xii Detailed Contents High-T Wha e Secondary and Tertiary Structures Ilumina Next-Gen Sequencing 358 :The Human Cenome RNA AIS Order Structure 1.2 What Sorts of Secondary Structures Car e-5 anded D p 2360 re Are oli cifically selected for Their Ligand-Binding Ability 393 SUMMARY 393 Molecules 362 founDATIONAL BIOCHEMISTRY 395 Watson-Crick Base Pairs Have Virtually Identical PROBLEMS 395 Di FURTHER READING 397 e DNA Doub Helixsa Stable Str A DEEPE Why Just Two s36 Adopt a Number of Stable 12 Recombinant DNA,Cloning,Chimeric ctures can Genes,and Synthetic Biology 399 A-Form DNA Is an Alternative Form of Right-Handed 12.1 What Does It Mean "To Clone"?399 DNA 366 Plasmids Are Very Useful in Cloning Genes 400 ninthe Form Shuttle Ve nic Structure 369 Be Create 12.2 What Is a DNA Library?406 Alternative Hydrogen-Bonding Interactions Give Rise red from the Total DNA in an Oreanism 406 13 CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: Combinatorial Libraries 40 tion of DNA Can Be Observed an for the Presenc of by Changes in UV Absorbance 374 Probes for scree ne libraries can be prepared in a H-onding Solutes Denature Variety of Ways 40 PCR Is Used to Clone and Amplify Specific Genes 408 nded DNA Can Renature to Form DNA DNA Libraries Prepared PMENTS IN BIOCHEMIS Specific DNA Se nces b A D PER LOO he Buoyant Density of DNA 376 606ouhemBog A Stra DNA M 1.4 123 Kind of s of High plexity?377 the Clo enes in Libraries d41 in DNA 377 ad so That the n.5 What Is the Str e of Fuka es Are the Fundamental Structural Unit es?379 in Chromatin 380 meric DNA M Next to an Easily Expressible Gene Product 416 Gives Rise to 05383 nization east Iw 1.6 Can Nucleic Acids Be Synthesized Chemically?383 419 orm 12.4 How Is RN Jsed to Revea nes?41 Genes Can Be Synthesized Chemically 385 Jsing Synthetic shRN A5420xii Detailed Contents 11.7 What Are the Secondary and Tertiary Structures of RNA? 386 Transfer RNA Adopts Higher-Order Structure Through Intrastrand Base Pairing 387 Messenger RNA Adopts Higher-Order Structure Through Intrastrand Base Pairing 390 Ribosomal RNA Also Adopts Higher-Order Structure Through Intrastrand Base Pairing 391 Aptamers Are Oligonucleotides Specifically Selected for Their Ligand-Binding Ability 393 SUMMARY 393 Foundational Biochemistry 395 PROBLEMS 395 Further Reading 397 12 Recombinant DNA, Cloning, Chimeric Genes, and Synthetic Biology 399 12.1 What Does It Mean “To Clone”? 399 Plasmids Are Very Useful in Cloning Genes 400 Shuttle Vectors Are Plasmids That Can Propagate in Two Different Organisms 405 Artificial Chromosomes Can Be Created from Recombinant DNA 405 12.2 What Is a DNA Library? 406 Genomic Libraries Are Prepared from the Total DNA in an Organism 406 Critical Developments in Biochemistry: Combinatorial Libraries 406 Libraries Can Be Screened for the Presence of Specific Genes 407 Probes for Screening Libraries Can Be Prepared in a Variety of Ways 408 PCR Is Used to Clone and Amplify Specific Genes 408 cDNA Libraries Are DNA Libraries Prepared from mRNA 409 Critical Developments in Biochemistry: Identifying Specific DNA Sequences by Southern Blotting (Southern Hybridization) 410 DNA Microarrays (Gene Chips) Are Arrays of Different Oligonucleotides Immobilized on a Chip 412 12.3 Can the Cloned Genes in Libraries Be Expressed? 413 Expression Vectors Are Engineered So That the RNA or Protein Products of Cloned Genes Can Be Expressed 413 Reporter Gene Constructs Are Chimeric DNA Molecules Composed of Gene Regulatory Sequences Positioned Next to an Easily Expressible Gene Product 416 Specific Protein–Protein Interactions Can Be Identified Using the Yeast Two-Hybrid System 417 In Vitro Mutagenesis 419 12.4 How Is RNA Interference Used to Reveal the Function of Genes? 419 RNAi Using Synthetic shRNAs 420 High-Throughput DNA Sequencing by the Light of Fireflies 356 Illumina Next-Gen Sequencing 358 Emerging Technologies to Sequence DNA Are Based on Single-Molecule Sequencing Strategies 358 Human Biochemistry: The Human Genome Project 360 11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt? 360 Conformational Variation in Polynucleotide Strands 360 DNA Usually Occurs in the Form of Double-Stranded Molecules 362 Watson–Crick Base Pairs Have Virtually Identical Dimensions 362 The DNA Double Helix Is a Stable Structure 362 A Deeper Look: Why Just Two Base Pairs? 363 Double Helical Structures Can Adopt a Number of Stable Conformations 365 A-Form DNA Is an Alternative Form of Right-Handed DNA 366 Z-DNA Is a Conformational Variation in the Form of a Left-Handed Double Helix 367 The Double Helix Is a Very Dynamic Structure 369 Human Biochemistry: DNA Methylation, CpG Islands, and Epigenetics 369 Alternative Hydrogen-Bonding Interactions Give Rise to Novel DNA Structures: Cruciforms, Triplexes, and Quadruplexes 371 11.3 Can the Secondary Structure of DNA Be Denatured and Renatured? 374 Thermal Denaturation of DNA Can Be Observed by Changes in UV Absorbance 374 pH Extremes or Strong H-Bonding Solutes also Denature DNA Duplexes 375 Single-Stranded DNA Can Renature to Form DNA Duplexes 375 The Rate of DNA Renaturation Is an Index of DNA Sequence Complexity 375 A Deeper Look: The Buoyant Density of DNA 376 Nucleic Acid Hybridization: Different DNA Strands of Similar Sequence Can Form Hybrid Duplexes 376 11.4 Can DNA Adopt Structures of Higher Complexity? 377 Supercoils Are One Kind of Structural Complexity in DNA 377 11.5 What Is the Structure of Eukaryotic Chromosomes? 379 Nucleosomes Are the Fundamental Structural Unit in Chromatin 380 Higher-Order Structural Organization of Chromatin Gives Rise to Chromosomes 381 SMC Proteins Establish Chromosome Organization and Mediate Chromosome Dynamics 383 11.6 Can Nucleic Acids Be Synthesized Chemically? 383 Phosphoramidite Chemistry Is Used to Form Oligonucleotides from Nucleotides 384 Genes Can Be Synthesized Chemically 385 Copyright 2017 Cengage Learning. 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