DNA Microarray Technology and Applications

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Table of Contents

Abstract
Introduction
Methods
Results
Discussion
Conclusion
Works Cited

Abstract

DNA microarray technology is an influential, as well as a newly flagged device for studying genetic appearance in many life forms. The microarray technique authorizes quantitative scrutiny of RNAs copied out from known, as well as from unknown genes. DNA microarray technology is quickly tuning out to be a vital platform for useful genomics. This appraisal portrays the experimental plan, as well as array manufacturing and its use in gene invention, as well as its expression (Afshari et al.154). In this assessment, the latest progressions in DNA microarray technology, as well as their applications are scrutinized. The many assortments of DNA chips and also DNA microarray schemes, as well as strategies, are elaborated along with their methods of manufacture and their purpose. This embraces both the low-density microarrays for a range of analytical applications and the higher-density microarrays that are designed for high-throughput program appliances. Application analysis of hybridization in DNA microarray consists of vital vicinity of gene appearance sturdy, short tandem replicates, single nucleotide polymorphism and genotyping for point mutations. The review also entails the vast applications of microarray diplomacy, as well as schemes for drug interventions, tumor diagnosis, and hereditary diseases, and also for pharmacogenomic research.

Introduction

DNA microarray technology refers to additional skills applied by scientists in order to examine a lot of genes at once. DNA microarray is a set of minute DNA spots that are attached to a solid façade (Collins 684). These DNA microarrays are used by scientists in order to determine the appearance levels of a big number of genes, and also to the manifold region of a genome. They also use it to provide knowledge on which genes are active, as well as those which are inactive in diverse cell kinds. It is of great assistance to scientists as they are able to understand how these cells are impinged on why these genes do not function as they should. The human body cells have analogous genetic materials, but these genes are not active in each cell. A diverse number of genes, including their products that are the proteins and RNA, in a living being function in a complex and coordinated manner that generates the secrecy of life. With the interventions of DNA microarray technology, the researchers are in a position to scrutinize the entire genome on a solitary fragment, hence having an enhanced illustration of the relations among thousands of genes at the same time. Earlier techniques used in molecular biology could only examine one gene in an experiment making it hard for scientists to analyze different functions of these genes.

There have been technologies that have been used to illustrate the DNA microarray technology which comprises of:

Gene collection
Gene collection
DNA chip
Biochip
DNA microarray

An array is referred to as a systematic arrangement of illustration that offers a medium for corresponding known, as well as unknown DNA models based on base-pairing policy and also mechanizing the method of spotting the unknowns. The difference in sample spots size describes the two arrays that are macro and microarrays. The macro arrays sample size is about 300 microns in diameter or more, they can be imaged with no trouble by blot scanners, as well as existing gel. The microarrays are normally less than 200 microns in diameter with numerous spots. Each DNA spot contains picomoles of an exact DNA series referred to as a probe. The microarray entails specific imaging apparatus that is commercially obtainable as a whole system. The microarray techniques are also applicable in:

Phamacogenomic research
Communicable and hereditary diseases diagnostic
Forensic purposes
Hereditary detection
Tumor diagnostic

The microarray technology is of a great value to researchers, as it helps them in categorizing the various kinds of tumors based on the prototype of genetic material action in the cancerous cell. With this fundamental skill, the researchers will be in a position to devise treatment policies aimed directly at every kind of tumor. Moreover, the researches will be able to comprehend how dissimilar treatments have an effect on tumors and be in a position to develop more efficient treatments (Hacia 43-44). The microarray skill continues to perk up in performance facet concerning selectively, as well as sensitivity and also a more economical research device. In a characteristic microarray, the probes are produced and then affixed through surface engineering to solid facade by a covalent link to a chemical medium. The solid surface can either be a silicon fragment or a glass. Illumine is another microarray platform that uses minute blobs in place of large solid support. The DNA microarrays can be useful in assessing alterations in appearance levels, as well as in detection of either of these genotype, resecuence mutation genomes and single nucleotide polymorphisms. The microarrays vary in accurateness, manufacture, cost, effectiveness as well as in their mechanism.

The DNA microarrays are formed through arrangement of very small amounts of numerous genetic material series on a single microscope glide by an automatic apparatus. When a genetic material is triggered, the cellular apparatus starts to duplicate certain sections of that gene, ensuing to products referred to as messenger RNA. The messenger RNA is the stencil for producing proteins. The messenger RNA formed by the cell is paired and as a result it will bind to the original segment of the DNA filament from which it was copied.

Methods

In a microarray technology, there are various techniques, as well as procedures that are conducted and an example of it is a simple DNA microarray experiment.

Gene expression analysis is done to determine which genes in genome are up or down regulated between samples
An appropriate collection of genes is selected
RNA was extracted from different samples
Different fluorescent dyes were used to label samples
Samples were hybridised to microarrays
The collections were scanned for fluorescent signals.

