What advantage do oligonucleotide based microarrays have over cDNA based arrays?

What advantage do oligonucleotide based microarrays have over cDNA based arrays?

Oligonucleotide-based microarrays offer a number of advantages over cDNA microarrays, including (i) more controlled specificity of hybridization, which makes them particularly useful for the analysis of single nucleotide polymorphisms (17) or mutational analysis (18,19); (ii) versatility to address subtle questions …

What is cDNA based microarray?

cDNA microarray is an innovative technology that facilitates the analysis of the expression of thousands of genes simultaneously. The utilization of this methodology, which is rapidly evolving, requires a combination of expertise from the biological, mathematical and statistical sciences.

What is the difference between spotted and oligonucleotide arrays?

A major difference between the platforms is how the genes are probed. In the case of cDNA arrays, full length cDNA is spotted on the DNA array for each gene to be queried. Oligonucleotide arrays are comprised of k-mer nucleotide probes for each gene (k is typically 25-40).

What is oligonucleotide microarray?

Oligonucleotide microarray (DNA chip)-based hybridization analysis is a promising new technology which potentially allows rapid and cost-effective screens for all possible mutations and sequence variations in genomic DNA.

How does oligonucleotide microarray work?

Oligonucleotide microarrays is the name used to describe a specific way of manufacturing probes for an array by producing short oligonucleotide sequences which represent a gene. This sequence is synthesized directly onto the array.

What is Oligo microarray?

An oligo DNA microarray is a DNA microarray whose probe is the chemically synthesized oligo DNA after genes corresponding to exons in the region of 20-100 nts are selected. Since the probe is shorter than a cDNA microarray, its specificity is high and cross hybridization can be inhibited.

Why is cDNA used in microarray instead of mRNA?

cDNA is a more convenient way to work with the coding sequence than mRNA because RNA is very easily degraded by omnipresent RNases. This the main reason cDNA is sequenced rather than mRNA. Likewise, investigators conducting DNA microarrays often convert the mRNA into cDNA in order to produce their probes.

What is Oligo DNA microarray?

What are cDNA arrays?

The cDNA microarray is the most powerful tool for studying gene expression in many different organisms. It has been successfully applied to the simultaneous expression of many thousands of genes and to large-scale gene discovery, as well as polymorphism screening and mapping of genomic DNA clones.

What are oligo arrays?

An oligonucleotide array consists of a series of short (typically 20~30 bases) single-stranded DNA sequences (oligonucleotides, or “oligos”) attached to a glass chip about the size of a microscope cover slip. In the arrangement shown here, each adjacent oligo differs from its neighbor only at the last base.

What is oligo DNA microarray?

What is the difference between cDNA and mRNA?

cDNAs are synthesized in vitro. First, mRNAs are isolated from a population of tissue-specific cells. The isolated mRNAs represent only those genes that are being expressed in those particular cells. Each mRNA serves as a tem- plate in the synthesis of a complementary strand of DNA—the cDNA.

What is oligo microarray?

What are the steps involved in cDNA microarray?

Steps involved in cDNA based microarray:

  • Sample collection.
  • Isolation of mRNA.
  • Creation of labeled cDNA.
  • Hybridization.
  • Collection and analysis.

What is the purpose of cDNA?

cDNA is often used to clone eukaryotic genes in prokaryotes. When scientists want to express a specific protein in a cell that does not normally express that protein (i.e., heterologous expression), they will transfer the cDNA that codes for the protein to the recipient cell.

What is the main difference between DNA and cDNA?

The main difference between DNA and cDNA is that DNA is composed of both coding and non-coding sequences whereas cDNA only contains the coding sequences. The coding sequences are the exons of a gene, which codes for a functional protein. The non-coding sequences are the remaining DNA sequences of the genome.

What is the principle of cDNA microarray?

The principle of cDNA microarray is illustrated in Figure 34.1. In brief, cDNA clones, which generally range from several hundred base pairs to several kilobases, are printed on a glass surface, either by mechanical or inkjet microspotting.

How are oligonucleotide microarrays made?

Oligonucleotide microarrays may also be fabricated by using ink-jet printing technology. Nucleotide monomers are printed onto the chip and coupled using phosphoramidite chemistry (Hughes et al., 2001 ). Agilent has adopted this technology to create a 60-mer oligonucleotide array.

Why are oligo arrays typically used for chip-ChIP experiments?

For mammalian genomes, the intergenic regions are large and the TF often bind many kbp away from the gene of interest. Hence, for mammalian genomes, oligo arrays with oligo’s spaced evenly across the entire genome are typically used for ChIP-chip experiments.

What is the difference between spotted microarray and high-density oligonucleotide microarrays?

Typically, the high-density oligonucleotide microarrays contain many more elements as compared to the spotted microarray chips, that is Koligo >> Kspotted in the general case. Owing to fundamental production differences, the characteristics of the biases are quite different compared to spotted microarray data.