NUCLEIC ACIDS

Bial’s Orcinol Test (Test for Ribose)

Test that gives a positive result of blue-green coloration.

Orcinol in HCl (yellow solution)

Reagent gives a positive result of blue-green coloration.

Diphenylamine Test (Test for Deoxyribose)

Test that gives a positive result of blue complex/compound (λmax = 595 nm) coloration.

Diphenylamine in conc. sulfuric acid

Reagent that gives a positive result of blue complex/compound (λmax = 595 nm) coloration.

Test for Phosphates

Test that gives a positive result of yellow crystalline precipitate.

10% ammonium orthomolybdate ((NH₄)MoO₄) Solution

Reagent that gives a positive result of yellow crystalline precipitate.

Murexide Test (Test for Purines)

Test that gives a positive result of red residue.

10%KOH, Conc. HNO₃

Reagent that gives a positive result of red residue.

Wheeler-Johnson Test (Test for Pyrimidines; cytosine and uracil)

Test that gives a positive result of purple solution due to the interaction of barium ions (Ba2+) with dialuric acid.

Bromine water, barium hydroxide (Ba(OH)₂) solution

Reagent that gives a positive result of purple solution due to the interaction of barium ions (Ba2+) with dialuric acid.

Heating with dilute NaOH

RNA isolation: What separates, extracts, and inactivates the nucleases of RNA?

Glacial acetic acid (pH 4-5)

RNA isolation: What separates nucleic acids associated with proteins and other substance?

Ethanol w/ concentrated HCl

RNA isolation: What precipitates RNA?

Alcohol (EtOH) and ether (organic solvents)

RNA isolation: What removes lipids?

SSC (Standard Saline Citrate) Solution

RNA isolation: What preserves the integrity of DNA by maintaining the pH of the solution?

1% NaOH

RNA isolation: What is used to recrystallize RNA?

0.15 M NaCl

DNA isolation (onions): What causes the precipitating of nucleoproteins (salting-out of DNA bound in proteins like histones)?

5% SDS (sodium dodecyl sulfate)

DNA isolation (onions): What breaks the ionic interaction between protein and nucleic acid?

0.15 M sodium citrate and 1 M EDTA

DNA isolation (onions): What chelates Ca²⁺ and Mg²⁺ ions (cofactors)?

Heating at 60°C

DNA isolation (onions): What dissolves the nucleic acids?

Cooling in ice bath

DNA isolation (onions): What retards nuclease activity?

6% Papain or meat tenderizer

DNA isolation (onions): What denatures protein?

Ice-cold 95% EtOH

DNA isolation (onions): What precipitates DNA and RNA?

Ice-cold 100% isopropyl alcohol

DNA isolation (onions): What precipitates DNA only?

5 M Sodium chloride

DNA isolation (animal): What causes osmosis in the cell?

Tris HCl

DNA isolation (animal): What was used as the Buffer?

0.5M EDTA

DNA isolation (animal): What chelates the metals in the DNAses?

5% SDS

DNA isolation (animal): What disrupts cell membrane and nuclear envelope?

Chloroform

DNA isolation (animal): What denature the proteins and lipids to maintain separation of organic and aqueous phases?

Isoamyl alcohol

DNA isolation (animal): What prevents foaming?

EDTA (EthyleneDiamineTetra Acetic acid)

DNA isolation (microbes): What is used as the chelating agent for divalent cations (Mg++) for the metals present in DNases as well as inactivating the enzyme.

Lysozyme

DNA isolation (microbes): What is used to cause lysis of bacterial cells by hydrolyzing the peptidoglycan present in cell walls, causing the disruption of the bacterial cell wall and letting the DNA into the solution?

CTAB (Cetyl TrimethylAmmonium Bromide)

DNA isolation (plant): What is the cationic detergent used to separate polysaccharides during purification of DNA samples from plants.

NaCl

DNA isolation (plant): What removes proteins that are conjugated to the DNA where the proteins are kept dissolved in the aqueous portion, preventing alcohol from precipitating it along with DNA?

0.001M sodium azide

What inhibits growth of microorganisms?

4°C (frozen state)

Suitable storage for preservation

pH 3-12

phosphodiester linkages in the DNA backbone are stable between

pH 3 or less (apurinic sites)

β-N-glycosidic bonds to purine bases are hydrolyzed at

less than 3 or greater than 12.

DNA is hydrolyzed at pH 

80-90°C

DNA unwinds at what temperature?

100˚C

phosphodiester and β-N-glycosidic bonds are stable up to

Mechanical Stress

Causes cleavage (shearing or scission) of the DNA chains, not necessarily in the secondary structure, but cuts the molecule into parts, thereby reducing the length.

hyperchromic effect; increase

Unwinding (denaturation) of DNA results into a _______, with ______ absorbance at 260 nm

hypochromic effect; decrease

Rewinding (renaturation or annealing) of DNA causes _________, with _________ absorbance at 260 nm

More dense DNA will migrate downward, less dense upwards forming bands

Cesium chloride (CsCl) forms a density gradient with the most dense solutions at the bottom. With that, where will DNA migrate?