Saturday, 8 August 2026

DNA/RNA & Protein Purification

DNA/RNA & Protein Purification – Methods in Biology

CSIR-NET | GATE Biotechnology | DBT BET | ICAR JRF | ICMR JRF

This comprehensive study material covers the major laboratory methods used for DNA isolation, RNA isolation, protein isolation, purification of biomolecules, and quantification of DNA, RNA and proteins. The notes are designed especially for competitive examinations and include important principles, reagents, mechanisms, calculations, comparisons and exam-oriented concepts.

Topics Covered

  • DNA isolation – principle, steps and important reagents
  • Genomic DNA isolation
  • Plasmid DNA isolation
  • Phenol-chloroform extraction
  • DNA precipitation and washing
  • RNA isolation and RNase-free techniques
  • TRIzol/guanidinium-based RNA extraction
  • mRNA enrichment and poly(A) selection
  • Protein isolation and cell lysis
  • Protein extraction buffers and protease inhibitors
  • Protein purification techniques
  • Ammonium sulfate precipitation
  • Dialysis and ultrafiltration
  • Chromatographic purification
  • Ion-exchange chromatography
  • Gel-filtration/size-exclusion chromatography
  • Affinity chromatography
  • Hydrophobic interaction chromatography
  • DNA/RNA quantification by UV spectrophotometry
  • Protein quantification by Bradford, Lowry and BCA assays
  • Important CSIR-NET and GATE concepts
  • 10 interactive MCQs with answers

1. Introduction to Biomolecule Isolation and Purification

Biomolecular techniques are fundamental to molecular biology, biotechnology, biochemistry, genetics, microbiology and biomedical research. Most biological experiments require the isolation of relatively pure DNA, RNA or protein from a complex biological sample. Cells contain thousands of different molecules, including nucleic acids, proteins, lipids, carbohydrates, pigments, salts, metabolites and other cellular components. Therefore, isolation and purification methods are required to separate the molecule of interest from unwanted components.

  • Isolation refers to obtaining the molecule of interest from a biological material.
  • Extraction generally refers to releasing the molecule from cells or tissues.
  • Purification means increasing the proportion or purity of the target biomolecule.
  • Quantification determines the amount or concentration of the biomolecule.
  • Quality assessment determines whether the isolated biomolecule is suitable for downstream applications.
Basic principle: Most purification procedures exploit differences between the target biomolecule and contaminants in properties such as size, charge, solubility, hydrophobicity, binding affinity and density.

For example, DNA and RNA are negatively charged because of their phosphate backbone. This property can be exploited using ion-exchange matrices. Proteins have different net charges depending on pH and their isoelectric points. Their size can be exploited using size-exclusion chromatography, while specific binding interactions can be exploited using affinity chromatography.

2. DNA Isolation

DNA isolation is the process of obtaining DNA from cells or tissues in a form that is sufficiently pure for downstream applications such as PCR, restriction digestion, cloning, sequencing, Southern blotting, genotyping and molecular diagnostics.

2.1 General Steps of DNA Isolation

  • Sample collection: Biological material such as blood, bacterial cells, plant tissue or animal tissue is collected.
  • Cell disruption: Cells are broken to release their intracellular contents.
  • Lysis: Detergents and other chemicals disrupt cellular and nuclear membranes.
  • Removal of proteins: Proteins are denatured or digested using proteases.
  • Removal of RNA: RNase may be used when RNA contamination must be minimized.
  • DNA separation: DNA is separated from cellular debris and contaminants.
  • DNA precipitation: DNA is precipitated using alcohol in the presence of salt.
  • Washing: The DNA pellet is washed, commonly with 70% ethanol.
  • Resuspension: Purified DNA is dissolved in TE buffer or nuclease-free water.
  • Quality assessment: DNA concentration and purity are evaluated.

2.2 Cell Lysis

Cell lysis is one of the most important steps in nucleic acid isolation. The method of lysis depends on the biological material.

  • Mechanical lysis: Grinding, homogenization, bead beating or sonication can disrupt cells.
  • Detergent-mediated lysis: SDS and other detergents disrupt lipid membranes.
  • Enzymatic lysis: Lysozyme is commonly used for bacterial cell walls.
  • Plant tissue disruption: Grinding in liquid nitrogen is frequently used to break tough plant tissues.
  • Proteinase treatment: Proteinase K helps degrade proteins associated with nucleic acids.

