MLSCI360 > MOLECULAR TECHNIQUES > Flashcards

MOLECULAR TECHNIQUES Flashcards

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1
Q

Explain the principle of Qiagen Symphony

A
  • automated nucleic acid purification
  • lysis buffer containing chaotropic salt (Proteinase K) lyse cells and cellular components are released
  • magnetic silica beads are added; nucleic acids adsorb to silica
  • a magnetic rod transfers beads to a series of reaction vessels; DNA is washed to remove contaminants
  • DNA eluted in a low salt buffer
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2
Q

Concentration of dsDNA when A(260) = 1.000

A

50 µg/mL

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3
Q

Concentration of ssDNA when A(260) = 1.000

A

33 µg/mL

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4
Q

Concentration of ssRNA when A(260) = 1.000

A

40 µg/mL

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5
Q

If a solution of dsDNA has an A(260) of 0.81, what is the concentration of dsDNA ?

A

(50 µg/mL / 1.000) = ( x / 0.810), so x = 40.5 µg/mL

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6
Q

List the reagents used in endpoint PCR

A
  • DNA polymerase
  • dNTPs
  • PCR buffer
  • Primers
  • MgCl2
    NOTE: Master Mixes can include all reagents to reduce repetitive measurements
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7
Q

What is the function of Taq polymerase ?

A
  • used in endpoint PCR
  • replicates template DNA
  • recognizes 3’ end of primer
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8
Q

What can occur if [dNTPs] is not optimal ?

A

Taq polymerase can be inhibited

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9
Q

What is the function of PCR buffers ?

A
  • maintains optimal pH = 8.3 for Taq polymerase
  • provides cofactors (Mg2+) for enzymatic activity
  • provides salt for annealing/ hybridization
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10
Q

What can occur if [salt] is too high in endpoint PCR ?

A

Taq polymerase can be inhibited

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11
Q

Which formula is used to calculate the reagent amounts required for endpoint PCR ?

A

C1V1 = C2V2

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12
Q

What is endpoint PCR and identify the thermocyler program steps used

A
  • agarose gel electrophoresis used to PCR amplicons
  • denaturation, annealing/ hybridization, extension
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13
Q

Describe the unidirectional workflow requirements of a molecular lab

A

Amplicons produced in the post-room cannot re-enter the pre-room
- this also applies to PPE and equipment

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14
Q

How many primers are necessary for endpoint PCR ?

A
  • two primers that are complementary to opposite strands of DNA target sequence
  • must have similar melting temperature (Tm)
  • provides 3’ end for Taq polymerase
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15
Q

What is the function of Mg2+ in endpoint PCR ?

A

A required cofactor for Taq polymerase

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16
Q

What can occur if [Mg2+] is too high in endpoint PCR ?

A

DNA replication can be inhibited

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17
Q

Why is a master mix used in endpoint PCR ?

A

Reduces error introduced by repeated pipetting of small volumes

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18
Q

How is the master mix prepared in the “clean room” ? What is added outside of the clean room ?

A
  • all reagents EXCEPT the template is added into a single vessel in the clean room = master mix
  • no enzymes are added
  • DNA template is added outside the clean room
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19
Q

Describe the denaturation step in the PCR thermocyler program

A
  • At 92 - 95°C:
  • dsDNA breaks to form ssDNA
  • 10 to 30 sec, but GC-rich targets can take longer
  • hot start Taq DNA polymerase prevents non-specific DNA replication at lower temp. until desired denaturation temp. is reached
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20
Q

Describe the annealing step in PCR thermocyler program

A

At 50 to 60°C:
- specific temp is determined by melting point (Tm) of primer and ionic concentration of rxn = (Tm - 5°C)
Tm = 4(G+C) + 2(A+T)
- takes approx. 30 sec
- primers bind to complementary sequences on ssDNA template

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21
Q

How is Tm of PCR primers calculated ?

A

Tm = 4(G+C) + 2(A+T)

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22
Q

Describe the extension step in PCR thermocyler program

A

At 72°C (dependent on which polymerase used ie. Taq):
- DNA polymerase adds free deoxynucleotides to 3’-end of annealed primer = forms dsDNA

a). one min/ 1kb
b). 30 sec for targets < 1kb

  • template DNA is doubled
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23
Q

What is RT-PCR ?

A
  • reverse transcription PCR uses an RNA template instead of DNA
  • RNA is converted to cDNA (complementary DNA) via reverse transcriptase = first strand synthesis
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24
Q

What is first strand synthesis ?

