The Structure of DNA

The Structure of DNA The Structure of DNA Bởi: OpenStaxCollege In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure of DNA Other scientists, such as Linus Pauling and Maurice Wilkins, were also actively exploring this field Pauling had discovered the secondary structure of proteins using X-ray crystallography Xray crystallography is a method for investigating molecular structure by observing the patterns formed by X-rays shot through a crystal of the substance The patterns give important information about the structure of the molecule of interest In Wilkins’ lab, researcher Rosalind Franklin was using X-ray crystallography to understand the structure of DNA Watson and Crick were able to piece together the puzzle of the DNA molecule using Franklin's data ([link]) Watson and Crick also had key pieces of information available from other researchers such as Chargaff’s rules Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types were always present in equal amounts and the remaining two types were also always present in equal amounts This meant they were always paired in some way In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine for their work in determining the structure of DNA Pioneering scientists (a) James Watson and Francis Crick are pictured here with American geneticist Maclyn McCarty Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure (credit a: modification of work by Marjorie McCarty; b: modification of work by NIH) 1/7 The Structure of DNA Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) The building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base ([link]) There are four types of nitrogenous bases in DNA Adenine (A) and guanine (G) are double-ringed purines, and cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines The nucleotide is named according to the nitrogenous base it contains (a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base (b) Cytosine and thymine are pyrimidines Guanine and adenine are purines The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, and so on, forming a long polymer of nucleotide monomers The sugar–phosphate groups line up in a “backbone” for each single strand of DNA, and the nucleotide bases stick out from this backbone The carbon atoms of the five-carbon sugar are numbered clockwise from the oxygen as 1', 2', 3', 4', and 5' (1' is read as “one prime”) The phosphate group is attached to the 5' carbon of one nucleotide and the 3' carbon of the next nucleotide In its natural state, each DNA molecule is actually composed of two single strands held together along their length with hydrogen bonds between the bases Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C In other words, adenine and thymine are complementary base pairs, and cytosine and 2/7 The Structure of DNA guanine are also complementary base pairs This is the basis for Chargaff’s rule; because of their complementarity, there is as much adenine as thymine in a DNA molecule and as much guanine as cytosine Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds The two strands are anti-parallel in nature; that is, one strand will have the 3' carbon of the sugar in the “upward” position, whereas the other strand will have the 5' carbon in the upward position The diameter of the DNA double helix is uniform throughout because a purine (two rings) always pairs with a pyrimidine (one ring) and their combined lengths are always equal ([link]) DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and cytosine pairs with guanine (credit a: modification of work by Jerome Walker, Dennis Myts) The Structure of RNA There is a second nucleic acid in all cells called ribonucleic acid, or RNA Like DNA, RNA is a polymer of nucleotides Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group In the case of RNA, the five-carbon sugar is ribose, not deoxyribose Ribose has a hydroxyl group at the 2' carbon, unlike deoxyribose, which has only a hydrogen atom ([link]) The difference between the ribose found in RNA and the deoxyribose found in DNA is that ribose has a hydroxyl group at the 2' carbon RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine However, they not contain thymine, ... Copyright  2011 Pearson Canada Inc. 15 - 1 Chapter 15 The Structure of Central Banking and the Bank of Canada Copyright  2011 Pearson Canada Inc. 15 - 2 Origins of the Bank of Canada I • The Bank was created by the Bank of Canada Act in 1934 and started operations in 1935 • Initially the Bank was a private institution but was nationalized in 1938, so is now a national institution with headquarters in Ottawa • The Bank also has regional offices in Toronto, Vancouver, Calgary, Montreal, and Halifax • Unlike a private bank that operates in pursuit of profit, the Bank of Canada is responsible for the country’s monetary policy and for the regulation of Canada’s deposit-based financial institutions. Copyright  2011 Pearson Canada Inc. 15 - 3 Origins of The Bank of Canada II Copyright  2011 Pearson Canada Inc. 15 - 4 Formal Structure of the Bank of Canada I • Responsibility for the operation of the Bank rests with a Board of Directors, which consists of fifteen members: • the governor (currently Mark Carney, who is the chief executive officer and chairman of the Board of Directors) • the senior deputy governor, • the deputy minister of finance, and • twelve outside