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Dna Microarray

DNA microarrays allow scientists to analyze the expression of thousands of genes simultaneously. Microarrays work by exploiting the principle of complementary base pairing - DNA or RNA from a sample will hybridize to complementary sequences attached to the array surface. This allows researchers to determine which genes are expressed under different conditions. Microarrays have many applications, including studying gene expression, detecting genetic variations, and identifying proteins and their interactions. They provide a high-throughput method for gathering large amounts of genomic and molecular information.

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0% found this document useful (0 votes)
65 views14 pages

Dna Microarray

DNA microarrays allow scientists to analyze the expression of thousands of genes simultaneously. Microarrays work by exploiting the principle of complementary base pairing - DNA or RNA from a sample will hybridize to complementary sequences attached to the array surface. This allows researchers to determine which genes are expressed under different conditions. Microarrays have many applications, including studying gene expression, detecting genetic variations, and identifying proteins and their interactions. They provide a high-throughput method for gathering large amounts of genomic and molecular information.

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The Basics of DNA Microarrays The Human Genome Project has created a massive amount of DNA sequence information.

To take full advantage of this latest information, scientists have developed ne techniques and tools for conducting research. DNA microarra!s, hich are also called DNA arra!s or gene chips, are an e"ample of a tool that uses genome sequence information to anal!#e the structure and function of tens of thousands of genes at a time. How Do Arrays Work? DNA arra!s come in man! varieties. $hether the! are created %! scientists or produced commerciall! %! one of several companies, arra!s depend on the same %asic principle& 'omplementar! sequences of nucleotides stick to, or (h!%ridi#e) to, one another. *or e"ample, a DNA molecule ith the sequence +A+T+T+G+'+ ill h!%ridi#e to another ith the sequence +T+ A+A+'+G+ to form dou%le+stranded DNA. *or the past ,- !ears, scientists have %een using h!%ridi#ation as a standard technique to detect specific DNA or .NA sequences. A single+stranded DNA molecule ith a kno n sequence is la%eled ith a radioactive isotope or fluorescent d!e and then used as a (pro%e) to detect a fragment of DNA or messenger .NA /m.NA, the molecule that is produced hen a gene is turned on or (e"pressed)0 ith the complementar! sequence. *or e"ample, if a researcher ants to kno hether gene A is e"pressed in a particular tissue, the researcher ould make a radio+la%eled DNA pro%e %! using a small piece of gene A, isolate m.NA from the tissue of interest, %ind the m.NA to a solid medium /such as a n!lon filter0, and then h!%ridi#e the pro%e to the filter. 1f gene A is e"pressed in the tissue, the researchers ill see a radioactive signal on the filter. This procedure is kno n as a Northern %lot. 1magine the po er of %eing a%le to do thousands of these e"periments at a time. DNA microarra!s use the same DNA pro%e detection method %ut on a much larger scale. 1nstead of detecting one gene or one m.NA at a time, microarra!s allo thousands of specific DNA or .NA sequences to %e detected simultaneousl! on a glass or plastic slide a%out 2.- centimeters square /a%out the si#e of !our thum%0. 3ach microarra! is made up of man! %its of single+ stranded DNA fragments arranged in a grid pattern on the glass or plastic surface. $hen sample DNA or .NA is applied to the arra!, an! sequences in the sample that find a match ill %ind to a specific spot on the arra!. A computer then determines the amount of sample %ound to each spot on the microarra!.

