148. A 30 Kb candidate gene linked to prostate cancer from a patient was digested with XhoI. Following Southern
hybridization of the digested products with the full-length gene probe, three bands of 15, 10 and 5 Kb sizes
were obtained. However, an identical experiment in normal individuals gave a 15 Kb fragment. This could be
due to:
1. Presence of SNP in the candidate gene
2. Deletion of a fragment of DNA from the candidate gene
3. The probe could not identify the 10 and 5 Kb fragments
4. The probe could only identify the 15 Kb fragment

Question

A 30 Kb candidate gene linked to prostate cancer from a patient was digested with XhoI. Following Southern hybridization of the digested products with the full-length gene probe, three bands of 15, 10, and 5 Kb sizes were obtained. However, an identical experiment in normal individuals gave a 15 Kb fragment. This could be due to:

1. Presence of SNP in the candidate gene

2. Deletion of a fragment of DNA from the candidate gene

3. The probe could not identify the 10 and 5 Kb fragments

4. The probe could only identify the 15 Kb fragment

Detailed Explanation

In this case, Southern blotting has been used to analyze the digestion pattern of a candidate gene linked to prostate cancer. The analysis compares the gene’s behavior in a patient with prostate cancer and a normal individual. Let’s break down the possible explanations for the different results.

Southern Hybridization and XhoI Digestion

• The Southern blotting technique is a molecular biology method used to detect specific sequences of DNA. After digestion with a restriction enzyme (XhoI, in this case), the DNA fragments are separated by size, transferred to a membrane, and then probed with a labeled DNA probe that binds to the target sequence.

• The normal individual produces a single 15 Kb fragment, while the patient with prostate cancer shows three bands of sizes 15 Kb, 10 Kb, and 5 Kb.

Possible Explanations

1. Presence of SNP in the Candidate Gene:

   • SNPs (single nucleotide polymorphisms) can cause variations in the restriction enzyme recognition sites. However, this would typically result in a change in the pattern or size of the bands, but not a complete absence of bands as seen here in the normal individual’s result (only a 15 Kb band).

   • This is unlikely to explain the results.

2. Deletion of a Fragment of DNA from the Candidate Gene:

   • A deletion in the gene could cause the patient’s DNA to produce additional fragments that are not present in the normal individual. For example, if the patient has a deletion between the 10 Kb and 5 Kb regions of the gene, it could result in fragments of 10 Kb and 5 Kb being missing in the normal individual’s DNA.

   • This seems likely, as it could explain why the normal individual’s digestion yields only a 15 Kb fragment, whereas the patient’s DNA produces fragments of 15 Kb, 10 Kb, and 5 Kb, suggesting a loss of a fragment.

3. The Probe Could Not Identify the 10 and 5 Kb Fragments:

   • If the probe used in the hybridization experiment were unable to detect the 10 Kb and 5 Kb fragments, it could explain why only the 15 Kb fragment is observed in the normal individual. However, this would not explain the presence of the 10 Kb and 5 Kb bands in the patient’s DNA.

   • This is unlikely because it would not explain the full profile of bands in the patient’s DNA.

4. The Probe Could Only Identify the 15 Kb Fragment:

   • This option suggests that the probe specifically recognizes only the 15 Kb fragment, which would explain why only the 15 Kb band is observed in both the normal and patient samples. However, if the 10 Kb and 5 Kb bands were present in the patient’s sample but were not visible due to the probe’s limitations, it would not account for the observed differences between the patient and normal individual.

   • This is unlikely because the 10 Kb and 5 Kb fragments should be detected by the probe if they are present.

Answer

The most likely explanation for the observed results is:

2. Deletion of a fragment of DNA from the candidate gene

This could explain why the normal individual only has a single 15 Kb fragment, whereas the patient has three fragments, with the difference indicating a deletion in the patient’s candidate gene.

Conclusion

In molecular genetics, Southern hybridization provides critical insights into genetic variations. The difference in the digestion pattern of the candidate gene between a patient with prostate cancer and a normal individual suggests a deletion in the patient’s gene. The deletion leads to missing fragments in the patient’s DNA, which is detected as additional bands during the hybridization process. This highlights the power of Southern blotting in identifying structural changes in genes that may be linked to diseases like prostate cancer.