NUCLEIC ACID AMPLIFICATION PART 2

Question 1

difference of probe amplification to target amplification

Answer 1

number of targets nucleic acid sequences in the sample is not changed

Question 2

purpose ofoligonucleotide

Answer 2

prime the dna polymerase

Question 3

3 types of nucleic acid amplification technique

Answer 3

target, signal, probe

Question 4

the amplified targets in dna sequence is called as

Answer 4

amplicons

Question 5

short stretches of nucleic acids

Answer 5

probes

Question 6

are synonymous to primer

Answer 6

probes

Question 7

in probe amplification, what we are amplifiying is

Answer 7

probe itself

Question 8

probes are attached to a fluorogenic dye such as

Answer 8

reported dye or guencher dye

Question 9

__ detects particular infectious
organisms as well as gene rearrangements (ex. sickle
cell anemia)

Answer 9

Probe amplification

Question 10

PROBE AMPLIFICATION

Can also detect chromosomal translocations (ex._____ ), and chromosomal breakages

Answer 10

down syndrome

Question 11

Also used to detect changes in oncogenes (promotes
cancer development), and tumor suppressor genes

Answer 11

PROBE AMPLIFICATION

Question 12

probe amplification is Also used to detect diagnosis of inherited disorders (ex.
_______

Answer 12

cystic fibrosis

Question 13

Also used to detect carrier status, polymorphic markers,
and establish identity or non-identity

Answer 13

probe amplification

Question 14

Also used to aid in donor selections and confirming an
organism isolated in the culture

Answer 14

probe amplification

Question 15

probe amplification is used to confirm what organism

Answer 15

mycobacterium legionella
salmonella
E coli (diarrheagenic e.coli)
campylobacter

fungi
blastomyces dermatitidis
coccidiodes imitis
cryptococcus neoformans
histoplasma capsulatum

Question 16

probe amplification

Can also detect agents of sexually transmitted disorder
such a

Answer 16

Chlamydia trachomatis,
Neisseria gonorrhoeae, cytomegalovirus, Epstein Barr Virus,
herpes simplex virus,
and detection of viral loads of HIV and HCV

Question 17

3 major procedures of probe amplification

Answer 17

ligase chain reaction
strand displacement amplification
qb replicase

Question 18

ligase chain reaction is manufactured and marketed by

Answer 18

abbott

Question 19

strand displacement amplification is manufactured and marketed by

Answer 19

beckton dickinson

Question 20

qb replicase is manufactured and marketed by

Answer 20

vysis

Question 21

PCR and probe amplification is similar, however, there’s one step that is added in probe amplification.

Answer 21

ligation - connecting probe together using ligase enzymes and that probe will automatically analyzed and amplified

Question 22

In LCR, __ is used to
ligate the adjacent primers
together

Answer 22

DNA ligase

Question 23

a method for amplifying synthethic primers/probes complementary to target nucleic acid

Answer 23

ligase chain reaction

Question 24

in LCR, the ligated primers can serve as ___ for annealing and ligation of additional primers

Answer 24

template

Question 25

product of LCR is

Answer 25

ligated primer thus classifying it as a probe amplification

Question 26

Lcr can be used to detect point-mutation in a target sequence

Answer 26

the point mutation that occurs in B globulin of patients with SICKLE CELL DISEASE is one of the first applications for LCR

Question 27

SDA or strand displacement amplification is an example of what process

Answer 27

isothermal amplification process

Question 28

isothermal amplification process means there will no changed in what parameter

Answer 28

no changes on temperature

Question 29

STRAND DISPLACEMENT AMPLIFICATION is Originally developed and patented by

Answer 29

Beckton dickinson in new jersey year 1991

Question 30

primers of strand displacement amplification is incorporated to a specific __

Answer 30

restriction enzyme

Question 31

strand displacement amplification creates a __ using restriction endonuclease enzyme

Answer 31

nick

Question 32

target in strand displacement amplification si

Answer 32

double stranded dna

Question 33

DNApolymerase will elongate the

Answer 33

dATPase

Question 34

two stages to SDA process

Answer 34

◆ Target Generation Phase ◆ Exponential Probe or Target Amplification Phase

Question 35

Target DNA is denatured by heating to ______°C

Answer 35

95

Question 36

which stage of SDA is this

Answer 36

at each stage end of the target sequence, a primer and a probe bind close to each other