An Array of Applications Gene Expression Arrays DNA arra!s are commonl! used to stud! gene e"pression. 1n this t!pe of stud!, m.NA is e"tracted from a sample /for e"ample, %lood cells or tumor tissue0, converted to complementar! DNA /cDNA0, hich is easier to ork ith than .NA, and tagged ith a fluorescent la%el. 1n a t!pical microarra! e"periment, cDNA from one sample /sample A0 is la%eled ith red d!e and cDNA from another /sample 40 ith green d!e. The fluorescent red and green cDNA samples are then applied to a microarra! that contains DNA fragments corresponding to thousands of genes. /*or certain organisms hose genomes have %een sequenced, such as the round orm Caenorhabditis elegans, there are arra!s that represent all the genes in the genome.0 1f a DNA sequence is present %oth on the arra! and on one or %oth samples, the sequences %ind, and a fluorescent signal sticks to a specific spot on the arra!. The signals are picked up using a (reader) or (scanner) that consists of lasers, a special microscope, and a camera, hich ork together to create a digital image of the arra!. 5pecial computer programs then calculate the red to green fluorescence ratio in each spot. The calculated ratio for each spot on the arra! reflects the relative e"pression of a given gene in the t o samples. /*or e"ample, a red signal indicates that a particular gene is e"pressed in sample A %ut not sample 46 a green signal that the gene is e"pressed in sample 4 %ut not sample A6 and a !ello signal that the gene is e"pressed at roughl! equal levels in %oth samples. No signal means that the gene is not e"pressed in either sample.0 The result of a gene e"pression e"periment is referred to as a gene e"pression (profile) or (signature.) 3"pression arra!s can %e used to ans er %asic %iolog! pro%lems. *or e"ample, %! comparing the e"pression profile of a cell that is in a resting state to the profile of one that is dividing, scientists can determine hich genes are turned on during cell division. 7icroarra!s also have medical applications. *or e"ample, %! comparing the e"pression profile of a cancer cell ith that of a normal cell, scientists can use microarra!s to diagnose different cancers. 4etter diagnosis can lead to more+informed treatment choices.

3ric 8ander9s group as the first to sho that gene e"pression arra!s could %e used to distinguish %et een t o t!pes of leukemia, acute l!mpho%lastic leukemia /A880 and acute m!eloid leukemia /A780. 1n a paper pu%lished in 2::: in the journal Science, the scientists used e"pression results from ;,<== human genes measured on arra!s to accuratel! predict hether a patient had A78 or A88. >ntil then, doctors distinguished %et een the t o cancers %! using a %atter! of e"pensive tests that could cost critical time. 5ince that stud!, a num%er of studies have sho n similar results ith different t!pes of cancers. DNA Sequence Arrays ?ther t!pes of arra!s can %e used to measure genetic variations among individuals. *or e"ample, single nucleotide variations, or 5NPs /pronounced (snips)0, hich occur throughout the genome, can %e detected %! using genot!ping arra!s or 5NP chips. These t!pes of arra!s carr! all the possi%le variations of one gene or several genes in a grid pattern. A DNA sample is e"tracted, multiple copies of the gene or genes of interest are generated using pol!merase chain reaction /P'.0, and the sample is then applied to the chip. The spots that light up correspond to the particular gene variants the individual has. 8ike the e"pression arra!s, these t!pes of arra!s provide %asic information, such as the range of variation in human genomes. 4ut the! can also have clinical applications. 4! looking at several 5NPs at once, researchers can identif! (5NP signatures) associated ith a specific disease or a response to a drug. 1ndividuals at risk for a particular disease could then %e tested for the telltale signature. A ne er technique called microarra! comparative genomic h!%ridi#ation /microarra! 'GH0 has %een developed to identif! large regions of DNA that are either missing /deletions0 or present in more copies /amplifications0. .earrangements in the DNA, such as deletions and amplifications, are often involved in diseases such as cancer. ?ther t!pes of arra!s are a%le to detect DNA sequences that %ind to proteins or sequences that are chemicall! modified in the genome, such as %! meth!lation or acet!lation. Protein Arrays A different %ut conceptuall! similar approach is %eing applied directl! to proteins. 5cientists have developed microarra!s that can %e used either to identif! and quantif! thousands of different proteins at once or to find associations %et een different kinds of proteins and %et een proteins and other molecules. These t!pes of arra!s are collectivel! referred to as protein arra!s. Protein arra!s that are used to identif! proteins t!picall! consist of man! anti%odies arra!ed on a glass or plastic slide. 3ach anti%od! can %ind to a different target protein. $hen a mi"ture of proteins@for e"ample, in a %lood sample@is applied to the arra!, the proteins recogni#ed %! the different anti%odies ill %ind to the arra!. 4ound proteins can %e detected either %! adding a second anti%od! tagged ith a fluorescent molecule or %! chemicall! la%eling all the proteins in the %lood sample %efore adding the sample to the arra!. 3ach %ound protein can therefore %e detected as a signal on the arra!, and the intensit! of the signal roughl! represents the amount of protein in the %lood sample. This t!pe of arra!, like a gene e"pression arra!, can %e used to generate (signatures) for different cell t!pes and tissues. Another t!pe of protein microarra! is used to glean insights into the function of different proteins %! looking at the molecules the! %ind to. *or this application, the proteins themselves, rather than their anti%odies, are arra!ed on a slide. 5tuart 5chrei%er9s group as one of the first to sho that more than 2=,=== different proteins could %e (stuck) to a single glass microscope slide and still retain their %iological activit!. 1n a t!pical e"periment,

