich Miescher, is composed of four bases (guanine, cytosine, adenine, thymine). The bases are connected to a sugar (deoxyribose), and sugars are interconnected through phosphate linkages to form a long, unbranched chain. For much of the first half of the 20th century, the chemical agent responsible for heredity was not known. Most scientists, however, believed that genes were composed of proteins, not DNA. DNA seemed too simple (only 4 different bases) compared to proteins (20 different amino acids) to encode the complex information of life. Two important experiments, one by Avery, MacLeod, and McCarty (1944) and the other by Hershey and Chase (1952), provided compelling evidence that DNA, and not protein, is the chemical agent responsible for heredity. The first important breakthrough in understanding the structure of DNA was made in 1938 by Florence Bell, a graduate student working with William Astbury in Leeds, England. Bell found a method to align fibers of DNA and then took X-ray photographs of the fibers. Her results (14 years before the famous photograph of Rosalind Franklin) revealed that DNA has a regular structure and that the bases are stacked at regular 3.4 angstrom intervals. Another important clue was found by Edwin Chargaff who determined the ratios of the four bases in DNA. He found that guanine and cytosine are present at a 1:1 ratio, as are adenine and thy- mine. The implication of this finding was not understood at first. Several scientists were chasing after the DNA structure (structure meaning understanding how the DNA chain adopts a three-dimensional shape). Watson and Crick, two young scientists at the Cavendish Laboratory in Cambridge, England, wanted to make a model, effectively a “guess” or hypothesis of what DNA might look like based upon a minimal amount of data. Linus Pauling, a famous senior scientist at Caltech, was doing the same. Rosalind Franklin and Maurice Wilkins, 5 The Structure of DNA like Florence Bell previously, were taking X-ray photographs and trying to determine the structure using more information from their experimental work. To make a model of DNA, you need to ascertain (1) how many chains of DNA are present in the biological form of DNA, and, if more than one chain, (2) whether those chains run in the same or opposite directions, (3) whether they pack straight or twist around one another, and (4) how the chains interact. Failed models of DNA preceded the correct one. The first (unpublished) Watson and Crick model and the published Pauling model both proposed an incorrect DNA triple helix. Rosalind Franklin made a key breakthrough by preparing a pure and “biologically relevant” form of DNA (B-form DNA) and generated her famous X-ray photograph: photograph 51. When Jim Watson saw photograph 51 (a half-year after it was produced), he immediately knew that DNA was a helix, thanks to earlier theoretical work by Francis Crick. This insight triggered an intense episode of model building by Watson and Crick. Crick also found a clue in the X-ray data that revealed that DNA was composed of two strands oriented in opposite directions. It was a double helix. A key eureka moment was Watson’s realization that guanine pairs with cytosine and adenine pairs with thymine at the center of the double helix. This insight explained how the two DNA strands are held together, how the double helix can maintain a constant width regardless of its nucleotide sequence, and most importantly, how DNA can replicate. The close collaboration between Watson and Crick and their combined insights allowed their model for the DNA double helix to come together in just 1 month. The DNA double helix was a model that was supported with some but not extensive data and many scientists remained skeptical. The experiment by Meselson and Stahl in 1958 showed that DNA replicates just as Watson and Crick proposed and led to the general acceptance of the Watson–Crick model. Watson, Crick, and Wilkins won the Nobel Prize in 1962. Franklin died of cancer in 1958. Part II: Knowledge Overview: The Structure of DNA DNA (deoxyribonucleic acid) stores information that can be read out to make RNAs and ultimately proteins. DNA can be copied, allowing life to propagate. DNA can mutate, allowing biological variation. The building blocks of DNA are nucleotides, small organic compounds consisting of one of four bases attached to a sugar (deoxyribose) and a phosphate. DNA in a chromosome is a single long chain of millions of connected nucleotides. The nucleotides are connected through phosphodiester bonds, in which one phosphate is linked to the 5′ carbon of one deoyxribose and to the 3′ carbon of another deoxyribose. The asymmetry of 5′ and 3′ phos- phodiester bonds confers a polarity to the DNA chain. 6 The Structure of DNA The most common biological form of DNA is the “B-form” (see Journey to Discovery), which is a double helix in which the two chains align in opposite directions. It is a right-handed helix that repeats its twist every ~10 nucleotides. The phosphate-sugar groups constitute the backbone of the helix; the bases, which lie perpendicular to the long axis, are spaced at 3.4 angstrom intervals. The DNA double helix has two grooves: the major groove and minor groove. Proteins can bind to these grooves, most commonly, the major groove where proteins can recognize a particular sequence of bases.
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