2.3 Role of Important Reagents in DNA Isolation

Reagent Major Function
Tris-HCl Maintains a stable pH.
EDTA Chelates divalent cations such as Mg2+ and Ca2+, thereby inhibiting nucleases.
SDS Detergent that disrupts membranes and denatures proteins.
Proteinase K Digests proteins and helps remove nucleases.
RNase Removes contaminating RNA.
NaCl Provides ionic strength and helps DNA precipitation by neutralizing phosphate charges.
Isopropanol Precipitates DNA efficiently, usually requiring a smaller volume than ethanol.
Ethanol Used for DNA precipitation and washing.
TE buffer Provides buffering and EDTA-mediated protection from nucleases.
CSIR-NET Important: EDTA protects DNA primarily by chelating Mg2+ and other divalent metal ions required by many nucleases.

3. Phenol-Chloroform Extraction of DNA

Phenol-chloroform extraction is a classical method for purification of nucleic acids. The method depends on differential partitioning of biomolecules between an aqueous phase and an organic phase.

  • Phenol denatures proteins.
  • Chloroform improves phase separation and removes lipids.
  • After centrifugation, the mixture separates into aqueous and organic phases.
  • DNA generally remains in the aqueous phase under appropriate conditions.
  • Denatured proteins accumulate at or near the interface.
  • The aqueous phase is carefully transferred to another tube.
  • DNA is subsequently precipitated using salt and alcohol.
Important: Phenol-chloroform is a classical laboratory technique involving hazardous organic chemicals. Modern laboratories often use safer column-based or magnetic-bead-based extraction systems.

3.1 DNA Precipitation

DNA precipitation is based on reducing the solubility of DNA in an aqueous solution. Salt and alcohol are commonly used.

  • DNA has a negatively charged phosphate backbone.
  • Cations such as Na+ help neutralize the negative charges.
  • Ethanol or isopropanol decreases the dielectric constant of the solution.
  • Reduced charge repulsion and reduced solvation promote aggregation of DNA.
  • The DNA can then be collected by centrifugation.
  • The pellet is usually washed with 70% ethanol.
  • The pellet is air-dried briefly and resuspended in an appropriate buffer.
Exam Point: Over-drying a DNA pellet can make it difficult to dissolve. The DNA pellet should generally not be excessively dried.

4. Plasmid DNA Isolation

Plasmids are small, usually circular, extrachromosomal DNA molecules commonly found in bacteria. Plasmid isolation is important in recombinant DNA technology, cloning and genetic engineering.

4.1 Alkaline Lysis Method

The alkaline lysis method is widely used for plasmid DNA purification. It takes advantage of the different renaturation properties of plasmid DNA and large bacterial chromosomal DNA.

  • Resuspension: Bacterial cells are resuspended in a suitable buffer, often containing Tris and EDTA.
  • RNase: RNase is commonly included to remove RNA.
  • Alkaline lysis: SDS and NaOH disrupt membranes and denature proteins and nucleic acids.
  • Neutralization: Potassium acetate-based neutralization causes plasmid DNA to renature while large chromosomal DNA and cellular debris precipitate.
  • Centrifugation: Insoluble material is removed.
  • Supernatant collection: Plasmid DNA remains in the cleared supernatant.
  • Purification: The plasmid can be further purified using silica columns, precipitation or other methods.
Key principle: Small covalently closed circular plasmid DNA can renature efficiently after neutralization, whereas large chromosomal DNA becomes tangled and precipitates with proteins and cell debris.

5. RNA Isolation

RNA isolation is more technically challenging than DNA isolation because RNA is highly susceptible to degradation by RNases. RNases are abundant in the environment and can remain active under conditions where many proteins are denatured.

5.1 Major Challenges in RNA Isolation

  • RNases are widely distributed in biological materials.
  • RNases can be present on skin, laboratory surfaces and equipment.
  • Some RNases are highly stable.
  • RNA degradation can occur rapidly if appropriate precautions are not taken.
  • RNA samples should be handled using RNase-free tubes, tips and solutions.

