Handbook of Chemical Biology of Nucleic Acids
- Reference work
- © 2023
- Naoki Sugimoto 0
Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
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- Commemorates the 70th anniversary of the DNA double helix discovery
- Provides comprehensive coverage of fundamentals and applications of nucleic acids
- Broadens the reader's understanding of nucleic acids
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About this book
This handbook is the first to comprehensively cover nucleic acids from fundamentals to recent advances and applications. It is divided into 10 sections where authors present not only basic knowledge but also recent research. Each section consists of extensive review chapters covering the chemistry, biology, and biophysics of nucleic acids as well as their applications in molecular medicine, biotechnology and nanotechnology. All sections within this book are: Physical Chemistry of Nucleic Acids (Section Editor: Prof. Roland Winter), Structural Chemistry of Nucleic Acids (Section Editor: Prof. Janez Plavec), Organic Chemistry of Nucleic Acids (Section Editor: Prof. Piet Herdewijin), Ligand Chemistry of Nucleic Acids (Section Editor: Prof. Marie-Paule Teulade-Fichou), Nucleic Acids and Gene Expression (Section Editor: Prof. Cynthia Burrows), Analytical Methods and Applications of Nucleic Acids (Section Editor: Prof. Chaoyong Yang), Nanotechnology and Nanomaterial Biology of Nucleic Acids (Section Editor: Prof. Zhen Xi), Nucleic Acids Therapeutics (Section Editor: Prof. Katherine Seley-Radtke), Biotechnology and Synthetic Biology of Nucleic Acids (Section Editor: Prof. Eriks Rozners), Functional Nucleic Acids (Section Editor: Prof. Keith R. Fox).
The handbook is edited by outstanding leaders with contributions written by international renowned experts. It is a valuable resource not only for researchers but also graduate students working in areas related to nucleic acids who would like to learn more about their important role and potential applications.
- Molecular Crowding
- Drug Discovery
- DNA Origami
Table of contents (90 entries)
Front matter, physical chemistry of nucleic acids, high-pressure single-molecule studies on non-canonical nucleic acids and their interactions.
- Sanjib K. Mukherjee, Jim-Marcel Knop, Roland Winter
Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids
- Shuntaro Takahashi, Hisae Tateishi-Karimata, Naoki Sugimoto
The Effect of Pressure on the Conformational Stability of DNA
- Tigran V. Chalikian, Robert B. Macgregor Jr.
Quadruplexes Are Everywhere…On the Other Strand Too: The i-Motif
- Jean-Louis Mergny, Mingpan Cheng, Jun Zhou
i-Motif Nucleic Acids
- Zoë A. E. Waller
Structural Chemistry of Nucleic Acids
Nmr study on nucleic acids.
- Janez Plavec
- Doyoun Kim, Vinod Kumar Subramani, Soyoung Park, Joon-Hwa Lee, Kyeong Kyu Kim
Structures of G-Quadruplexes and Their Drug Interactions
- Yichen Han, Jonathan Dickerhoff, Danzhou Yang
In Cell 19F NMR for G-Quadruplex
Structures and catalytic activities of complexes between heme and dna.
- Yasuhiko Yamamoto, Atsuya Momotake
Studying Nucleic Acid-Ligand Binding by X-Ray Crystallography
- Christine J. Cardin, Kane T. McQuaid
Predicting the 3D Structure of RNA from Sequence
- James Roll, Craig L. Zirbel
Organic Chemistry of Nucleic Acids
Hexitol nucleic acid (hna): from chemical design to functional genetic polymer.
