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Colony Blotting

Colony Blotting –



Colony blotting (also called colony hybridization) is an important molecular biology technique used to screen and identify bacterial colonies that contain a specific DNA sequence or recombinant plasmid. It is widely applied in recombinant DNA technology for the identification of positive clones from a large population of transformants. The technique was first described by Grunstein and Hogness (1975).
Colony blotting is based on the principle of nucleic acid hybridization, where a labeled DNA or RNA probe binds specifically to its complementary sequence present in the bacterial DNA immobilized on a membrane.


Principle


The principle of colony blotting involves:
Transfer of bacterial colonies from an agar plate onto a nitrocellulose or nylon membrane.
Lysis of cells directly on the membrane to release DNA.
Denaturation of DNA to single strands and immobilization on the membrane.
Hybridization of the immobilized DNA with a labeled probe complementary to the target gene.
Detection of colonies that give a positive signal, indicating the presence of the desired DNA sequence.


Materials Required


Bacterial colonies on agar plate
Nitrocellulose or nylon membrane
Lysis solution (alkali/SDS)
Denaturation and neutralization solutions
Labeled DNA/RNA probe (radioactive or non-radioactive)
Hybridization buffer
Washing solutions
Detection system (autoradiography or colorimetric/chemiluminescent)


Procedure / Steps Involved


1. Preparation of Master Plate


Bacterial cells transformed with recombinant plasmids are spread on selective agar medium and allowed to form well-separated colonies. This original plate is preserved as the master plate.

2. Transfer of Colonies to Membrane

A sterile nitrocellulose or nylon membrane is gently placed over the agar plate. The positions of colonies are marked for reference. Some cells from each colony adhere to the membrane.


3. Cell Lysis

The membrane is removed and treated with lysis solution to break open bacterial cells and release DNA.

4. Denaturation of DNA


The DNA is denatured using an alkaline solution, converting double-stranded DNA into single-stranded DNA suitable for probe binding.


5. Neutralization and Fixation


The membrane is neutralized and the DNA is fixed onto the membrane by baking at 80°C or by UV cross-linking.


6. Hybridization


The membrane is incubated with a labeled nucleic acid probe under suitable conditions. The probe hybridizes with complementary DNA sequences present on the membrane.


7. Washing


Excess and non-specifically bound probe is removed by washing with appropriate buffers.
8. Detection
Hybridized probes are detected by:
Autoradiography (radioactive probes)
Colorimetric or chemiluminescent methods (non-radioactive probes)
Colonies showing signals correspond to positive clones.



A typical colony blotting diagram shows:


Agar plate with bacterial colonies
Transfer of colonies to membrane
Lysis and denaturation
Hybridization with probe
Detection of positive spots
(Diagram can be drawn in exams for better scoring)


Applications


Screening of recombinant bacterial colonies
Identification of clones containing desired genes
Gene library screening
Confirmation of successful transformation
Molecular genetics and biotechnology research


Advantages


Allows screening of thousands of colonies simultaneously
High specificity and sensitivity
No need for prior DNA isolation
Time-saving and cost-effective


Limitations


Requires labeled probes
False positives may occur if washing is inadequate
Cannot quantify gene expression
Radioactive probes need special handling


Conclusion


Colony blotting is a reliable and widely used technique in molecular cloning for the rapid identification of bacterial colonies containing a specific gene of interest. Its simplicity, specificity, and efficiency make it an indispensable method in genetic engineering and biotechnology laboratories.


Colony Blotting – 50 MCQs with Answers



1. Colony blotting is mainly used for
A. Protein separation
B. RNA isolation
C. Screening recombinant colonies
D. DNA sequencing
Answer: C


2. Colony blotting is also known as
A. Southern hybridization
B. Colony hybridization
C. Northern hybridization
D. Western hybridization
Answer: B


3. Colony blotting was first developed by
A. Watson and Crick
B. Grunstein and Hogness
C. Sanger
D. Mullis
Answer: B


4. The membrane commonly used in colony blotting is
A. Cellulose paper
B. Agarose
C. Nitrocellulose
D. Glass fiber
Answer: C


5. Which molecule is detected in colony blotting?
A. Protein
B. Lipid
C. DNA
D. Carbohydrate
Answer: C


6. Colony blotting is based on the principle of
A. Electrophoresis
B. Immunodiffusion
C. Nucleic acid hybridization
D. Chromatographic separation
Answer: C


7. Which probe is used in colony blotting?
A. Antibody probe
B. Enzyme probe
C. Nucleic acid probe
D. Fluorescent protein
Answer: C


8. The DNA is denatured in colony blotting to
A. Increase molecular weight
B. Form single strands
C. Degrade DNA
D. Remove RNA
Answer: B


9. The colonies are transferred from agar plate to
A. Filter paper
B. Polyacrylamide gel
C. Membrane
D. Test tube
Answer: C


10. The master plate is used to
A. Detect signal
B. Store DNA
C. Recover positive colonies
D. Denature DNA
Answer: C


11. Which step releases DNA from bacterial cells?
A. Hybridization
B. Washing
C. Cell lysis
D. Fixation
Answer: C


12. DNA fixation on membrane is done by
A. Centrifugation
B. Heating or UV cross-linking
C. Freezing
D. Shaking
Answer: B