5.2 General RNA Isolation Procedure

  • Rapidly disrupt the biological sample.
  • Inactivate endogenous RNases.
  • Lyse cells using an appropriate chaotropic reagent.
  • Separate RNA from DNA, proteins and other cellular components.
  • Purify RNA using organic extraction, silica columns or magnetic beads.
  • Treat with DNase when genomic DNA contamination is a concern.
  • Elute RNA using RNase-free water or an appropriate buffer.
  • Assess RNA concentration and integrity.

5.3 Guanidinium-Based RNA Isolation

Guanidinium salts are powerful chaotropic agents that denature proteins, including RNases. Guanidinium-containing solutions are therefore commonly used in RNA extraction protocols.

  • Chaotropic salts disrupt protein structure.
  • RNases are denatured and inactivated.
  • RNA is protected from enzymatic degradation.
  • RNA can subsequently be separated using organic extraction or silica-based purification.

5.4 TRIzol-Type Extraction Principle

Phenol and guanidinium-based reagents can be used to isolate RNA from biological samples. After phase separation, RNA is recovered from the appropriate aqueous fraction and subsequently precipitated or purified.

  • Cells are homogenized in the reagent.
  • Proteins and nucleases are denatured.
  • Chloroform or another phase-separation step produces distinct phases.
  • RNA is recovered from the aqueous phase under appropriate conditions.
  • DNA and proteins are distributed differently between phases.
  • RNA is precipitated and washed.
  • The RNA pellet is dissolved in RNase-free water.
Very Important: During RNA purification, preventing RNase contamination is more critical than simply preventing DNase contamination during DNA isolation.

6. RNA Quality Assessment

RNA concentration alone does not indicate whether RNA is suitable for experiments. RNA integrity is also extremely important.

  • UV spectrophotometry: Used to estimate RNA concentration.
  • A260/A280: Gives an indication of protein contamination.
  • A260/A230: Helps identify contamination by salts, phenol and other compounds.
  • Gel electrophoresis: Can provide information about RNA integrity.
  • Bioanalyzer-type systems: Can provide quantitative RNA integrity measurements.
For nucleic acids: Concentration is commonly estimated from absorbance at 260 nm.

A260 × conversion factor × dilution factor = concentration

For pure nucleic acid samples, an A260/A280 ratio near approximately 1.8 is often associated with relatively pure DNA, whereas RNA often has a ratio near approximately 2.0. These values are approximate indicators rather than absolute proof of purity.

7. DNA/RNA Quantification by UV Spectrophotometry

Nucleic acids absorb ultraviolet radiation strongly at approximately 260 nm because of their aromatic nitrogenous bases.

  • DNA and RNA absorb strongly around 260 nm.
  • Proteins, particularly aromatic amino acids, contribute strongly near 280 nm.
  • A260 is therefore used for nucleic acid concentration estimation.
  • A280 is useful for evaluating protein-related contamination.
  • A230 can indicate contamination by organic compounds, salts or other substances.

7.1 Beer-Lambert Law

A = εcl
  • A = absorbance
  • ε = molar extinction coefficient
  • c = concentration
  • l = path length

The Beer-Lambert law explains the relationship between absorbance and concentration under appropriate experimental conditions.

7.2 Approximate Conversion Factors

  • For double-stranded DNA, an A260 of 1 is commonly approximated as about 50 µg/mL.
  • For RNA, an A260 of 1 is commonly approximated as about 40 µg/mL.
  • For single-stranded DNA, a commonly used approximate factor is about 33 µg/mL.
These conversion factors are approximate and depend on the nucleic acid, buffer, sequence and experimental conditions.

8. Protein Isolation

Protein isolation begins with disruption of cells or tissues and extraction of proteins into a suitable buffer. Unlike DNA, proteins have diverse physicochemical properties, so the extraction buffer must be selected according to the target protein.

8.1 Important Considerations in Protein Extraction

  • Protein stability
  • pH
  • Temperature
  • Salt concentration
  • Detergent compatibility
  • Presence of proteases
  • Redox conditions
  • Requirement for cofactors
  • Subcellular localization of the protein

8.2 Cell Disruption Methods

  • Mechanical homogenization: Suitable for tissues and cells.
  • Sonication: Uses ultrasonic energy to disrupt cells.
  • French press: Uses high pressure to disrupt cells.
  • Bead beating: Uses beads to mechanically break cells.
  • Detergent lysis: Detergents disrupt lipid membranes.
  • Enzymatic lysis: Enzymes can digest specific cell wall components.