- Elisabetta Groaz, Piet Herdewijn
The Effects of FANA Modifications on Non-canonical Nucleic Acid Structures
- Roberto El-Khoury, Miguel Garavís, Masad J. Damha
Isomorphic Fluorescent Nucleoside Analogs
- Kfir B. Steinbuch, Yitzhak Tor
Bridged Nucleic Acids for Therapeutic Oligonucleotides
- Md Ariful Islam, Satoshi Obika
Editors and Affiliations
Naoki Sugimoto
About the editor
Naoki Sugimoto received Ph.D. degree in 1985 from Kyoto University, Japan. After postdoctoral work at University of Rochester, USA, he joined Konan University, Kobe, Japan in 1988 and is a full professor since 1994. From 2003, he also holds a director of Frontier Institute for Biomolecular Engineering Research (FIBER) at Konan University. He is a member of the Editorial Board of Nucleic Acids Research from 2007 and Scientific Reports from 2015 to the present, was the first President of the Japan Society of Nucleic Acids Chemistry (JSNAC) from 2017 to 2020 and is now the Fellow of JSNAC. He received the Dr. Masao Horiba’s Award in 2004, Distinguished Scientist Award from ICA (International Copper Association), USA in 2005, Hyogo Science Award from Hyogo prefecture, Japan in 2006, the Chemical Society Japan (CSJ) Award for Creative Work in 2007, JSCC Contribution Award, Japan Society of Coordination Chemistry (JSCC) in 2014, The Iue Cultural Award in Scienceand Technology in 2015, The Imbach-Townsend Award, IS3NA in 2018, The 72th CSJ Award (Top Award in CSJ) in 2019, and so on. His research interests focus on biophysical chemistry, biomaterials, bionano-engineering, molecular design, biofunctional chemistry, biotechnology, and therapeutic application of nucleic acids.
Bibliographic Information
Book Title : Handbook of Chemical Biology of Nucleic Acids
Editors : Naoki Sugimoto
DOI : https://doi.org/10.1007/978-981-19-9776-1
Publisher : Springer Singapore
eBook Packages : Chemistry and Materials Science , Reference Module Physical and Materials Science , Reference Module Chemistry, Materials and Physics
Copyright Information : Springer Nature Singapore Pte Ltd. 2023
Hardcover ISBN : 978-981-19-9775-4 Published: 30 July 2023
eBook ISBN : 978-981-19-9776-1 Published: 29 July 2023
Edition Number : 1
Number of Pages : XXXIV, 2861
Number of Illustrations : 321 b/w illustrations, 790 illustrations in colour
Topics : Chemistry/Food Science, general , Biomaterials , Biochemistry, general , Organic Chemistry , Biotechnology , Nanochemistry
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Nucleotides and Nucleic Acids - Lehninger Chapter8
Dec 20, 2019
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Nucleotides and Nucleic Acids - Lehninger Chapter8. 8.1 Basics 8.2 Structure 8.3 Chemistry 8.4 Nucleotide Function. 8.1 Basics. Building Blocks Phosphodiester bonds Naming and Drawing Base Stacking and Pairing. Building Blocks. Nucleotides = Base + Sugar + Phosphate
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Nucleotides and Nucleic Acids - Lehninger Chapter8 • 8.1 Basics • 8.2 Structure • 8.3 Chemistry • 8.4 Nucleotide Function
8.1 Basics • Building Blocks • Phosphodiester bonds • Naming and Drawing • Base Stacking and Pairing
Building Blocks • Nucleotides = Base + Sugar + Phosphate • Nucleosides = Base + Sugar • Nitrogen Bases • Purines (5 + 6 membered rings) – numbering • Adenine Guanine • Pyrimidines (6 membered ring) – numbering • Thymine Cytosine Uracil • Pentose Sugars (numbering) • – Ribose • – Deoxy Ribose
Pyrimidines
Phosphodiester bonds • Formed by Polymerase and Ligase activities • C-5' OH carries the phosphate in nucleotides • C5' - O - P - O - C3' • Phosphate pKa ~ 0 • Natural Oligonucleotides have 5' P and 3' 0H • Base hydrolysis due to ionizaiton of 2' OH in RNA
Oligonucleotide naming / drawing conventions • 5’ - Left to Right - 3’ • pACGTOH • ACGT
Base Stacking and Base Pairing • Bases are very nearly planar • Aromaticity => large absorbance at 260nm • Flat surfaces are hydrophobic • Dipole-Dipole and Van Der Waals interactions also stabilize stacked structures • Bases have hydrogen bond donors and acceptors • H-bonding potential satisfied in paired structures
8.2 Structure • DNA contains genetic Information • Distinctive base composition foretells base pairing patterns • Double helical structures • Local structures • mRNAs - little structure • Stable RNAs - complex structures