13. Colony blotting is mainly used in
A. Protein purification
B. Gene cloning
C. Metabolomics
D. Enzyme kinetics
Answer: B


14. Which organism is commonly used in colony blotting?
A. Yeast
B. Virus
C. Bacteria
D. Protozoa
Answer: C


15. Colony blotting can screen
A. One colony at a time
B. Only plasmid-free cells
C. Thousands of colonies simultaneously
D. Only proteins
Answer: C


16. Radioactive probes are detected by
A. ELISA
B. Autoradiography
C. Spectrophotometry
D. Chromatography
Answer: B


17. A positive colony blot indicates
A. Absence of gene
B. Presence of target gene
C. Cell death
D. DNA degradation
Answer: B


18. Which solution is used for DNA denaturation?
A. Acidic solution
B. Alkaline solution
C. Buffer only
D. Alcohol
Answer: B


19. Which blotting technique is used to detect proteins?
A. Southern
B. Northern
C. Colony
D. Western
Answer: D


20. Colony blotting does NOT require
A. Agar plate
B. DNA extraction
C. Labeled probe
D. Membrane
Answer: B


21. Which is a non-radioactive probe label?
A. ³²P
B. ³H
C. Biotin
D. ¹⁴C
Answer: C


22. Washing step in colony blotting is used to
A. Lyse cells
B. Remove excess probe
C. Denature DNA
D. Transfer colonies
Answer: B


23. Colony blotting is most useful for
A. Gene expression analysis
B. Clone identification
C. Protein structure analysis
D. Metabolite detection
Answer: B
24. The DNA on membrane must be
A. Double stranded
B. Circular
C. Single stranded
D. Supercoiled
Answer: C
25. Which step ensures specific binding of probe?
A. Hybridization
B. Cell lysis
C. Transfer
D. Fixation
Answer: A
26. False positive results can occur due to
A. Proper washing
B. High specificity
C. Non-specific probe binding
D. Correct hybridization
Answer: C
27. Colony blotting cannot be used to
A. Screen gene libraries
B. Identify recombinant clones
C. Quantify gene expression
D. Detect target DNA
Answer: C
28. Which membrane has higher binding capacity?
A. Paper
B. Nylon
C. Agar
D. Plastic
Answer: B
29. Colony blotting is an example of
A. Immunological technique
B. Hybridization technique
C. Electrophoretic technique
D. Chromatographic technique
Answer: B
30. The hybridization temperature depends on
A. Membrane type
B. Probe length and GC content
C. Agar concentration
D. Colony size
Answer: B
31. Which enzyme is NOT involved in colony blotting?
A. Lysozyme
B. DNase
C. Alkaline phosphatase
D. Proteinase K
Answer: B
32. Colony blotting is mainly qualitative because it
A. Measures enzyme activity
B. Identifies presence or absence of gene
C. Measures absorbance
D. Separates proteins
Answer: B
33. Which step comes first in colony blotting?
A. Hybridization
B. Detection
C. Growth of colonies
D. Washing
Answer: C
34. What is used to mark colony positions?
A. Ink pen
B. Needle marks
C. Radioisotopes
D. Enzymes
Answer: B
35. Colony blotting is NOT suitable for
A. Recombinant screening
B. Gene library analysis
C. Protein detection
D. Clone selection
Answer: C
36. Which blotting technique detects RNA?
A. Southern
B. Northern
C. Colony
D. Western
Answer: B
37. The probe must be
A. Identical to target
B. Complementary to target
C. Random sequence
D. Protein based
Answer: B
38. Colony blotting helps in
A. DNA sequencing
B. Selecting positive clones
C. Measuring transcription rate
D. Protein folding
Answer: B
39. Which chemical is commonly used for cell lysis?
A. SDS
B. Ethanol
C. Acetone
D. Phenol
Answer: A
40. Colony blotting is a
A. In vivo technique
B. In vitro screening technique
C. Clinical diagnostic test
D. Imaging method
Answer: B
41. The original agar plate is preserved as
A. Replica plate
B. Master plate
C. Control plate
D. Test plate
Answer: B
42. DNA binds to nitrocellulose membrane by
A. Covalent bonds
B. Hydrogen bonds
C. Hydrophobic interactions
D. Electrostatic interactions
Answer: C
43. Colony blotting requires DNA to be
A. Amplified
B. Isolated
C. Immobilized
D. Circular
Answer: C
44. Which method is safer than radioactive labeling?
A. ³²P labeling
B. Biotin labeling
C. Tritium labeling
D. Carbon labeling
Answer: B
45. Colony blotting is commonly used in
A. Biochemistry labs
B. Genetic engineering labs
C. Ecology labs
D. Physics labs
Answer: B
46. Hybridization buffer helps in
A. Cell lysis
B. DNA precipitation
C. Specific probe binding
D. Gel electrophoresis
Answer: C
47. Detection of signal shows
A. Cell death
B. DNA degradation
C. Probe binding
D. Protein expression
Answer: C
48. Colony blotting is performed after
A. PCR
B. Electrophoresis
C. Transformation
D. Sequencing
Answer: C
49. The most common host for colony blotting is
A. Bacillus
B. E. coli
C. Yeast
D. Algae
Answer: B
50. Colony blotting is essential in
A. Cloning experiments
B. Photosynthesis studies
C. Enzyme purification
D. Cell culture
Answer: A









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