8.3 Protease Inhibitors

Proteases released during cell disruption can degrade proteins of interest. Protease inhibitors are therefore frequently included in extraction buffers.

  • Protease inhibitors reduce unwanted proteolysis.
  • The inhibitor cocktail should be selected according to the proteases likely to be present.
  • Protein extraction is often performed at low temperature.
  • Rapid processing reduces protein degradation.
Important: Not every protein is stable under the same extraction conditions. Detergents, reducing agents, salt and pH must be optimized for the specific target protein.

9. Protein Purification

Protein purification involves a sequence of steps designed to remove contaminating proteins and other cellular components while maintaining the biological activity of the target protein.

A typical purification strategy may involve:

  • Cell lysis
  • Centrifugation
  • Clarification
  • Precipitation or concentration
  • Dialysis or buffer exchange
  • Chromatographic purification
  • Polishing step
  • Protein concentration
  • Activity and purity assessment

10. Ammonium Sulfate Precipitation

Ammonium sulfate precipitation is a classical method for protein fractionation. It is based on the reduced solubility of proteins at high ionic strength, a phenomenon commonly called salting out.

  • Ammonium sulfate is highly soluble in water.
  • Increasing salt concentration reduces protein solubility for many proteins.
  • Different proteins precipitate at different salt concentrations.
  • The precipitated protein can be collected by centrifugation.
  • The pellet can be dissolved in an appropriate buffer.
  • Dialysis or desalting may be required before further purification.
Salting out vs salting in: At low salt concentrations, protein solubility may increase due to shielding of charged groups. At sufficiently high salt concentrations, competition for water molecules decreases protein solubility and promotes precipitation.

11. Dialysis

Dialysis is used to remove small molecules from a protein solution while retaining larger molecules such as proteins.

  • A semipermeable membrane is used.
  • Small molecules can diffuse through the membrane.
  • Larger proteins are retained.
  • Dialysis can remove salts, reducing agents and other small molecules.
  • The external buffer is usually changed several times to improve removal.
CSIR-NET Point: Dialysis separates molecules mainly on the basis of their ability to pass through a semipermeable membrane, not by specific binding affinity.

12. Ultrafiltration

Ultrafiltration uses a membrane with a defined molecular weight cutoff. Pressure or centrifugal force drives solvent and small molecules through the membrane while larger proteins are retained.

  • Useful for protein concentration.
  • Useful for buffer exchange.
  • Much faster than traditional dialysis for many applications.
  • Membrane selection depends on molecular size.
  • Protein adsorption to the membrane can sometimes reduce recovery.

13. Chromatography

Chromatography is one of the most important techniques for biomolecule purification. It separates molecules based on differences in their interactions with a stationary phase and a mobile phase.

Sample → Stationary Phase + Mobile Phase → Differential Retention → Separation

Major Types of Chromatography

  • Ion-exchange chromatography
  • Size-exclusion chromatography
  • Affinity chromatography
  • Hydrophobic interaction chromatography
  • Reverse-phase chromatography

14. Ion-Exchange Chromatography

Ion-exchange chromatography separates molecules based on charge. The stationary phase contains charged functional groups that interact with oppositely charged molecules.

14.1 Cation-Exchange Chromatography

  • The stationary phase is negatively charged.
  • It binds positively charged proteins.
  • Therefore, cation exchangers bind cations.
  • Examples include carboxymethyl-type and sulfopropyl-type matrices.

14.2 Anion-Exchange Chromatography

  • The stationary phase is positively charged.
  • It binds negatively charged molecules.
  • DNA and RNA can interact strongly with positively charged matrices because of their phosphate backbone.
  • Examples include DEAE and quaternary ammonium matrices.
Memory Trick:
Cation exchanger → binds cations → negatively charged matrix.
Anion exchanger → binds anions → positively charged matrix.

