DNA microarray

A DNA microarray (also commonly known as gene chip, DNA chip, or biochip) is a collection of microscopic DNA spots attached to a solid surface.Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome.
A DNA microarray is a multiplex technology used in molecular biology and in Medicine. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles (10⁻¹² moles) of a specific DNA sequence, known as probes (or reporters). This can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample (called target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic tests in parallel. Therefore arrays have dramatically accelerated many types of investigation.

In standard microarrays, the probes are attached via surface engineering to a solid surface by a covalent bond to a chemical matrix (via epoxy-silane, amino-silane, lysine, polyacrylamide or others). The solid surface can be glass or a silicon chip, in which case they are colloquially known as an Affy chip when an Affymetrix chip is used. Other microarray platforms, such as Illumina, use microscopic beads, instead of the large solid support. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system.

DNA microarrays can be used to measure changes in expression levels, to detect single nucleotide polymorphisms (SNPs) , to genotype or resequence mutant genomes.

Denaturation

Denaturation is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), or heat. If proteins in a living cell are denatured, this results in disruption of cell activity and possibly cell death. Denatured proteins can exhibit a wide range of characteristics, from loss of solubility to communal aggregation. Denaturization in this sense is not used in preparing the industrial chemical denatured alcohol.

Denaturation is the alteration of a protein shape through some form of external stress (for example, by applying heat, acid or alkali), in such a way that it will no longer be able to carry out its cellular function.

Denatured proteins can exhibit a wide range of characteristics, from loss of solubility to communal aggregation.

Proteins are very long strands of amino acids linked together in specific sequences.

A protein is created by ribosomes that "read" codons in the gene and assemble the requisite amino acid combination from the genetic instruction, in a process known as translation.

The newly created protein strand then undergoes post-translational modification in which additional atoms or molecules are added, for example copper, zinc, iron.

Once this post-translational modification process has been completed, the protein begins to fold (spontaneously, and sometimes with enzymatic assistance), curling up on itself so that hydrophobic elements of the protein are buried deep inside the structure and hydrophilic elements end up on the outside.

The final shape of a protein determines how it interacts with its environment.

Plasmid Isolation (Alkaline Lysis)

Bacterial plasmids, the non-genomic transferable DNA, can easily be purified from bacteria using numerous techniques. The purification of DNA is important for genetic research as it provides a source of transferable DNA and allows researchers to isolate large amounts of recombinant DNA. One common technique for plasmid purification is the alkaline lysis method, which breaks open bacteria with an alkaline solution, proteins are removed by precipitation and the plasmid DNA is recovered with alcohol precipitation.

Students purify bacterial plasmids from a liquid culture using this alkaline lysis method.