DNA contains genetic Information • Purified DNA can "transform" Bacteria • Avery, MacLeod & McCarty transferred the virulence trait to pneumococci • The genetic material contains 32P (DNA) and not 35S (protein – C, M) • Hershey and Chase grew bacteriophage on either 32P or 35S • Bacteriophage infection resulted in transfer of 32 P and not 35S
Distinctive Base composition foretell base pairing patterns • Hydrolysis of DNA and analysis of base composition • Same for different individuals of a given species • Same over time • Same in different tissues • %A = %T and %G = %C (Chargaff's Rules) • Amino acid compositions vary under all three conditions • No quantitative relationships in AA composition
Structural Basis of Chargaff’s Rules Two Strands have complementary sequences 2 logical operations to obtain complementary strand 5' to 3' 1. Reverse: Rewrite the sequence, back to front 2. Complement: Swap A with T, C with G
Double helical structures • Potentially Right or Left Handed • Actually Mostly Right Handed • Potentially Parallel or Anti-parallel • Actually anti-parallel • Sugar Pucker + 6 rotatable bonds gives 3 families • A, B, Z structures
Semi-conservative Replication
DNA Backbone Flexibility Multiple Degrees of Rotational Freedom
Glycosidic Bond Configurations
3 Canonical Helical DNA Structures
A, B and Z DNA A form – favored by RNA B form – Standard DNA double helix under physiological conditions Z form – laboratory anomaly, Left Handed Requires Alt. GC High Salt/ Charge neutralization
Local structures • Palindromes – Inverted repeats • Not quite the same as (Madam I’m Adam) • Symmetrical Sequence Elements Match Symmetry of Protein Homo-Oligomers • Symmetry often incomplete/imperfect • Direct Repeats • Hairpin and Cruciform Structures
Hoogstein Pairing in Base Triples
Messenger RNAs • Contain protein coding information • ATG start codon to UAA, UAG, UGA Stop Codon • A cistron is the unit of RNA that encodes one polypeptide chain • Prokaryotic mRNAs are poly-cistronic • Eukaryotic mRNAs are mono-cistronic • Base pairing/3D structure is the exception • Can be used to regulate RNA stability termination, RNA editng, RNA splicing
GG[GACU] code for Glycine UGG codes for Tryptophan UGA, UAG, UAA are stop codons AG[CU] and UC[GACU] code for Serine The Genetic Code
mRNA coding patterns
Stable RNAs with complex structures
RNA Helices are short, bulges, loops
RNA Secondary Structure Maps Calculated from helix thermodynamic parameters Loop entropy considerations
tRNA-Phe 2° Structure
tRNA - the prototype structure
8.3 Chemistry • Denaturation and reannealing • Hybridization • Spontaneous Chemical Reactions • Methylation • Sequencing • Chemical Synthesis
Denaturation and reannealing
Tm (transition midpoint) as a function of base composition Salt dependence is more dramatic
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IMAGES
COMMENTS
The first isolation of nucleic acid we now refer to as DNA was accomplished by Swiss physiologist Johann Friedrich Miescher circa 1870 while studying the nuclei of white blood cells. In the 1920's nucleic acids were found to be major components of chromosomes, small gene-carrying bodies in the nuclei of complex cells.
Chapter 28: Nucleosides, Nucleotides, and Nucleic Acids. Nucleic acids are the third class of biopolymers (polysaccharides and proteins being the others) Two major classes of nucleic acids deoxyribonucleic acid (DNA): carrier of genetic information ribonucleic acid (RNA): an intermediate in the expression of genetic information and other diverse roles The Central Dogma (F. Crick):
CHAPTER 2 STRUCTURES OF NUCLEIC ACIDS DNA and RNA are both nucleic acids, which are the polymeric acids isolated from the nucleus of cells. DNA and RNA can be represented as simple strings of letters, where each letter corresponds to a particular nucleotide, the monomeric component of the nucleic acid polymers. Although this conveys almost all the information content of the nucleic acids, it ...
Ribonucleic acid (RNA), the other kind of nucleic acid, is a related molecule to DNA. It is also a poly-mer of four nucleotides, three of which are the same as in DNA while the fourth one is slightly different. It has many functions in cells, notably acting as the intermediate between DNA and proteins. Some viruses even store their genome in the form of an RNA molecule rather than DNA.
