Introduction

Abstract

DNA microarray technology has revolutionized biological research by enabling genome-scale explorations. This chapter provides an overview of DNA microarray technology and its application to characterizing the physical genome, with a focus on cancer genomes. Specific areas discussed include investigations of DNA copy number alteration (and loss of heterozygosity), DNA methylation, DNA-protein (i.e., chromatin and transcription factor) interactions, DNA replication, and the integration of diverse genome-scale data types. Also provided is a perspective on recent advances and future directions in characterizing the physical genome.

Oligonucleotide Tagging for Copper-Free Click Conjugation

“…The pure fractions were combined, concentrated, taken up in EtOAc, filtered and concentrated. Yield over two steps: 1 2 Cl 2 (35.5 mL) was added dropwise then the reaction was stirred at RT for 90 min. TLC (hexane-acetone, 80:20, PMA stain) shows the complete consumption of starting material (Rf 0.15) and the appearance of a single new product (Rf 0.50).…”

“…Synthetic DNA and RNA oligonucleotides (ONs) are key tools in a broad variety of diagnostic and therapeutic applications, including microarray technology [1], antisense and gene-silencing therapies [2], nanotechnology [3] and materials sciences [4,5]. Generally, such applications require the introduction of a suitable handle in an oligonucleotide to enable selective conjugation to a functionality of interest [6][7][8].…”

“…For example, attachment of a cell-penetrating ligand is the most commonly applied strategy to tackle the low internalization rate of ONs into target cells [2], currently the main bottleneck in oligonucleotide-based therapeutics (antisense, siRNA). Similarly, the preparation of oligonucleotide-based microarrays requires the selective immobilization of ONs on a suitable solid surface, e.g., glass [1]. Conventional post-synthetic labeling protocols, based on amide bond formation or sulfide-based chemistry [8][9][10] typically suffer from low yield and long reaction times and often require a high concentration of the biomolecule in combination with a large excess of coupling partner.…”

RNA-Sequencing Analysis of HepG2 Cells Treated with Atorvastatin

“…Microarrays have been used in gene expression studies for nearly two decades, whereas RNA sequencing (RNA-seq) is a relatively new approach for this purpose [14], [15]. Briefly, RNA is converted into cDNA, which is fragmented and PCR-amplified before being subjected to parallel sequencing to generate millions of reads.…”

Preparation and Analysis of Glycan Microarrays

“…1989) was successfully applied to detection of nucleic acids in the form of DNA chips or microarrays arrays in the late 1980’s (Kulesh, D.A., Clive, D.R., et al 1987), as a multiplexing technique to study gene expression in a high throughput fashion (Heller, M.J. 2002, Pollack, J.R. 2009, Ramsay, G. 1998). This technology was extended to proteomic analysis by immobilization of a variety of captured molecules as microspots for binding of proteins (Kramer, S., Joos, T.O., Templin, M.F.…”