Buckingham - Chapter 3 - Nucleic Acid Extraction Methods

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1. Which whole-blood fraction is the most abundant source of genomic DNA?

A. Red blood cells

B. Buffy coat

C. Serum

D. Plasma

A. Red blood cells

2. Which of the following will yield the highest-quality DNA preparation?

A. Fixed tissue

B. Hemolyzed blood

C. Fresh blood

D. Stool

C. Fresh blood

3. Which of the following is the first step in DNA isolation from cells in a clinical sample?

A. DNA precipitation

B. Precipitation of proteins

C. Lysis of cells

D. Eluting DNA from a spin column

C. Lysis of cells

4. Phenol/chloroform and an aqueous solution will form what type of mixture?

A. Simple solution

B. Emulsion

C. Suspension

D. Supersaturated solution

B. Emulsion

5. In organic DNA extraction methods, the DNA is found in which fraction?

A. Upper aqueous

B. Lower aqueous

C. Upper hydrophobic

D. Lower hydrophobic

A. Upper aqueous

6. DNA in solution, after separation from other cellular constituents, is precipitated in which of the following?

A. Chloroform

B. Isopropanol

C. Ethylenediaminetetraacetic acid

D. Sodium dodecyl sulfate

B. Isopropanol

7. Which of the following is used to optimize the yield of nucleic acid by precipitation or column purification?

A. Carrier molecule

B. Detergent

C. TRIS buffer

D. Isotonic saline

A. Carrier molecule

8. In inorganic DNA isolation or "salting-out" procedures, in the presence of low pH and high salt concentrations, which intracellular component precipitates out of solution?

A. DNA

B. RNA

C. Carbohydrate

D. Protein

D. Protein

9. Which fixative is the least damaging to nucleic acids?

A. B5

B. Bouin's

C. Any mercury-based fixative

D. Buffered formalin

D. Buffered formalin

10. The most abundant form of RNA in all cells is

A. ribosomal.

B. transfer.

C. messenger.

D. small nuclear.

A. ribosomal.

11. Diethyl pyrocarbonate (DEPC) is a chemical that is used to

A. inactivate DNases.

B. measure DNA concentration.

C. isolate mitochondria.

D. inactivate RNases.

D. inactivate RNases.

12. Which of the following will not inhibit RNases?

A. Guanidine isothiocyanate (GITC)

B. Tris buffer

C. Strong reducing agents

D. High-salt buffers

B. Tris buffer

13. In procedures for the organic isolation of RNA, guanidinium isothiocyanate is added to

A. degrade DNA.

B. denature all proteins.

C. inhibit RNases.

D. separate RNA from DNA.

C. inhibit RNases.

14. PolyT oligomers bound to a matrix resin column will selectively isolate which of the following?

A. Ribosomal RNA

B. GC-rich DNA

C. Transfer RNA

D. Messenger RNA

D. Messenger RNA

15. Nucleic acid concentration can be assessed relatively simply and quickly by which of the following procedures?

A. Electrophoresis

B. Enzyme immunoassay

C. Sequencing

D. Spectrophotometry at 260 nm

A. Electrophoresis

16. What is the concentration of DNA whereby a 1:100 dilution has an absorbance reading of 0.015 at 260 nm?

A. 6.0 µg/mL

B. 60 µg/mL

C. 75 µg/mL

D. 750 µg/mL

C. 75 µg/mL

17. What is the yield of DNA from a sample with a concentration of 280 µg/mL and a volume of 0.5 mL?

A. 70 µg

B. 140 µg

C. 280 µg

D. 560 µg

B. 140 µg

18. What is the concentration of RNA whereby a 1:10 dilution has an absorbance reading of 0.675 at 260 nm?

A. 33.75 µg/mL

B. 337.5 µg/mL

C. 27 µg/mL

D. 270 µg/mL

D. 270 µg/mL

19. What is the yield of RNA from a sample with a concentration of 450 µg/mL and a volume of 0.3 mL?

A. 135 µg

B. 150 µg

C. 225 µg

D. 450 µg

A. 135 µg

20. DNA is isolated from a clinical sample. The absorbance at 260 nm is 0.489, and the absorbance at 280 nm is 0.257. Is this sample of sufficient quality for use in subsequent analyses?

A. Yes, this DNA is of acceptable quality.

B. No, there is unacceptable protein contamination.

C. No, there is unacceptable RNA contamination.

C. Quality cannot be determined with the data given.

A. Yes, this DNA is of acceptable quality.

21. Isolated DNA has an absorbance at 260 nm of 0.268 and an absorbance at 280 nm of 0.191. What is the 260 nm/280 nm ratio?

A. 1.2

B. 1.4

C. 1.6

D. 1.8

B. 1.4

22. When measuring the concentration of RNA by spectrophotometry at 260 nm, the absorbance reading is multiplied by the dilution and a conversion factor, which is

A. 20.

B. 30.

C. 40.

D. 50.

C. 40.

23. The 260 nm/280 nm ratio for isolated DNA was determined to be 1.2. What should be done next with this sample?

A. Proceed with DNA analysis as necessary.

B. Reprecipitate the DNA to remove excess protein.

C. Treat the sample with RNase to remove RNA.

D. Dilute the sample 1:10 and repeat spectrophotometry.

B. Reprecipitate the DNA to remove excess protein.

24. A DNA-specific dye that is used in fluorometry procedures to measure DNA concentration is

A. ethidium bromide.

B. diethyl pyrocarbonate.

C. SYBR green.

D. Hoechst 33258.

D. Hoechst 33258.

25. In what way is fluorometry more accurate than spectrophotometry?

A. Fluorescence is more specific for single nucleotides.

B. Spectrophotometry only measures absorbance from intact nucleic acid polymers.

C. Using specific stains, fluorometry only detects intact double-stranded DNA.

D. Absorbance may require dilution of the sample before reading.

C. Using specific stains, fluorometry only detects intact double-stranded DNA.

26. What is the purpose of microdissection of tissue sections in oncology?

A. Increased yield of nucleic acid

B. Enhanced detection of tumor-specific mutations

C. Identification of tumor-specific mutations

D. Protection of tumor-specific RNA

B. Enhanced detection of tumor-specific mutations

27. The quality of RNA isolated from fixed tissue will depend on which factors?

A. Presence of PCR inhibitors in the isolated sample

B. Random hexamer priming of cDNA

C. Type of tissue fixative and length of fixation

D. Paraffin embedding of the specimen

C. Type of tissue fixative and length of fixation

28. RNA collected in denaturant is stable at room temperature for how long?

A. 1 day

B. 3 days

C. 7 days

D. 14 days

C. 7 days

29. An NGS procedure calls for 5 µL DNA at 5 ng/µL. Your isolated preparation is at 30 ng/µL. How will you prepare the DNA for the procedure?

A. Precipitate with alcohol and resuspend in a larger volume.

B. Dilute the DNA 1/6 and use 5 µL of the diluted DNA.

C. Dilute the DNA 1/5 and use 5 µL of the diluted DNA.

D. Use 1 µL instead of 5 µL in the assay.

B. Dilute the DNA 1/6 and use 5 µL of the diluted DNA.

30. Which method is best for isolation of nucleic acid from plasma for a liquid biopsy?

A. Solid-phase isolation

B. Organic isolation

C. Elution from storage cards

D. Inorganic isolation

A. Solid-phase isolation