What Is a Genome Microarray?

DNA microarray is also called DNA array or DNA chip. The more popular name is gene chip. It is a special glass sheet with a DNA microarray (micorarray) coating. Thousands or tens of thousands of nucleic acid probes can be installed on an area of several square centimeters. With one test, it can provide a lot of information about gene sequences. It is a tool for genomics and genetics research. Using the gene chip, researchers can quantitatively analyze the expression level of a large number (thousands of thousands) of genes at the same time, which has fast, accurate and low-cost biological analysis and inspection capabilities.

Chinese name: DNA microarray
Foreign name: DNA microarray

Special color: DNA array or DNA chip
Types of: Clinical diagnostic chip

Introduction

Among them, cDNA-microarray, which can be used to detect the degree of gene expression, has been commercialized, and the market is mainly based on R & D laboratories. In addition, biolithography (photolithography) -based biochips that can detect polymorphisms are still in the experimental stage and microfluidics-based clinical diagnostic chips are still in the research and development stage.

DNA DNA microarray type

Gene chip manufacturing methods can be basically divided into the following types:

Stanford DNA microarray Stanford type

A method for preparing a cDNA array developed by Stanford University in the United States places a previously synthesized nucleic acid probe on a glass slide carrier. Advantages: Designing longer probe lengths increases specificity. Disadvantages: The chip density is lower than that of the photomask method, and it must have a good storage design.

This method can be divided into dot method and printing method.

The spot method is a small-scale production or laboratory-made low-density chip. The nucleic acid probe solution is spotted on a glass slide or a polyester fiber membrane with a micro-scored steel needle with a capillary action on a mechanical arm. Low cost, suitable for the situation with few probes or small manufacturing requirements.

The printing method is changed from the inkjet printer method, and the nucleic acid probe is printed on a glass slide by heating the bubble. High-density, long-probe gene chips can be achieved using well-produced showerheads; for example, PhalanxJet.

DNA microarray in situ synthesis

In situ synthesis (in situ synthesised) is a synthesis technique that was originally used for photolithography of electronic chips to convert nucleic acid sequences. The photomask is used to control the reaction position, and the nucleotide molecules are connected one by one according to the sequence; it can mass produce ultra-high density chips. Due to factors such as manufacturing process and mask cost, the probe length made by this method is less than 25-mer; therefore, multiple probes of the same gene are needed to avoid misjudgment. The main production plants are Affymetrix, Roche NimbleGen and so on.

DNA microarray microbead deployment method

Illumina has its unique microbead array, which makes nucleic acid probes on tiny particles and then arranges them on special slides.

qPCR array DNA microarray qPCR array

In 96-well or 384-well standard PCR disks or 384-well microfluidic disks, real-time PCR primers and probes are pre-synthesized, and the samples are injected for reaction and detection analysis by quantitative PCR. The amount of analysis is less than that of traditional chips, and it is a low-density array, but it has both accurate quantification and qualitative; and the threshold of equipment and technology is low, and general molecular biology laboratories can operate by themselves. New medium-density qPCr array: OpenArray is a product of Applied Biosystems (affiliated with Life Technologies Group), which is divided into dozens of matrix regions in a glass-sized hydrophobic substrate; the matrix is a hydrophilic surface The microwell has a set of pre-synthesized primers and probes. The current specification is that each slide has 12 * 4 (48) matrix areas, and each area has 8 * 8 (64) holes. It is expected that new 12K chips and special machines will be available in 2012.

DNA microarray types have commercialized chips

DNA microarray: detects the genomic DNA of a sample for genotyping.

cDNA-microarray: also known as expression array. The mRNA in a sample is converted to cDNA and then tested for detection and comparison of the degree of gene expression.

miRNA-microarray: Detects miRNA-related gene regulation mechanisms.

ChIP-chip: chromatin immunoprecipitation on chip

High-throughput nucleic acid sequencing chip: combining special PCR reactions and microarray detection technology for gene sequencing.

Microtube chip for clinical detection: A reagent set that attaches a low-density microarray to the bottom of a special test tube to detect specific pathogens or cancer indicators.

CGH chip: Chromosome chip (array Comparative Genomic Hybridization, aCGH or Chromosomal Microarray Analysis, CMA)

SNP chip: can detect polymorphisms (Polymorphisms).

Gene methylation chip: detects the degree of DNA modification by methylation.

DNA microarrays near commercialization or development

Electronic sequencing chip: A chip that combines nano-motors and electronics as a fast and high-throughput nucleic acid sequencing chip.

Microfluidics clinical diagnostic chip.

DNA Application of DNA microarray technology

-Detecting gene expression levels and identifying gene sequences.

In 1996, Schena et al. Used Arabidopsis light-modulated gene microarrays to detect mRNA expression levels in different organs using mRNA as probes. The results showed that leaf mRNA expression levels were 500 times that of roots. In 1996, Shelon et al. Cloned Saccharomyces cerevisiae genomic DNA into a microarray, and used 6 largest chromosomes and 10 smallest chromosomal DNA probes to mark the red and green fluorescent markers for hybridization detection. The results showed that 95% of the clones were on the chromosomes. Positioning is consistent with literature reports. Milosaljevic et al., In 1996, made 15328 clones of E. coli genomic DNA into microarrays and used 997 oligonucleotide probes for hybridization detection. The results were compared with the E.coli sequence database using a computer. Recognize the 4.6MbDNA sequence structure.

Second, check the expression and discover new genes.

Wodicka 1997 will cover 260,000 25mer probes covering the entire ORF of the yeast genome, arrayed on 4 slides, each 65,000 probes, will be divided into rich and low-end cultures to study gene expression under different growth conditions The results showed that 90% of genes were expressed under both conditions, 36 mRNAs were more expressed in enriched culture, and 140 mRNAs were expressed in low-limit culture. In addition, a number of new genes have not been reported.

Three detection mutations and polymorphisms were performed for genetic mapping.

Hacia et al. Used a 96600 oligonucleotide array in 1996 to detect mutations in the human oncogene BRCA1. 15 patient samples and control samples were labeled with two types of fluorescence. It was found that 14 people had a clip mutation in this gene, a total of 8 This polymorphism is mutated in codon 22 of exon 2 of the gene. The use of SNPs to make human genetic maps will be the third generation of genetic maps. This technology is based entirely on DNA microarrays. Fourth, DNA sequence analysis. Donnel et al. 1992, Pease et al. 1994, Yershow et al. 1996, and Wallraff et al. 1997 all reported DNA sequence analysis using DNA microarray technology. Most researchers make microarrays by first synthesizing oligonucleotide sequences, then hybridize with labeled unknown DNA sequences, scan them with a fluorescence confocal microscope, and analyze the data with computer software. Some researchers also array the tested DNA fragments to label them. The oligonucleotides were sequenced for probe hybridization.