14.3 Elution in Ion Exchange

  • Increasing salt concentration can compete with bound proteins.
  • Changing pH changes the charge of the protein.
  • Proteins with weaker interactions generally elute earlier.
  • A salt gradient can provide controlled separation.

15. Size-Exclusion Chromatography

Size-exclusion chromatography, also called gel filtration chromatography, separates molecules according to their effective size or hydrodynamic volume.

  • The stationary phase contains porous beads.
  • Large molecules cannot enter many pores.
  • Large molecules therefore travel through the column relatively quickly.
  • Small molecules enter the pores and take a longer path.
  • Large molecules generally elute before smaller molecules.
Key Rule: In size-exclusion chromatography, larger molecules elute first and smaller molecules elute later.

Important Terms

  • Void volume (V0): Volume outside the beads accessible to very large molecules.
  • Elution volume (Ve): Volume of mobile phase required for a molecule to elute.
  • Fractionation range: Range of molecular sizes that can be effectively separated by the matrix.

16. Affinity Chromatography

Affinity chromatography is one of the most selective purification methods. It uses a specific biological interaction between the target molecule and a ligand attached to the stationary phase.

  • The target protein specifically binds to an immobilized ligand.
  • Unbound proteins are washed away.
  • The target protein is subsequently eluted.
  • Elution may be achieved by adding a competing ligand.
  • Changes in pH, ionic strength or other conditions may also disrupt the interaction.

16.1 His-Tagged Protein Purification

Recombinant proteins are often engineered with a short polyhistidine tag. This tag can interact with immobilized metal ions such as nickel or cobalt in immobilized metal affinity chromatography.

  • His-tagged protein binds to the immobilized metal-containing matrix.
  • Many contaminating proteins do not bind strongly.
  • Washing removes weakly interacting proteins.
  • Imidazole can compete with histidine residues and promote elution.
Very Important: His-tag purification is an example of affinity chromatography, not size-exclusion chromatography.

17. Hydrophobic Interaction Chromatography

Hydrophobic interaction chromatography separates proteins based on exposed hydrophobic regions on their surfaces.

  • High salt concentrations promote hydrophobic interactions.
  • Proteins bind to hydrophobic ligands on the stationary phase.
  • A decreasing salt gradient weakens hydrophobic interactions.
  • Proteins are subsequently eluted.

Hydrophobic interaction chromatography is useful when maintaining native protein structure and biological activity is important.

18. Reverse-Phase Chromatography

Reverse-phase chromatography uses a highly hydrophobic stationary phase. Proteins or peptides interact with the hydrophobic stationary phase and are eluted using changes in organic solvent concentration.

  • Strong hydrophobic interactions are involved.
  • Organic solvents can be used for elution.
  • Reverse-phase chromatography is commonly used for peptides and analytical applications.
  • It may not preserve the native structure of many proteins.

19. Comparison of Major Protein Purification Techniques

Technique Separation Basis Major Application
Ammonium sulfate precipitation Solubility Initial fractionation
Dialysis Membrane permeability Desalting/buffer exchange
Ion exchange Charge Protein purification
Size exclusion Size/hydrodynamic volume Size separation and polishing
Affinity chromatography Specific molecular interaction Highly selective purification
Hydrophobic interaction Surface hydrophobicity Native protein purification
Reverse phase Hydrophobicity Peptide/protein analytical purification

20. Protein Quantification

Protein concentration can be measured using several colorimetric or spectrophotometric methods. The most commonly discussed methods for competitive examinations include Bradford, Lowry and BCA assays.

21. Bradford Protein Assay

The Bradford assay is based on the binding of Coomassie Brilliant Blue dye to proteins. Protein-dye binding produces a change in the absorption spectrum. The assay is commonly measured near 595 nm.

  • Uses Coomassie Brilliant Blue dye.
  • Protein binding shifts the dye toward a blue form.
  • Absorbance is commonly measured around 595 nm.
  • A standard curve is prepared using a known protein such as BSA.
  • Unknown protein concentration is determined from the standard curve.
Remember: Bradford assay → Coomassie Brilliant Blue → approximately 595 nm.

22. Lowry Protein Assay

The Lowry assay combines the Biuret reaction with reduction of the Folin-Ciocalteu reagent. The resulting color is measured spectrophotometrically.

