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Plaque Blotting Technique


Plaque Blotting Technique


Introduction


Plaque blotting is a molecular biology screening technique used to identify specific DNA or RNA sequences present in bacteriophage plaques formed on a bacterial lawn. It is especially useful in the screening of recombinant phage libraries such as λ (lambda) phage genomic or cDNA libraries.
This technique combines:
Plaque assay (to isolate individual phage clones)
Blotting technique (to transfer nucleic acids onto a membrane)
Hybridization (to detect specific sequences using labeled probes)


Principle of Plaque Blotting


The principle of plaque blotting is based on nucleic acid hybridization.
Each plaque represents a clone of phage particles containing identical DNA.
DNA from phage particles in plaques is:
Released
Denatured into single strands
Transferred onto a nitrocellulose or nylon membrane
The membrane is incubated with a labeled DNA/RNA probe complementary to the target sequence.
Hybridization between probe and target DNA identifies positive plaques.
These plaques can then be picked from the original agar plate for further analysis.


Materials Required


Bacteriophage (e.g., λ phage library)
Host bacteria (e.g., E. coli)
Agar plates with soft agar
Nitrocellulose or nylon membrane
Denaturing solution (NaOH)
Neutralizing solution
SSC buffer
Labeled DNA/RNA probe (radioactive or non-radioactive)
Hybridization oven/incubator
Autoradiography film or detection system


Procedure of Plaque Blotting

1. Preparation of Phage Plaques
Recombinant phage library is mixed with E. coli host cells.
The mixture is poured onto agar plates.
After incubation, clear zones (plaques) appear due to bacterial lysis.
Each plaque represents a single phage clone.

2. Transfer of Plaques to Membrane

A nitrocellulose or nylon membrane is gently placed over the agar plate.
The membrane picks up phage particles and DNA from plaques.
Orientation marks are made to align membrane with original plate.


3. Lysis and Denaturation


Membrane is treated with:
Denaturing solution (NaOH) → converts double-stranded DNA to single-stranded DNA.
Neutralizing buffer → stabilizes DNA.
DNA becomes fixed onto the membrane.

4. Fixation of DNA

DNA is permanently fixed by:
Baking at 80°C (nitrocellulose), or
UV cross-linking (nylon membrane)

5. Hybridization with Labeled Probe


Membrane is incubated in hybridization buffer.
A labeled probe complementary to the target gene is added.
Hybridization occurs between probe and target DNA.

6. Washing

Excess unbound probe is removed by stringent washing.
This reduces non-specific binding.


7. Detection

Depending on the probe:
Radioactive probes → autoradiography
Non-radioactive probes → colorimetric or chemiluminescent detection
Dark spots indicate positive plaques.

8. Recovery of Positive Plaques


Using orientation marks, corresponding plaques are identified on the original plate.
Positive plaques are picked and amplified.
Further confirmation is done by sequencing or restriction analysis.


Diagram (Description for Exam)
Diagram showing:
Agar plate with plaques
Membrane placed over plaques
DNA transfer to membrane
Hybridization with labeled probe
Detection of positive plaques
(Students are advised to draw a neat labeled diagram.)


Applications of Plaque Blotting


Screening of genomic libraries
Screening of cDNA libraries
Identification of recombinant phage clones
Isolation of specific genes
Detection of viral genomes
Molecular cloning and gene mapping


Advantages
Allows screening of large phage libraries
High specificity due to probe hybridization
Enables recovery of intact phage clones
Useful for gene isolation and characterization.


Limitations
Time-consuming
Requires prior knowledge of target sequence
Radioactive probes involve safety issues
Less sensitive compared to PCR-based methods

Conclusion
Plaque blotting is a powerful and classical molecular biology technique used for the identification and isolation of specific recombinant phage clones from phage libraries. By combining plaque assays with nucleic acid hybridization, this method plays a crucial role in gene cloning, genome analysis, and molecular genetics research.




