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Chapter 13

DNA Structure and Function

The DNA Helix
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most…
DNA Packaging
Eukaryotes have large genomes compared to prokaryotes. In order to fit their genomes into a cell, eukaryotes must pack their DNA tightly inside the…
Organization of Genes
The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. Genes…
Karyotyping
Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated…
Replication in Prokaryotes
DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to…
Replication in Eukaryotes
In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity…
Proofreading
Synthesis of new DNA molecules starts when DNA polymerase links nucleotides together in a sequence that is complementary to the template DNA…
Mismatch Repair
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires…
Nucleotide Excision Repair
Exposure to mutagens can damage DNA and result in bulky lesions that distort the double-helix structure or impede proper transcription. Damaged DNA…
Mutations
Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors.…
Transcription
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene…
Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it…
Bacterial Transformation
In 1928, bacteriologist Frederick Griffith worked on a vaccine for pneumonia, which is caused by Streptococcus pneumoniae bacteria. Griffith studied…
Folding and Characterization of a Bio-responsive Robot from DNA Origami
The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside.…
Targeted <em>in Situ</em> Mutagenesis of Histone Genes in Budding Yeast
We describe a PCR- and homologous recombination-based system for generating targeted mutations in histone genes in budding yeast cells. The resulting…
The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA…
A Simple Chelex Protocol for DNA Extraction from <em>Anopheles</em> spp.
Endemic countries are increasingly adopting molecular tools for efficient typing, identification and surveillance against malaria parasites and…
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
In mammalian cells, gene transcription is regulated in a cell type specific manner by the interactions of transcriptional factors with genomic DNA.…
Examination of the Telomere G-overhang Structure in <em>Trypanosoma brucei</em>
The telomere G-overhang structure has been identified in many eukaryotes including yeast, vertebrates, and Trypanosoma brucei. It serves as the…
Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein
Transient kinetic analysis is indispensable for understanding the workings of biological macromolecules, since this approach yields mechanistic…
Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
AFM imaging is a powerful technique for the study of protein-DNA interactions. This single molecule method allows the simultaneous resolution of…

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