  • Protein peptide bonds participate in the Biuret reaction.
  • Copper ions are involved under alkaline conditions.
  • The Folin-Ciocalteu reagent contributes to color development.
  • A standard curve is prepared.
  • Protein concentration is calculated from the standard curve.
Exam Point: Lowry assay is more chemically complex than Bradford and can be affected by several interfering substances.

23. BCA Protein Assay

The bicinchoninic acid (BCA) assay is based on the reduction of Cu2+ to Cu+ by proteins under alkaline conditions. Cu+ then reacts with bicinchoninic acid to produce a purple-colored complex.

  • Protein reduces Cu2+ to Cu+.
  • Cu+ reacts with BCA.
  • A purple-colored complex is formed.
  • Absorbance is commonly measured around 562 nm.
  • BSA is frequently used as a protein standard.
Assay Major Principle Typical Detection
Bradford Coomassie dye binding ~595 nm
Lowry Biuret + Folin reaction ~750 nm
BCA Cu2+ reduction + BCA complex ~562 nm

24. Standard Curve in Biomolecule Quantification

A standard curve is essential in many quantitative biochemical assays. Known concentrations of a standard are measured and plotted against absorbance.

  • Prepare several known concentrations of the standard.
  • Measure the absorbance of each concentration.
  • Plot absorbance versus concentration.
  • Determine the equation of the calibration curve.
  • Measure the absorbance of the unknown sample.
  • Use the calibration equation to determine the unknown concentration.
  • Apply dilution factors where necessary.
y = mx + c

Unknown concentration = (Absorbance − intercept) / slope
Always consider the dilution factor when calculating the concentration of the original sample.

25. DNA/RNA vs Protein Purification

Feature DNA/RNA Protein
Major chemical nature Nucleic acid polymer Polypeptide
Major charge feature Phosphate backbone is negatively charged Charge depends on amino acid composition and pH
Important degradation enzymes DNases/RNases Proteases
UV maximum commonly used 260 nm 280 nm for intrinsic absorbance
Common purification principle Charge, precipitation, silica binding Charge, size, affinity, hydrophobicity

26. Important CSIR-NET / GATE Exam Points

  • DNA and RNA absorb strongly at approximately 260 nm.
  • Proteins containing aromatic amino acids contribute strongly to absorbance near 280 nm.
  • EDTA chelates divalent cations.
  • Mg2+ is required by many nucleases.
  • SDS is an anionic detergent.
  • Proteinase K digests proteins.
  • RNase removes RNA contamination from DNA preparations.
  • DNase removes DNA contamination from RNA preparations.
  • Alcohol precipitation is used for nucleic acids.
  • DNA generally remains in the aqueous phase during appropriate phenol-chloroform extraction.
  • Ammonium sulfate precipitation is based on salting out.
  • Dialysis separates molecules using a semipermeable membrane.
  • Ion exchange separates based on charge.
  • Size exclusion separates based primarily on hydrodynamic size.
  • Large molecules generally elute first in size-exclusion chromatography.
  • Affinity chromatography depends on specific molecular interactions.
  • His-tag purification commonly uses immobilized metal affinity chromatography.
  • Bradford assay uses Coomassie Brilliant Blue.
  • Bradford assay is commonly read around 595 nm.
  • BCA assay commonly uses detection around 562 nm.
  • Lowry assay involves Biuret chemistry and Folin reagent.
  • RNA handling requires strict RNase-free conditions.
  • 70% ethanol is commonly used to wash nucleic acid pellets.
  • Over-drying nucleic acid pellets can make them difficult to dissolve.
  • Protein purification should minimize proteolysis and denaturation.

