1. Which of the following is favoured for primer design?
a) The melting temperature should be different for both the primers
b) Primers should be long in length
c) Primers should not be complementary to each other
d) Matching should be of whole primer to the template
Explanation: Primers should not be complementary to each other. It is so because if they are complementary, primer dimer formation takes place. If primer dimer is formed, proper elongation won’t be taking place.
2. What will happen if the amino acid sequence is used directly for primer designing?
a) There would be certainty because the genetic code is unique for each amino acid
b) There would be uncertainty as the genetic code is degenerate and none of the amino acid is having a unique code
c) There would be uncertainty as the genetic code is degenerate but some of the amino acids such as methionine are having a unique codon
d) The amount of uncertainty or certainty is a matter of chance
Explanation: If the amino acid sequence is used directly, there would be uncertainty. It is so because the genetic code is degenerate. It means that one codon can correspond to many amino acids. There are some exceptions such as methionine which are having a unique codon
3. In the case of uncertainty, if more than one nucleotide is included at a position it is called ____________
a) mixed site
b) polynucleotide site
c) unique site
d) degenerate site
Explanation: If uncertainty is there at times, more than one nucleotide can be included in one position. And in this condition it is called a mixed site.
4. What is the property of inosine?
a) Having narrow range of pairing capabilities
b) Having a broad range of pairing capabilities
c) The pairing capability is the same as the normal nucleotides
d) It is abbreviated as A
Explanation: It is having a broad range of pairing capabilities and thus can be used in order to have less amount of uncertainty
5. Which of the statement holds for long-range PCR and in its relation?
a) It is the PCR in which longer templates are used
b) DNA polymerases which don’t have proof-reading activity give larger products
c) DNA polymerases’ processivity is not a measure to have larger products
d) It is PCR in which a mixture of enzymes is used to have larger products
Explanation: Long range PCR is the PCR in which a mixture of enzymes is used to have larger products. If DNA polymerases are having proof reading activity then we can obtain larger products because in this case chain terminators are not used. Also, the processivity of the enzymes is also very important.
6. Which of the following conditions don’t contribute to wrong annealing to primer?
a) Chance complementarity
b) Conditions of annealing
c) The original sequence of the primers
d) Both the conditions of annealing and the original sequence don’t play any role
Explanation: There are cases when wrong annealing of the primer takes place. It can happen because of chance complementarity, conditions of annealing such as ionic concentration and temperature. The original sequence of the primers is very important
7. How can the specificity of primer annealing be increased?
a) Use of short primers
b) Raising temperature
c) Adjusting the concentration of sodium ions
d) Using polymerase with proof reading activity
Explanation: The specificity of primers annealing can be increased in various ways such as increasing temperature, using long primers. If long primers are used there are increased chances of having correct matching. Also, if the magnesium ion concentration is adjusted, annealing can be done more effectively. It is so because they stabilize primer-template binding.
8. There are basically two types of contamination, laboratory and external. If a PCR product is found to be contaminated by bacteria. It comes under laboratory contamination.
a) True
b) False
Explanation: Laboratory contamination consists of aerosols in pipettes from previously formed PCR products or related DNA sequences. External contamination includes contamination from bacteria, fungi and other human contamination.
9. Which can be used as a precaution in order to minimize contamination?
a) Careful use and design of pipettes
b) Placing the pre-PCR and post-PCR stages in the same rooms
c) Extracting the DNA along with surface layers
d) Use of primers carefully is not very important
Explanation: Pipettes are very important in minimizing contamination. Thus they should be designed and used carefully. The pre-PCR and post-PCR stages should be places in separate rooms. While extraction of DNA surface layers should be removed because they might be containing bacteria. Sometimes the use of species specific primers is also very important, thus they should be used carefully.
10. During amplification, there are chances of having a product of a mixture of different sequences. There are various ways to detect it. Which of the statement is true in regard to it?
a) Direct sequencing can’t be used in the case if the template DNA is heterozygous at the locus
b) Direct sequencing can be used if the template DNA is heterozygous at the locus
c) If cloning is done before sequencing, then it is detected via using only a single clone for sequencing
d) In the case several recombinants are used, it can’t go undetected
Explanation: If the template DNA is heterozygous at the locus, it can be detected via using direct sequencing. It is so because it would give rise to two different signals at the same nucleotide position at the sequence output. If the cloning is done before sequencing, a single clone won’t be helpful to detect heterogeneity. It is because single clones are derived from a single PCR product. Also, if several recombinants are used, there are chances that they go undetected.