Plaque Blotting – 50 MCQs with Answers


1. Plaque blotting is mainly used to screen
A. Plasmid libraries
B. cDNA libraries in plasmids
C. Phage libraries
D. Protein libraries
Answer: C
2. Each plaque represents
A. One bacterial cell
B. One plasmid
C. One phage clone
D. One ribosome
Answer: C
3. Plaque blotting is a modification of
A. Western blotting
B. Southern blotting
C. Northern blotting
D. ELISA
Answer: B
4. Host organism commonly used in plaque blotting
A. Yeast
B. Bacillus
C. Escherichia coli
D. Streptococcus
Answer: C
5. Vector commonly used in plaque blotting
A. pBR322
B. Cosmids
C. BAC
D. Lambda (λ) phage
Answer: D
6. Plaques are formed due to
A. Antibiotic resistance
B. Bacterial growth
C. Lysis of bacteria by phage
D. DNA replication
Answer: C
7. Membrane used in plaque blotting
A. Cellulose
B. PVDF
C. Nitrocellulose or nylon
D. Agarose
Answer: C
8. DNA in plaques is transferred to membrane by
A. Electrophoresis
B. Diffusion
C. Direct contact
D. Centrifugation
Answer: C
9. Denaturation of DNA is done using
A. HCl
B. Ethanol
C. NaOH
D. Acetone
Answer: C
10. Purpose of DNA denaturation
A. DNA precipitation
B. DNA fragmentation
C. Formation of single-stranded DNA
D. Protein removal
Answer: C
11. DNA is fixed to membrane by
A. Freezing
B. Ethanol
C. Baking or UV crosslinking
D. Centrifugation
Answer: C
12. Hybridization occurs between
A. Protein–protein
B. DNA–protein
C. DNA–DNA or DNA–RNA
D. RNA–protein
Answer: C
13. Probe used in plaque blotting is
A. Antibody
B. Enzyme
C. Labeled nucleic acid
D. Lipid
Answer: C
14. Common labeling method for probes
A. Fluorescence only
B. Enzyme only
C. Radioactive or non-radioactive
D. Heat labeling
Answer: C
15. Autoradiography is used when probes are
A. Fluorescent
B. Enzyme-labeled
C. Radioactively labeled
D. Unlabeled
Answer: C
16. Positive plaques are identified as
A. Clear zones on agar
B. Colorless spots
C. Dark spots on film or membrane
D. Bacterial colonies
Answer: C
17. Washing step is important to
A. Increase DNA amount
B. Fix DNA
C. Remove non-specifically bound probe
D. Denature DNA
Answer: C
18. Orientation marks are made to
A. Increase sensitivity
B. Identify probe type
C. Locate positive plaques on original plate
D. Improve hybridization
Answer: C
19. Plaque blotting detects
A. Proteins
B. Lipids
C. Specific nucleic acid sequences
D. Carbohydrates
Answer: C
20. After detection, positive plaques are
A. Discarded
B. Washed
C. Picked and amplified
D. Stained
Answer: C
21. Plaque blotting is NOT used for
A. Gene isolation
B. Library screening
C. Viral genome detection
D. Protein purification
Answer: D
22. Hybridization buffer contains
A. SDS and blocking agents
B. Proteins only
C. Salts, detergents, and blocking agents
D. Agarose
Answer: C
23. Plaque blotting is similar to colony blotting except
A. Probe type
B. Hybridization
C. Use of phage instead of plasmid
D. DNA denaturation
Answer: C
24. Soft agar is used to
A. Fix DNA
B. Allow phage diffusion and plaque formation
C. Denature DNA
D. Label probes
Answer: B
25. Main disadvantage of plaque blotting
A. Low specificity
B. Time-consuming process
C. Poor resolution
D. No gene recovery
Answer: B
26. Which blotting technique uses bacteriophage?
A. Southern
B. Northern
C. Western
D. Plaque blotting
Answer: D
27. Positive signal in plaque blotting indicates
A. Protein expression
B. Antibiotic resistance
C. Presence of target gene
D. Cell death
Answer: C
28. Stringency of washing affects
A. DNA size
B. Plaque number
C. Specificity of hybridization
D. Membrane type
Answer: C
29. Probe binding depends on
A. Temperature and salt concentration
B. DNA length
C. Agar thickness
D. Bacterial strain
Answer: A
30. Plaque blotting is mainly used in
A. Proteomics
B. Molecular cloning
C. Metabolomics
D. Cytology
Answer: B
31. Non-radioactive probes are detected by
A. Autoradiography
B. Chemiluminescence or color reaction
C. UV light only
D. Heat
Answer: B
32. DNA released from phage is
A. Circular
B. RNA
C. Double-stranded DNA
D. Protein
Answer: C
33. Lambda phage genome is
A. RNA
B. Single-stranded DNA
C. Double-stranded DNA
D. Protein
Answer: C
34. Main purpose of plaque assay in blotting
A. Protein detection
B. Isolation of individual phage clones
C. DNA sequencing
D. Enzyme assay
Answer: B
35. Plaque blotting is a type of
A. Immunoblotting
B. Nucleic acid blotting
C. Protein blotting
D. Lipid blotting
Answer: B
36. Nitrocellulose membrane binds DNA by
A. Covalent bonding
B. Ionic interaction
C. Hydrophobic interactions
D. Hydrogen bonding
Answer: C
37. Nylon membrane has advantage because it
A. Cannot bind DNA
B. Is fragile
C. Has high binding capacity and durability
D. Is opaque
Answer: C
38. Hybridization temperature is usually
A. 0°C
B. 25°C
C. 42–65°C
D. 100°C
Answer: C
39. The probe must be
A. Identical in length to target
B. Complementary to target sequence
C. Double-stranded
D. Unlabeled
Answer: B
40. After plaque blotting, confirmation of clone is done by
A. ELISA
B. Microscopy
C. Sequencing or restriction analysis
D. Staining
Answer: C
41. First step in plaque blotting
A. Hybridization
B. Plaque formation on agar
C. DNA fixation
D. Washing
Answer: B
42. Blotting refers to
A. DNA synthesis
B. DNA amplification
C. Transfer of biomolecules to membrane
D. DNA digestion
Answer: C
43. Blocking agents in hybridization prevent
A. DNA degradation
B. Probe labeling
C. Non-specific probe binding
D. DNA denaturation
Answer: C
44. Plaque blotting is most useful when
A. Target gene sequence is known
B. Target protein is known
C. No sequence information is available
D. Only antibodies are available
Answer: A
45. Which blotting technique detects RNA?
A. Southern
B. Northern
C. Western
D. Plaque
Answer: B
46. In plaque blotting, plaques appear as
A. Colored spots
B. Colonies
C. Clear zones
D. Turbid zones
Answer: C
47. Plaque blotting is generally less sensitive than
A. Southern blot
B. Northern blot
C. PCR-based methods
D. Western blot
Answer: C
48. Excess probe removal increases
A. Background noise
B. DNA damage
C. Signal clarity
D. Plaque size
Answer: C
49. Plaque blotting was widely used before
A. Sequencing
B. High-throughput PCR methods
C. Gel electrophoresis
D. ELISA
Answer: B
50. Final outcome of plaque blotting is
A. Protein isolation
B. Identification of desired recombinant phage clone
C. RNA purification
D. Enzyme activity measurement
Answer: B



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