27. Quick Revision Table

Question Answer
DNA absorbs maximally near? 260 nm
Protein aromatic residues absorb near? 280 nm
Bradford assay dye? Coomassie Brilliant Blue
Bradford wavelength? Approximately 595 nm
BCA wavelength? Approximately 562 nm
DNA protection by EDTA? Chelation of divalent cations
Protein precipitation by ammonium sulfate? Salting out
Ion exchange basis? Charge
Size exclusion basis? Hydrodynamic size
Affinity chromatography basis? Specific molecular interaction
Large molecule in SEC? Usually elutes first
RNA major threat? RNase degradation
His-tag purification? Immobilized metal affinity chromatography

28. 10 MCQs – DNA/RNA & Protein Purification

Q1. Which reagent protects DNA from many nucleases by chelating divalent metal ions?
Correct Answer: B. EDTA
EDTA chelates divalent cations such as Mg2+, which are required by many nucleases.
Q2. DNA and RNA show strong absorbance at which wavelength?
Correct Answer: B. 260 nm
The nitrogenous bases of nucleic acids contribute strongly to UV absorbance near 260 nm.
Q3. In size-exclusion chromatography, which molecules generally elute first?
Correct Answer: B. Large molecules
Large molecules cannot enter many pores in the stationary phase and therefore take a shorter path through the column.
Q4. Bradford protein assay primarily uses which dye?
Correct Answer: B. Coomassie Brilliant Blue
The Bradford assay is based on protein binding to Coomassie Brilliant Blue, with measurement commonly around 595 nm.
Q5. Ammonium sulfate precipitation of proteins is mainly based on:
Correct Answer: B. Salting out
High concentrations of ammonium sulfate can reduce protein solubility and cause proteins to precipitate.
Q6. Which chromatography technique separates molecules primarily according to charge?
Correct Answer: C. Ion-exchange chromatography
Ion-exchange chromatography separates biomolecules based on electrostatic interactions between the molecule and the charged stationary phase.
Q7. Which technique is particularly useful for purification of His-tagged recombinant proteins?
Correct Answer: A. Immobilized metal affinity chromatography
Histidine residues in a His-tag can interact with immobilized metal ions such as nickel or cobalt.
Q8. Which problem is particularly important during RNA isolation?
Correct Answer: A. RNase-mediated degradation
RNases are abundant and stable, making strict RNase-free handling essential for obtaining intact RNA.
Q9. The BCA assay involves formation of a colored complex between BCA and:
Correct Answer: A. Cu+
Protein reduces Cu2+ to Cu+ under alkaline conditions, and Cu+ forms a purple complex with bicinchoninic acid.
Q10. Which statement about affinity chromatography is correct?
Correct Answer: B. It uses specific molecular interactions
Affinity chromatography exploits highly specific interactions between a target molecule and an immobilized ligand.

29. MCQ Answer Key

Question Answer Concept
1BEDTA and nuclease inhibition
2BNucleic acid UV absorption
3BSize-exclusion chromatography
4BBradford assay
5BSalting out
6CIon-exchange chromatography
7AHis-tag purification
8ARNA degradation
9ABCA assay
10BAffinity chromatography

30. Final Revision Strategy

For CSIR-NET and GATE, remember these five connections:
  • DNA/RNA → 260 nm
  • Protein → 280 nm
  • Bradford → Coomassie Brilliant Blue → 595 nm
  • Ion exchange → Charge
  • Size exclusion → Size → Large molecules elute first
  • Affinity → Specific interaction
  • Ammonium sulfate → Salting out
  • EDTA → Chelates divalent cations
  • RNA isolation → RNase-free conditions
  • His-tag → Immobilized metal affinity chromatography

One-Line Memory Tricks

  • 260 = Nucleic acids
  • 280 = Proteins
  • 595 = Bradford
  • 562 = BCA
  • Charge = Ion exchange
  • Size = Size exclusion
  • Specific binding = Affinity
  • Salt out = Ammonium sulfate
  • RNase = RNA enemy
  • EDTA = Metal-ion chelator
Conclusion: DNA, RNA and protein isolation are foundational techniques in molecular biology. The choice of extraction and purification method depends on the chemical and physical properties of the target biomolecule. For competitive examinations, it is particularly important to understand the principle behind each method rather than memorizing only the names of reagents. A strong understanding of charge, size, solubility, hydrophobicity, affinity, spectrophotometric absorption and membrane permeability makes it much easier to solve conceptual questions in CSIR-NET, GATE Biotechnology, DBT BET, ICAR-JRF and other biotechnology examinations.
CSIR NET Life Science GATE Biotechnology DBT BET DNA Isolation RNA Isolation Protein Purification Biomolecule Quantification Methods in Biology Biotechnology Notes

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