directors Copyright  2011 Pearson Canada Inc. 15 - 5 Formal Structure of the Bank of Canada II • The Board appoints the governor and senior deputy governor with the government’s approval, for a renewable term of 7 years. • The outside directors are appointed by the minister of finance, with cabinet approval, for a 3-year term. • In 1994 the Board of directors established a new senior decision making authority called the Governing Council • The Council is chaired by the governor and is composed of the senior deputy governor and four deputy governors Copyright  2011 Pearson Canada Inc. 15 - 6 The Functions of the Bank The functions of the Bank of Canada are: • Bank Note Issue • Government Debt and Asset Management Services • Central Banking Services • Monetary Policy Copyright  2011 Pearson Canada Inc. 15 - 7 Bank Note Issue • Before the creation of the Bank, the federal government and the early banks issued notes designed to circulate as currency. • By 1945, however, the Bank had a monopoly over note issue in the country. • The Bank also conducts ongoing research, working closely with private sector partnerships and note-issuing authorities in other countries, in order to improve cost- effectiveness, increase the durability of bank notes, and reduce counterfeiting. Copyright  2011 Pearson Canada Inc. 15 - 8 Government Debt and Asset Management Services As the federal government’s fiscal agent, the Bank: • provides debt-management services for the federal government such as advising on borrowings, managing new debt offerings, and servicing outstanding debt • manages the government’s foreign exchange reserves held by the Exchange Visit the National Academies Press online, the authoritative source for all books from the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council: • Download hundreds of free books in PDF • Read thousands of books online for free • Explore our innovative research tools – try the “Research Dashboard” now! • Sign up to be notified when new books are published • Purchase printed books and selected PDF files Thank you for downloading this PDF. 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Gravitational Physics: Exploring the Structure of Space and Time Committee on Gravitational Physics, National Research Council Committee on Gravitational Physics Board on Physics and Astronomy Commission on Physical Sciences, Mathematics, and Applications National Research Council NATIONAL ACADEMY PRESS Washington, D.C. G ravitational P hysics E xploring the Structure of Space and Time Copyright © National Academy of Sciences. All rights reserved. Gravitational Physics: Exploring the Structure of Space and Time http://www.nap.edu/catalog/9680.html NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance. This project was supported by the National Aeronautics and Space Administration under Grant No. NAG5-4120, the Department of Energy under Contract No. DE-FG02-97ER41051, and the National Science Foundation under Grant No. PHY-9722102. Any opinions, findings, and conclu- sions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsors. Front cover: Gravitational waves are ripples in the curvature of space and time that propagate with the speed of light through otherwise empty space. Mass in motion is the source of gravitational waves. The figure shows the predicted gravitational wave pattern from a pair of neutron stars or black holes spiraling inward toward a final merger. The figure shows one polarization of the waves as seen by observers stationed throughout the plane THE INFLUENCE OF THE KU80 CARBOXY-TERMINUS ON ACTIVATION OF THE DNA-DEPENDENT PROTEIN KINASE AND DNA REPAIR IS DEPENDENT ON THE STRUCTURE OF DNA COFACTORS Derek S. Woods Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Department of Biochemistry and Molecular Biology, Indiana University November 2013 ii Accepted by the Graduate Faculty, of Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. John J. Turchi, Ph.D., Chairman Maureen A. Harrington, Ph.D. Doctoral Committee Anna L. Malkova, Ph.D. August 6, 2013 Yuichiro Takagi, Ph.D. iii ACKNOWLEDGEMENTS I would like to thank my family for their unfaltering support over the last several years. My parents have played such a key role in my development and well being throughout my life. I am very lucky to have their unconditional love and dedication. My brother and sister-in-law, who have expressed their support of science and my research in particular over the last 5 years. My affectionate and supportive wife, Carly Woods, whose love and commitment to me knows no end. She sacrifices so much in order to be with me and this does not go unnoticed. I can’t imagine my life without her. She is my rock, my biggest cheerleader, and my best friend. There is no way I can ever repay her for all that she has done for me but I intend to try everyday for the rest of my life. I also have to thank my advisor, Dr. John Turchi, for taking a risk by accepting me into his lab with basically no experience to work on a project that was not funded. Over the past 5 years he has given me direction when it was required as well as the freedom to explore my passion. I look forward to our next endeavor at NERx Biosciences, Inc. where he has once again decided to take a chance on me. Finally I would like to thank Dr. Katherine Pawelczak whose previous work is the basis for my thesis. She has taught me