4.5 ARRAY-BASED HYBRIDIZATION

Question 1

Which hybridization method is used when determining target size is not required?

Answer 1

Dot/Slot blots

Question 2

What types of samples are most efficiently analyzed using dot or slot blots?

Answer 2

Less complex samples (cloned plasmids, PCR products, selected mRNA)

Question 3

What control is necessary to ensure proper interpretation in dot or slot blot expression analysis?

Answer 3

Amplification or normalization control

Question 4

What serves as the baseline for interpretation in dot or slot blot hybridization assays?

Answer 4

Negative control (DNA without the targeted sequence)

Question 5

What is a key advantage of slot blots over dot blots for quantification?

Answer 5

More accurate quantification by densitometry scanning

Question 6

What can be used for depositing the target DNA or RNA onto the membrane in dot/slot blots?

Answer 6

Various devices, including vacuum systems or a pipet

Question 7

Why are dot blots especially useful for mutational screening?

Answer 7

Useful for multiple qualitative analyses where many targets are compared

Question 8

What type of technology allows for the simultaneous study of large numbers of targets or samples?

Answer 8

Array technology

Question 9

What type of arrays are used to study gene amplification or deletion?

Answer 9

Comparative genome hybridization arrays

Question 10

Which arrays are applied to the analysis of gene expression, such as RNA or protein?

Answer 10

Expression arrays

Question 11

Name four approaches to array technology

Answer 11

Macroarrays, microarrays, high-density oligonucleotide arrays, microelectronic arrays

Question 12

What is the primary advantage of macroarrays over Northern and Southern blots?

Answer 12

Larger sample capacity.

Question 13

What is a limitation of dot and slot blots regarding the number of genes?

Answer 13

Single gene testing.

Question 14

Array technique where unlabeled probes are immobilized on the membrane, and the test sample is labeled for hybridization.

Answer 14

Reverse dot blot technique.

Question 15

Type of blot that allows testing and analyzing larger numbers of samples simultaneously.

Answer 15

Macroarrays

Question 16

Type of signal typically used to detect hybridization in macroarrays.

Answer 16

Radioactive or chemiluminescent signals.

Question 17

Device used to read the hybridization of labeled sample material in macroarrays.

Answer 17

Phosphorimager

Question 18

Material that replaced nitrocellulose or nylon membranes for producing arrays in 1987.

Answer 18

Treated glass.

Question 19

Technology that allowed the evolution of macroarrays into microarrays by depositing very small target spots.

Answer 19

Improved spotting technology.

Question 20

Maximum number of targets that can be screened simultaneously on a microarray.

Answer 20

Tens of thousands.

Question 21

Size of the glass substrate used for microarrays compared to a common laboratory item.

Answer 21

Microscope slide.

Question 22

System used to automate the deposition of spots on microarrays.

Answer 22

Arrayers

Question 23

Number of spots that automated systems can place on a glass substrate.

Answer 23

More than 80,000 spots.

Question 24

Year the first automated arrayer was described by Patrick Brown.

Answer 24

1995

Question 25

Institution where the first automated arrayer was developed.

Answer 25

Stanford University

Question 26

Technology used by the first automated arrayers to place probe material.

Answer 26

Pen-type contact

Question 27

Type of printing systems incorporated into modified arrayers for target deposition.

Answer 27

Ink-jet printing systems

Question 28

Methods of expulsion used in ink-jet printing systems for target material.

Answer 28

Thermal, solenoid, or piezoelectric

Question 29

What replaces the larger nitrocellulose membrane in microarrays?

Answer 29

Glass microscope slide.

Question 30

What is the common term used for the glass slide carrying the array of targets?

Answer 30

Chip

Question 31

What types of targets are usually immobilized on the glass slide of a microarray?

Answer 31

DNA (cDNAs, PCR products, or oligomers).

Question 32

How are targets typically arranged on a microarray chip?

Answer 32

In triplicate and spaced across the chip.

Question 33

What are test samples usually generated from in microarray experiments?

Answer 33

cDNA generated from sample RNA

Question 34

Besides cDNA, what other types of test samples can be used in microarrays?

Answer 34

Genomic DNA, RNA, or protein.

Question 35

What is the field that studies the entire genome or sets of related genes?

Answer 35

Genomics

Question 36

What term describes the complete set of transcripts encoded by a genome?

Answer 36

Transcriptome

Question 37

What term refers to the set of encoded proteins in an organism?

Answer 37

Proteome

Question 38

Who predicted that the proteome is likely to be 10 times more complex than the genome?

Answer 38

Stanley Fields

Question 39

What is the study of entire sets of proteins called?

Answer 39

Proteomics

Question 40

What technologies facilitate the study of proteomics?

Answer 40

Array technology and mass spectrometry

Question 41

What method is used to deposit targets for array analysis directly on glass or silicon support?

Answer 41

DNA synthesis

Question 42

What technology allows for the synthesis of short oligomers (10 to 25 bases long) on high-density arrays?

Answer 42

Proprietary photolithography techniques.

Question 43

What type of arrays are used for mutation and polymorphism analysis, DNA methylation analysis, and sequencing?

Answer 43

High-density oligonucleotide arrays.

Question 44

What is required for sample preparation in array analysis for reading microarrays?

Answer 44

Fluorescent labeling of the test sample.

Question 45

What method is frequently used for labeling RNA in array analysis?

Answer 45

Synthesis of cDNA or RNA copies with labeled nucleotides

Question 46

What are arrays used to assess gene expression classified as?

Answer 46

Expression arrays

Question 47

What technique is designed to test DNA for deletions and amplifications in comparative genome hybridization?

Answer 47

Array CGH (comparative genome hybridization).

Question 48

What advantage does array CGH provide over traditional cytogenetic analysis?

Answer 48

Higher resolution and more defined genetic information.

Question 49

What is necessary for reading microarrays?

Answer 49

A fluorescent reader and analysis software.

Question 50

In bead array technology, where are the probes immobilized?

Answer 50

beads

Question 51

What allows hybridization of targets in bead array technology?

Answer 51

complementary base pairing

Question 52

How can multiple suspensions be tested simultaneously in bead array technology?

Answer 52

Using a 96-well plate.

Question 53

How are different probes on beads distinguished in bead array technology?

Answer 53

color-coding the beads with a particular shade of red fluorescent dye.

Question 54

What color dye is used to label the sample in bead array technology?

Answer 54

Green dye

Question 55

For what types of targets is bead array technology used?

Answer 55

Protein and nucleic acid targets

Question 56

What clinical applications are available for bead array systems?

Answer 56

Tests for infectious diseases and tissue typing.