From the experiment above the results were obtained which will be presented and elaborated below:

There were tiny spots with a diameter of approximately between a hundred to two hundred and fifty micrometers – the spots on the surface of the slide were arranged in a regular grids
A vast number of copies of specific DNA molecules that had been dried and also attached to surface were contained in each spot.
The formed spots were ready for hybridisation to sample

The product spots that came out of the experiment were found to be between one hundred to two hundred and fifty micrometers in diameter indicating that they are microarrays, adding weight to this these spots were found out to be numerous in number. In a distinctive test, a microarray is primed and mounted in a well compartment after which the DNA is hybridized. Silica atmosphere suspension that is negatively charged is scattered via gravitational sedimentation over the microarray façade. Due to the fact that the substrate façade of the microarray is positively charged the atmospheres of silica, it will stretch across the whole façade and attach to it. On surfaces with double-stranded DNA however, which is exceedingly negatively charged, as well as the region with single stranded DNA which is also negatively charged but with a slightly small degree as compared to DNA that is double-stranded.

Results

In the microarray surfaces, there are electrostatic connections that consequence into charge-density disparity that is readily experiential (Chen et al. 364). A snowy or semi-transparent appearance is observed on surfaces with DNA sections. These facade areas can be linked to definite hybridizations that divulge the existence of pathogens, genetic materials as well as alterations.

For a thriving execution of microarray technologies there is a necessity for advancement of many procedures, as well as techniques for making microarrays and also for marking the probes. These procedures are also required for carrying out and marking out hybridization reaction as well as informatics for evaluating the data. The microarrays in DNA hybridization analysis engrosses the identification of an indicator produced from attachment of reporter probe to the intended DNA series. The microarray is scrutinized or, otherwise, imaged with an aim of attaining the whole hybridization. The heart principle in microarrays is hybridization involving two DNA filaments and also the process of complementary nucleic acid chains to particularly pair to form hydrogen bonds between complementary nucleotide base pairs. Subsequent to washing off of non-precise bonding progression, it is only the steadily paired strands that will be left hybridized (Collins 686). Target series that are fluorescently marked attaches to a prod sequence to generate a signal that varies on the vigor of the hybridization established by:

The number of corresponding bases
Rinsing after hybridization
Hybridization setting like the temperatures

The indicators vigor from the feature depends on the quantity of the intended test binding to the prod on the spot. After the preparation of the cleansed replica, the models are independently spotted. A complementary DNA microarray practice is another technique based on the precise, as well as on the shared affinity of balancing strands of DNA. The technique is suitable in a laboratory setting, as it miniaturizes the measure of information enclosed within a genome. When the preferred genes have been selected, individual replica for every one of them must be attained. For the polymerase chain reaction, common primers are used in the amplification of each one of the genetic material. These primers could have originated form bacterial carrier or from plasmid preparation.

SAMPLE TYPE	GENE COMMON NAME	GENE SYMBOL
B	ACTSA	ACTA2
B	MYH 11	MYH11
B	AAT4	MYH11
B	ATCE	ACTG2
B	MRF4	MYF6
A	CAP 23	BASP1
A	SLC17A7	SLC17A7
A	BAI2	BAI2
A	FLJ41988	BAI1
A	BETA2	NEUROD1

From the above table, different tissues were obtained and tested in sample A and B for gene presence or absence. ACTSA, MYH11, AAT4, ATCE and MRF4 are some of the genes that were found present in sample B but absent in sample A whereas CAP23, SLC17A7, BAI2, FLI41988 and BATA2 were found to be present in sample A and absent in sample B. This is because some genes are only present in some body tissues and absent in others.

Discussion

The trickiest constituent of microarray test is possibly the assessment of the information. The examination of genome interactions may precisely be made probable by the assortment design, although the design does not make simpler the intricacy. The results have got to be authenticated via duplication, and this is one of the things that make the assessment of data to be more complex. Another factor that makes data assessment to be complex is the fact that the characteristic microarray experiment may possibly make use of twenty or even thirty slides and generate an enormous magnitude of data. The generated data ought to be scrutinized, as well as pieced collectively to make a logic picture of the scheme that is being studied (Lipshutz 20-21). Biotechnology industry can build up software packages that may be useful in contrasting experiments and also produce collective illustrations that may be based on statistical assessment. In spotting universal prototypes these kinds of statistics are helpful in the information that could be used to direct additional experiments.