thousands of proteins that are found in a cell are %ound to an arra!. Then a particular t!pe of molecule@for e"ample, a fat molecule /or lipid0@is fluorescentl! la%eled and applied to the protein arra!. The spots on the arra! that light up ith a fluorescent signal correspond to proteins that associate ith lipids. This kno ledge provides important insights into the function of man! proteins at once. Protein %inding information can also %e o%tained %! using a small molecule microarra!, in hich thousands of different small s!nthetic molecules are arra!ed on a slide. An advantage of this t!pe of arra! is that small molecules tend to %e more sta%le and rugged, hich simplifies storage and handling requirements and makes the process suita%le for mass production. 4! letting a single protein species react to this t!pe of arra!, one can identif! different small molecules that %ind to proteins. 5ome of these small molecules ma! %e candidates for a reagent that interferes ith the functions of a protein, or the! ma! even lead to ne drug discover!.

An! chromosome other than a se" chromosome. Humans have ,, pairs of autosomes.

Cytogenic Map The visual appearance of a chromosome hen stained and e"amined under a microscope. Particularl! important are visuall! distinct regions, called light and dark %ands, hich give each of the chromosomes a unique appearance. This feature allo s a personAs chromosomes to %e studied in a clinical test kno n as a kar!ot!pe, hich allo s scientists to look for chromosomal alterations.

DNA .eplication The process %! hich the DNA dou%le heli" un inds and makes an e"act cop! of itself.

EXON The region of a gene that contains the code for producing the geneAs protein. 3ach e"on codes for a specific portion of the complete protein. 1n some species /including humans0, a geneAs e"ons are separated %! long regions of DNA /called introns or sometimes Bjunk DNAB0 that have no apparent function.

fl orescence in sit hy!ri"i#ation $%&'H( A process hich vividl! paints chromosomes or portions of chromosomes ith fluorescent molecules. This technique is useful for identif!ing chromosomal a%normalities and gene mapping.

Gene 3"pression Proteins are made from instructions encoded DNA

Marker Also kno n as a genetic marker, a segment of DNA ith an identifia%le ph!sical location on a chromosome hose inheritance can %e follo ed. A marker can %e a gene, or it can %e some section of DNA ith no kno n function. 4ecause DNA segments that lie near each other on a chromosome tend to %e inherited together, markers are often used as indirect a!s of tracking the inheritance pattern of genes that have not !et %een identified, %ut hose appro"imate locations are kno n.

Nonco"ing DNA The strand of DNA that does not carr! the information necessar! to make a protein. The non+ coding strand is the mirror image of the coding strand and is also kno n as the antisense strand.

)oly*erase Chain +eaction , )C+ A fast, ine"pensive technique for making an unlimited num%er of copies of an! piece of DNA. 5ometimes called Bmolecular photocop!ing,B P'. has had an immense impact on %iolog! and medicine, especiall! genetic research.

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