Basically, nucleic acids can be subdivided into two types: deoxy-ribonucleic acid (DNA) and ribonucleic acid (RNA). Both DNA and RNA have been shown to consist of three groups of molecules: pentose (5-carbon-atom) sugars; organic bases; and inorganic phosphate.
Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry genetic information which is read in cells to make the RNA and proteins by which living things function.
Module 14 Nucleic Acids Lecture 36 Nucleic Acids I Nucleic acids are targets of many important drugs, including several anticancer agents. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA encodes the hereditary details and controls the growth and division of the cells. The genetic information stored in DNA is then transcribed into RNA, and the ...
n DNA are responsible for the efficient control of a cell's metabolism. How-ever, the production of protein molecules is under th. control of the nucleic acids, the primary control molecules of the cell. The structure of the nucleic acids, DNA and RNA, determines the structure of the proteins, whereas the struct.
The document is a lecture on nucleic acids and DNA replication. It contains the following key points: 1. Nucleic acids are made up of nucleotides, which contain a nitrogenous base, a 5-carbon sugar (ribose in RNA, deoxyribose in DNA), and a phosphate group. RNA contains uracil and DNA contains thymine. 2. DNA stores and transmits genetic information through replication and transcription ...
Nucleic acids Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are made up of nucleic acids found in the nuclei of living cells. They are the vehicles of genetic inheritance. Nucleic acids are condensation polymers of nucleotides.
Chem 2223b Intersession 2008: Nucleic Acids This chapter focuses on some of the biological and chemical aspects of nucleic acids, specifically DNA. We will examine its properties, sequencing, and laboratory synthesis.
8.1 Some Basics Nucleotides, Building Blocks of Nucleic Acids The amino acid sequence of every protein in a cell, and the nucleo-tide sequence of every RNA, is specified by a nucleo-tide sequence in the cell's DNA. A segment of a DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA, is referred to as a gene. A cell ...
This handbook is the first to comprehensively cover nucleic acids from fundamentals to recent advances and applications. It is divided into 10 sections where authors present not only basic knowledge but also recent research. Each section consists of extensive review chapters covering the chemistry, biology, and biophysics of nucleic acids as ...
Assignment # 8 Genes & Nucleic Acids - Free download as Word Doc (.doc / .docx), PDF File (.pdf), Text File (.txt) or read online for free. The document discusses nucleic acids, DNA, RNA, and their functions. It defines a karyotype as an individual's complete set of chromosomes. It describes the key differences between DNA and RNA, such as DNA containing deoxyribose while RNA contains ribose ...
Nucleic acids in chemistry and biology Publication date 1990 Topics Nucleic acids, Nucleic Acids, Acides nucleiques, Acides nucleiques, Nucleic acids, Nucleinsauren, Acides nucleiques, 11030 nucleic acids, Nucleic acids Publisher Oxford ; New York : IRL Press at Oxford University Press Collection internetarchivebooks; inlibrary; printdisabled ...
Assignment No.1 On Nucleic Acids - Free download as Word Doc (.doc / .docx), PDF File (.pdf), Text File (.txt) or read online for free. The document summarizes key concepts about nucleic acids: Nucleic acids are polymers of nucleotides that serve as the genetic material of cells. DNA stores and transfers genetic information found in the cell nucleus. RNA is involved in protein synthesis and ...
Resonance assignment of nucleic acids follows a similar strategy to that of proteins for the identification of residue type. The nucleotide type is identified from a combination of HSQC, Hb(C)Nb and Hs(Cs)N(Cb)Hb experiments (Table 4).
Nucleic Acid - Assignment (1) - Free download as PDF File (.pdf), Text File (.txt) or read online for free. Assignment about real examples of Nucleic Acid
Chemistry Class 12th Project - DNA and RNA 2 (Complete Content PDF) - Free download as PDF File (.pdf), Text File (.txt) or read online for free. This document provides background information on nucleic acids and their components.
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PP1. Nucleic Acids - Free download as Powerpoint Presentation (.ppt / .ppsx), PDF File (.pdf), Text File (.txt) or view presentation slides online. lifesciences grade 12 nucleic acids(DNA)
Assignment on Nucleic acids (Biochemistry) - Free download as Word Doc (.doc / .docx), PDF File (.pdf), Text File (.txt) or read online for free.