numerous valuable lessons in science and in life. I truly appreciate her friendship and mentorship. iv ABSTRACT Derek S. Woods The Influence of the Ku80 Carboxy-Terminus on Activation of the DNA-Dependent Protein Kinase and DNA Repair is Dependent on the Structure of DNA Cofactors In mammalian cells DNA double strand breaks (DSBs) are highly variable with respect to sequence and structure all of which are recognized by the DNA- dependent protein kinase (DNA-PK), a critical component for the resolution of these breaks. Previously studies have shown that DNA-PK does not respond the same way to all DSBs but how DNA-PK senses differences in DNA substrate sequence and structure is unknown. Here we explore the enzymatic mechanism by which DNA-PK is activated by various DNA substrates. We provide evidence that recognition of DNA structural variations occur through distinct protein-protein interactions between the carboxy terminal (C-terminal) region of Ku80 and DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Discrimination of terminal DNA sequences, on the other hand, occurs independently of Ku 80 C-terminal interactions and results exclusively from DNA-PKcs interactions with the DNA. We also show that sequence differences in DNA termini can drastically influence DNA repair through altered DNA-PK activation. Our results indicate that even subtle differences in DNA substrates influence DNA-PK activation and ultimately Non-homologous End Joining (NHEJ) efficiency. John J. Turchi, Ph.D., Chairman v TABLE OF CONTENTS 1. Introduction 1 1.1 DNA Damage and Repair 1 1.2 Double Strand Breaks (DSBs) 2 1.3 DNA Damaging Agents in Cancer Therapy 7 1.4 Ku70/80 9 1.5 DNA-PKcs 14 1.6 Ku/DNA-PKcs THE MATHEMATICS OF DNA STRUCTURE, MECHANICS, AND DYNAMICS DAVID SWIGON∗ Abstract A brief review is given of the main concepts, ideas, and results in the fields of DNA topology, elasticity, mechanics and statistical mechanics Discussion includes the notions of the linking number, writhe, and twist of closed DNA, elastic rod models, sequence-dependent base-pair level models, statistical models such as helical worm-like chain and freely jointed chain, and dynamical simulation procedures Experimental methods that lead to the development of the models and the implications of the models are also discussed Emphasis is placed on illustrating the breadth of approaches and the latest developments in the field, rather than the depth and completeness of exposition Key words DNA topology, elasticity, mechanics, statistical mechanics, stretching Introduction The discovery of DNA structure 55 years ago marked the beginning of a process that has transformed the foundations of biology and medicine, and accelerated the development of new fields, such as molecular biology or genetic engineering Today, we know much about DNA, its properties, and function We can determine the structure of short DNA fragments with picometer precision, find majority of the genes encoded in DNA, and we can manipulate, stretch and twist individual DNA molecules We can utilize our knowledge of gene regulatory apparatus encoded in DNA to produce new microorganisms with unexpected properties Yet, there are aspects of DNA function that defy our understanding, mostly because the molecule is just one, albeit essential, component of a complex cellular machinery From the very beginning, abstraction and modeling played a significant role in research on DNA, since the molecule could not be visualized by any available experimental methods These models gave rise to mathematical concepts and techniques for study of DNA configurations at the macroscopic and mesoscopic levels, which are the subject of this short review The paper begins with a brief description of DNA atomic-level structure, followed by a discussion of topological properties of DNA such as knotting, catenation, and the definitions of linking number and supercoiling It continues with an outline of continuum and discrete models of DNA elasticity, focusing on local energy contributions and analysis of equilibrium states Modeling of long range electrostatic interactions is described next, followed by the treatment of thermal fluctuations and statistical mechanics The paper concludes with an outline of dynamical models of DNA, and ∗ Department of Mathematics, University of Pittsburgh, 301 Thackeray Hall, Pittsburgh, PA 15260 (swigon@pitt.edu) The work was supported by Institute for Mathematics and its Applications (IMA), Alfred P SLoan Fellowship and NSF Grant DMS 0516646 293 C.J Benham et al (eds.), Mathematics of DNA Structure, Function and Interactions, The IMA Volumes in Mathematics and its Applications 150, DOI 10.1007/978-1-4419-0670-0_14, © Springer Science+Business Media, LLC 2009 294 DAVID SWIGON Fig Side view (left) and a view along the axis (right) of DNA double helix in atomic level detail, .. .The Structure of DNA Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) The building blocks of DNA are nucleotides,... linked to the next one by a short strand of DNA that is free of histones This is also known as the “beads on a string” structure; the nucleosomes 4/7 The Structure of DNA are the “beads” and the short... animation of DNA packaging Section Summary The model of the double-helix structure of DNA was proposed by Watson and Crick The DNA molecule is a polymer of nucleotides Each nucleotide is composed of