Quiz 6 – Analysis And Uses Of Cloned DNA

Explanation
Southern blotting is a method used to transfer DNA fragments from a gel onto a membrane for detection of specific sequences by hybridization. It involves the separation of DNA fragments by gel electrophoresis, followed by transfer onto a membrane and subsequent hybridization with a labeled probe. This technique is commonly used to analyze gene expression, DNA methylation patterns, and to detect genetic mutations. Nothern blotting is used for RNA detection, Western blotting is used for protein detection, and Eastern blotting and Zoo blotting are not valid techniques.

Explanation
The statement is false because nucleic acid molecules are not transferred to a nylon or nitrocellulose membrane after agarose gel electrophoresis. After gel electrophoresis, the nucleic acid molecules are typically stained or visualized using a dye, and then the gel is analyzed directly or further processed for downstream applications such as DNA sequencing or Southern blotting. The transfer of nucleic acid molecules to a membrane is a separate technique called blotting, which is not a step in agarose gel electrophoresis.

Explanation
Northern blots cannot help to identify whether a genomic clone has regions that are transcribed. Northern blots are a laboratory technique used to detect and measure the expression of a specific gene or RNA molecule in a sample. They involve the separation of RNA molecules by size through gel electrophoresis and their subsequent transfer to a membrane for detection using a labeled probe. Therefore, Northern blots can only provide information about the expression of a specific gene or RNA molecule, not the presence of transcribed regions in a genomic clone.

Explanation
The given statement is true. The procedure mentioned involves using hybridisation analysis to test if a nucleic acid probe from one species can hybridize with the DNA fragment of another species. Hybridisation analysis is a technique used to determine the degree of similarity or complementarity between nucleic acid sequences. In this case, the ability of the probe to hybridize with the DNA fragment of another species is being tested, which suggests that the statement is true.

Explanation
Sanger's method, also known as DNA sequencing, does indeed use deoxynucleotides as chain terminators. These chain terminators, also called dideoxynucleotides, lack the 3'-OH group necessary for further DNA chain extension. When incorporated into the growing DNA strand by DNA polymerase, they halt further extension, resulting in the production of a ladder of DNA fragments of different lengths. This ladder can then be analyzed to determine the sequence of the original DNA template. Therefore, the statement is true.

Explanation
The statement is false because the Gilbert chemical method does not involve base-specific cleavage reactions by restriction enzymes. Instead, this method involves the use of chemicals to cleave the DNA at specific sites, allowing for the determination of the DNA sequence.

Explanation
Agarose gel electrophoresis analysis is a commonly used technique in molecular biology that separates DNA fragments based on their size. By running a DNA sample through an agarose gel and applying an electric current, the DNA fragments migrate through the gel at different speeds. This allows scientists to visualize and analyze the DNA fragments, including determining their sequence. Therefore, it is true that agarose gel electrophoresis analysis allows the sequence to be read.

Explanation
Formic acid is a weak acid that can react with nucleic acids, but it does not specifically target pyrimidines (C + T). It can react with both pyrimidines and purines (A + G). Therefore, the statement that formic acid will attack only pyrimidines is false.

Explanation
Formic acid is a weak acid and does not have the ability to attack or react with pyrimidines (C + T). Therefore, the statement that formic acid will attack pyrimidines is false.

Explanation
The Southern blot technique is not used to verify the presence or absence of a specific amino acid sequence in a protein. Instead, it is a molecular biology technique used to detect and analyze specific DNA sequences. It involves the separation of DNA fragments by gel electrophoresis, followed by transfer to a membrane and hybridization with a labeled DNA probe. Therefore, the given statement is false.

Explanation
The Southern blot technique is indeed used to identify the size of the restriction fragment that contains the specific DNA sequence. This method involves the separation of DNA fragments through gel electrophoresis, followed by transferring them onto a membrane and hybridizing with a labeled probe that is complementary to the target sequence. By visualizing the resulting bands, the size of the restriction fragment containing the desired sequence can be determined. Therefore, the given statement is true.

Explanation
A probe is a labelled molecule that is indeed used in hybridization procedures. Hybridization is a process where two complementary strands of DNA or RNA come together to form a double-stranded molecule. Probes are often used to detect specific sequences of DNA or RNA in a sample by binding to the target sequence. The label attached to the probe, such as a fluorescent dye or a radioactive isotope, allows for easy detection and visualization of the target sequence. Therefore, the statement "Probe is a labelled molecule used in hybridisation procedures" is true.

Explanation
The explanation for the given answer, FALSE, is that the Walter Gilbert method, also known as dideoxy sequencing, is not the most commonly used method of DNA sequencing. The most commonly used method of DNA sequencing is the Sanger sequencing method, which was developed by Frederick Sanger and is based on the dideoxy sequencing principle. The Sanger sequencing method is widely used due to its accuracy and reliability, making the statement false.

Explanation
Dideoxy sequencing actually involves the extension of a short DNA primer by DNA polymerase in 4 separate reactions, not by RNA polymerase. Therefore, the given statement is false.

Explanation
A dideoxynucleotide differs from a deoxynucleotide in that it lacks a 3'-OH group on the deoxyribose sugar, rather than having it. This difference is significant because the 3'-OH group is essential for the formation of phosphodiester bonds during DNA synthesis. Dideoxynucleotides are commonly used in DNA sequencing methods, as they lack the 3'-OH group needed for further nucleotide addition, causing chain termination and allowing the determination of the DNA sequence. Therefore, the statement that dideoxynucleotides have a 3'-OH group is incorrect.

Explanation
The absence of a 3'-OH on the dideoxynucleotide prevents the formation of a phosphodiester bond with an incoming DNA nucleotide. This means that when a dideoxynucleotide is incorporated into a growing DNA strand during DNA synthesis, it acts as a chain terminator, preventing further addition of nucleotides and causing synthesis to terminate. Therefore, the statement is true.

Explanation
The statement is false because when a deoxynucleotide is inserted, it actually promotes the elongation of the newly synthesized strand. Deoxynucleotides are the building blocks of DNA, and they are added to the growing DNA strand during replication. This process allows for the continuous elongation of the DNA strand, rather than causing it to stop.

Explanation
The explanation for the answer being FALSE is that in the Southern blot technique, RNA is not isolated and digested with a specific restriction enzyme. Instead, the Southern blot is used to detect and analyze DNA fragments. It involves the isolation of DNA from a sample, digestion of the DNA with restriction enzymes, separation of the digested DNA fragments using gel electrophoresis, transfer of the fragments onto a membrane, and hybridization with a labeled probe to detect specific DNA sequences. Therefore, the statement in the question is incorrect.

Explanation
The statement is false because in the Southern blot technique, it is actually DNA, not RNA, that is transferred from the gel to a nylon filter. The Southern blot is a method used to detect specific DNA sequences in a sample, where the DNA fragments are separated by gel electrophoresis and then transferred to a solid support like a nylon membrane for further analysis.