Question 37

the probe will have a site or a recognition sequence specific for ___

Answer 37

restriction enzyme

Question 38

the modified nucleotide (dATPas) will be elongated and the ____ will extend the primers incorporating to a modified nucleotide

Answer 38

Exonuclease-deficient DNA polymerase derived from E. coli

Question 39

a stage of SDA in which the product of this amplification is millions of copies of the initial probe

Answer 39

exponential probe/target amplification phase

Question 40

application of SDA

Answer 40

detection of M. Tuberculosis C. trachomatis N. gonorrhea

Question 41

In SDA, addition of a ___ to the reaction produces a fluorescent signal that corresponds to the amount of amplified target

Answer 41

fluorogenic probe

Question 42

method for amplifying probes that have specificity for a target sequence

Answer 42

QB replicase

Question 43

QB replicase is named for the major enzyme that is used to amplify probe sequences true or false

Answer 43

true

Question 44

the RNA dependent RNA polymerase/ QB replicase came from

Answer 44

bacteriophage QB

Question 45

2 types of probes that is used by QB replicase

Answer 45

reporter probe capture probes

Question 46

4 steps of QB replicase methodology

Answer 46

hybridization, capture, wash, and release

Question 47

how many hybridization procedure are done in QB replicase

Answer 47

2 hybridization

Question 48

steps in QB REPLICASE

Answer 48

capture probe A - will capture target RNA in hybridization connected to magnetic bead. Upon connecting to magnetic bead, it will under go capture, washing, and release. Once release, it will go under hybridization again using capture B. Will under go capture, washing, and release again. It will become purified reported probe, this reporter probe will be act upon by the QB replicase enzyme in order to amplify or target this reporter probe. These reporter probe will have the specificity for the target sequence because of the so called MIDVARIANT 1

Question 49

Reporter probes–RNA molecules that have specificity for the target sequence and also contain a promoter sequence that is recognized by the QB replicase

Answer 49

midivariant-1

Question 50

the qb replication is very efficient with the generation of _____ RNA molecules/probes in less than 15 mns

Answer 50

10^6-10^9 RNA

Question 51

application of QWB replicase

Answer 51

detection of infection organisms such as mycobacteria chlamydia HIV CMV and genetic disorders such as sickle cell anemia, cystic fibrosis, huntington's disease duchenne muscular dystrophy vwillebrand diseases

Question 52

signal amplification will amplify

Answer 52

signals that are attached to targets

Question 53

signal are attached to labeled enzymes, and used upon by the technique called

Answer 53

chemilluminescence

Question 54

chemilluminescence is measured using

Answer 54

luminometer

Question 55

applications of signal amplification

Answer 55

designed to increase signal strength by increasing concentrations of the label

Question 56

labels example in signal amplification

Answer 56

enzyme label or antibody labels

Question 57

signal amplification is used in detection of what organisms

Answer 57

HCV, HIV, Legionella

Question 58

4 methods of signal amplification

Answer 58

branched DNA amplification hydrid capture assay cleavage-based amplification cycling probe

Question 59

branched DNA amplification is developed by

Answer 59

chiron corp

Question 60

target nucleic acid of branched dna amplification is can be

Answer 60

DNA or RNA

Question 61

series of ____ are used to capture to target nucleic acid and then additional extended probes bind to target nucleic acid, and then to multiple reporter molecule, loading the tarhet nucleic acid with isgnal

Answer 61

short oligomer probes

Question 62

enzyme used in branched DNA amplification is

Answer 62

alkaline phosphatase

Question 63

the target nucleic acid is released from the cells, the DNA is denatured if DNA is the target, and the target nucleic acid binds to capture probes that are fixed to a solid support

Answer 63

branched dna amplification

Question 64

generations of branched DNA amplification

Answer 64

first, second, and third

Question 65

substrate used for the alkaline phosphatase

Answer 65

dioxetane