A

When RNA is converted to complementary DNA (cDNA) via reverse transcriptase in RT-PCR

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25
Can mRNA be used as the template in RT-PCR ?
yes, RNA sub-fractions like mRNA can be used instead of total RNA
26
What is reverse transcriptase ?
It is a RNA-dependant DNA polymerase used in RT-PCR - normally isolated from Avian Myeloblastosis Virus (AMV) or Maloney Murine Leukemia Virus (MMLV)* *MMLV is better for RT-PCR bc it has lower endogenous RNAse activity
27
Is AMV or MMLV better suited for RT-PCR ? Why ?
Moloney Murine Leukemia Virus is better suited bc it has lower endogenous RNAse activity
28
What do RT buffers contain ?
Reverse transcription buffers contain: - cofactors for enzyme activity (Mg2+) - salts that aid in hybridization of primer to template cDNA - REDUCING AGENTS to inhibit RNA template from forming secondary structures
29
Differentiate one-step vs two-step RT-PCR
One-step: - cDNA and PCR are synthesized in the same reaction vessel - uses target (gene)-specific primers - faster bc less pipetting steps - lower possibility of contamination bc reaction vessel is never opened Two-step: - cDNA is synthesized in one tube and transferred to a second reaction vessel for PCR - advantageous when there are multiple (gene) targets - allows storage of cDNA for later use
30
The size of the pores in agarose __ as the concentration of agarose __
The size of the pores in agarose decreases as the concentration of agarose increases
31
If agarose = 0.5%, Range of separation of linear DNA = ?
1-30 kb
32
If agarose = 1.0%, Range of separation of linear DNA = ?
500 bp - 10 kb
33
If agarose = 1.5%, Range of separation of linear DNA = ?
200 bp - 3 kb
34
If agarose = 2.0%, Range of separation of linear DNA = ?
100 bp - 2.5 kb
35
Identify the 2 most common DNA electrophoresis buffers
1. Tris-acetate-EDTA (TAE) 2. Tris-borate-EDTA (TBE)
36
Which is more expensive: TAE or TBE ? Why ?
TBE is more expensive bc it has a higher buffer capacity
37
Why is loading dye added in DNA gel electrophoresis ?
- add color to DNA samples for loading process - dyes migrate towards anode at predictable rates = monitors sufficient migration - ficoll, glycerol, or sucrose component increases density of DNA sample and ensures sample sinks down/ is not lost in the buffer
38
Describe the dye used for visualization in DNA gel electrophoresis
- Ethidium bromide is an intercalating dye - It binds between complementary bp of dsDNA - fluorochrome is excited by UV light and observed as red light
39
Why are DNA ladders used ?
- used as a reference to calculate sample molecular weights - monitors progress of electrophoresis run - estimates concentration of sample
40
In DNA gel electrophoresis, DNA samples migrate from __ to __.
In DNA gel electrophoresis, DNA samples migrate from cathode (black) to anode (red).
41
Describe capillary gel electrophoresis
- used for DNA sequencing and fragment analysis - nucleic acid sample must be labelled with a fluorescent tag by PCR reaction - uses long silica tube reinforced with polyimide coating - thin walls efficiently dissipates heat = allows HIGH VOLTAGE = FASTER - small volumes of sample are introduced via electrokinetic injection - DNA migrates through flowable polymer based on mass to charge ratio TOWARDS ANODE - fluorescent label is excited by a laser = emitted light is detected
42
Describe Sanger Sequencing
- aka DNA termination sequencing due to random incorporation of fluorescently-labeled ddNTPs - ddNTPs lack 3’ hydroxyl (OH) group = DNA replication terminates - DNA strands of various lengths are formed, each with a terminal ddNTP - capillary electrophoresis will detect the emitted light from fluorophores attached to terminal ddNTPs - each signal is assigned a base code (GCAT) = visualized as an electropherogram
43
Describe quantitative PCR
- aka real-time PCR - does not require electrophoresis for detecting amplification products - qPCR products are fluorescently-labeled, allowing for “real-time” detection - intercalation of SYBR green dyes in dsDNA = signal intensity increases with accumulation of products
44
Pros and Cons of qPCR, target-specific probes vs SYBER green
Pros: - better sensitivity - faster testing - reduced risk of contamination - SYBER green is less expensive than target-specific probes Cons: - target-specific probes are more expensive - SYBER green lacks specificity; binds non-specifically to dsDNA = false positive signal
45
Identify 2 most common qPCR probe techniques
1. Hydrolysis probes (5’ nuclease) 2. Dual hybridization probes
46
Describe qPCR hydrolysis probes
- “Taqman”; 5’-nuclease - probe is an oligonucleotide sequence complimentary to target - modified with a 5’-fluorophore and 3’-quencher (complex does not fluoresce) - during EXTENSION phase of qPCR, Taq DNA polymerase 5’-3’ exonuclease activity cleaves the probe = FLUORESCENT SIGNAL - detectable fluorescent signal is proportional to amount of PCR product