The scrutiny of the raw arithmetical data is useful in the recognition of exact genes presentation and leads to an alteration in their appearance intensity. The limits of implication are resolute by a variety of arithmetical investigation carried out, as well as the denotation of the queries that are asked in the experiment. The scrutiny of functional data hinges upon appropriately appreciating the center of attention of the test. It is also crucial to take in hand the study to the precise objectives of the experiment for the sake of fruitfully employing the wonderful quantity of information made from a microarray glide. Microarray technology, at its most basic stage, illness, as well as growth crop up, due to alterations in the gene expression makes it appropriate in an extended range of experimental states (Brown 8). DNA microarray technology permits experimental contrast between abnormal and ordinary ones that is the normal tissues with the articulate reason of determining why certainly one is normal and the other one is not. This microarray technique can be used by biologist to supervise genetic material changes during progression. This is due to the fact that genetic material expression is adjusted throughout the process of embryonic growth. In the process of establishing the genetic material that has been turned on or off in a specified cell, the researcher ought to gather the messenger RNA bits present in that particular cell (Ermolaeva 19). This is followed by labeling of messenger RNA particles with the use or an enzyme called reverse transcriptase. The enzyme reverse transcriptase produces a complementary cDNA to the mRNA and it is at this time that fluorescent nucleotides get attached to cDNA. Varying fluorescent pigments are used to label the normal and the tumor samples.

Tumor cells occur in two different forms that is, those which are chemotherapy resistant and those which are not chemotherapy resistance. This is done on the base of their microarray expression profile. The process of profiling a tumor sample by use of DNA microarray assists the patient, as well as the clinician in making more conversant option in the design of the tumor treatment.

Conclusion

In conclusion, DNA microarray technique is an easy notion but in a practical situation the technology is an essential part of experimental examination. For the recent years, there have been supreme chances for innovations in the field of molecular biology, and this DNA microarray technology has taken part in a great position in making an image of scientists a realistic truth and technology will keep on being implicated in handing out, as well as applying the apparently continuous flow of information attainment that has consequence from those ideas (Debouck and Goodfellow 48).This is a clear indication that in some years to come the technology will have advanced even further and more discoveries will have emerged. This is encouraging, so in the field of medicine more innovations will have emerged leading to possibilities of coming up with more ways of treating, as well as diagnosing the diseases. Since microarray is a basic technique for classifying new areas for research wellbeing, it can therefore not be taken out of perspective and used to set up endings that are not propped up in other settings and therefore, extra means for gene analysis expression ought to be employed in to substantiate microarray conclusions. It is important to ensure that the cells and tissues studied are grown under specific conditions, and also with the aim to understand how genetic material expression changes when cells are exposed to toxic chemicals and also what happens when cells are shifted to varying temperatures (Khan et al. 5013).The biologist should also understand the genes that have amplified expression in tumor cells as compared to normal cells.

On the other hand, a complete amount of data articulated on a microarray chip opens the likelihood of inaccurate labeling. On the same, if an inaccuracy is made at PCR intensification phase in the procedure of printing, the mistake can be conveyed through the hybridisation step hence, this will lead to gene being wrongly identified. This is an indication that should be ensured in order to avoid errors that would eventually lead to incorrect identification of the genetic materials (Duggan 11).The principle aim of the experiment was to make the scholar to gasp that the supremacy of DNA microarray technology in medical appliance relies chiefly on monitoring a general modification in the gene expression prototype in patient with similar kind of illness. It is, therefore, crucial that emphasis is put on the study of this technology, as it is of a great value for the medical field.

Works Cited

Afshari, Cynthia, Emile Nuwaysir, Michael Bittner, Jeffrey Tent, and J. Carl Barrett. “Microarrays and Toxicology: The Advent of Toxicogenomics.” Molecular Carcinogenesis 24 (1999): 153-159.

Brown, Pat, and David Botstein. “Exploring the New World of the Genome with DNA Microarrays.” Nat Genet 21 (1999): 7-33.

Chen, Yidong, Edward R. Dougherty, and Michael L. Bittner. “Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images.” Journal of Biomedical Optics 2(4) (1997): 364-374.

Collins, Nick, Harry Patrinos, et al. “New Goals for the U.S. Human Genome.” Science 282(5389) (1998): 682-9.

Debouck, Christine, and Peter N. Goodfellow. “DNA Microarrays in Drug Discovery and Development.” Nature Genetics Supplement 21 (1999): 48-50.

Duggan, Jamie, Alexander Bittner, Yunmei Chen, Erica Meltzer, and Jeffrey Trent. “Expression Profiling Using cDNA Microarrays.” Nat Genet 21 (Jan. 1999): 4-10.

Ermolaeva Olga, Swati Rastodi, et. al. “Data Management and Analysis for Gene Expression Arrays.” Nat Genet 20 (1998): 19-23.

Hacia G. Joseph. “Resequencing and Mutational Analysis Using Oligonucleotide Microarrays.” Nature Genetics 21 (1999): 42-47.

J-Khan, Simon R. Green, Alexander Bittnet, et. al. “Gene Expression Profiling of Alveolar Rhabdomyosarcoma with cDNA Microarrays.” Cancer Res 58(22) (1998): 5009-13.

Lipshutz, Robert, Stephen Fodor, Thomas Gingeras, and David J. Lockhart. “High Density Synthetic Oligonucleotide Arrays.” Nature Genetics Supplement 21 (1999): 20-24.

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