47
Describe qPCR dual hybridization probes
- PCR with fluorescence resonance energy transfer (FRET) - uses 2 labeled oligonucleotide probes that bind PCR product in close proximity (5 nucleotides) = ENERGY TRANSFER from donor fluorophore to acceptor fluorophore - FLUORESCENCE IS DETECTED AT HYBRIDIZATION proportional to PCR product - FRET uses 2 primers and 2 probes
48
Analysis of qPCR requires plotting __ against __.
Analysis of qPCR requires plotting fluorescent signal intensity against cycle number.
49
T or F: the signal detected during the initial 3-15 cycles of PCR is background noise
TRUE; the signal detected during the initial 3-15 cycles of PCR is background noise
50
What is the threshold cycle/ crossing point ?
The cycle at which the amplification plot crosses the threshold
51
What do values above the threshold represent in a qPCR analysis plot ?
A true amplification product signal
52
The concentration of DNA in a patient sample can be determined by generating a __.
The concentration of DNA in a patient sample can be determined by generating a standard curve.
53
Identify the 4 controls required in a PCR run
1. Positive control = POSITIVE 2. Negative control = NEGATIVE 3. No-template control = NEGATIVE 4. Internal positive control = POSITIVE
54
What does a positive control do ?
Validates that PCR conditions were sufficient to amplify and detect the target = POSITIVE amplification of target
55
What does a negative control do ?
Nucleic acid sample does NOT contain target = NEGATIVE for target but amplification of DNA works
56
What does a no-template control do ?
The NTC contains all reagents EXCEPT for a DNA template = should be NEGATIVE; detection of PCR products indicates contamination
57
What does an internal positive control do ?
- tests presence of PCR inhibitors - is simultaneously extracted and amplified with DNA template = POSITIVE
58
Identify 2 types of positive internal controls
1. Endogenous; found in specimen ie. actin 2. Exogenous; added into samples during extraction or before PCR amplification ie. MS2
59
What additional control is required for reverse transcription PCR ?
- REVERSE TRANASCRIPTASE is NOT ADDED = NEGATIVE - RNA cannot be transcribed to cDNA - presence of PCR product indicates contamination
60
What is transcription mediated amplification used to detect ?
- Chlamydia trachomatis rRNA - Neisseria gonorrhoeae rRNA
61
How is the rRNA in transcription mediated amplification obtained ?
- buffer lyses C. trachomatis and N. gonorrhoeae and protects rRNA - capture oligo binds complementary rRNA - poly-adenosine sequence of capture oligo hybridizes to magnetic particle - magnetic field is applied and captured targets are washed
62
Describe the 3 functions of reverse transcriptase in transcription mediated amplification (TMA)
1. RNA-dependent DNA polymerase = converts RNA to cDNA 2. RNAse H activity = digests the RNA of RNA:cDNA hybrid 3. DNA dependent DNA polymerase = synthesizes second strand of DNA
63
When do capture oligo T7 and non T7 bind during transcription mediated amplification (TMA) ?
- T7 binds to target rRNA; provides 3’ for reverse transcriptase TO FORM cDNA - non T7 binds cDNA; provides 3’ for DNA dependent reverse transcriptase TO FORM dsDNA
64
How are RNA products in transcription mediated amplification (TMA) detected ? What is this called ?
- RNA products are detected by ssDNA probes labeled with acridinium esters = CHEMILUMINESCENCE
65
What A(260/280) is considered “pure” for DNA ?
~1.8
66
What A(260/280) ratio is considered “pure” for RNA ?
~2.0
67
What A(260/230) ratio is considered “pure” for both DNA and RNA ?
Approximately 2.0 - 2.2
68
Why may A(260/280) be low ?
- residual phenol or other reagents from extraction - protein contamination
69
T or F: High A(260/280) ratios are indicative of purity problem
FALSE; high A(260/280) ratios are NOT INDICATIVE OF PURITY PROBLEMS - can indicate issue with spectrophotometer
70
Why may A(260/230) be low ?
- carbohydrate carryover - residual phenol or guanidine HCl from extraction - glycogen was used in the precipitation
71
Why may A(260/280) be high ?
- not associated with contamination; MORESO PROCEDURAL ERRORS - using an inappropriate blanking solution ie. not similar ionic strength as sample solution
72
What is a chaotropic agent ? Give an example.
- molecules that distrupt intramolecular bonds that fold proteins together (hydrogen bonding between water molecules) = denaturant Eg. GUANIDINE
73
What substance is most commonly used in enzymatic digestion ?
Proteinase K; cleaves adjacent carboxylic groups
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