PRIMER DESIGN

Question 1

It is a short nucleotide sequence that is paired with one strand of DNA and provides a free 3’-OH end at which a DN A polymerase starts synthesis of a DNA chain

Answer 1

Primer

Question 2

This is the site where the incoming nucleotide will be added

Answer 2

3’-OH

Question 3

True or False:
DNA polymerase cannot start synthesis without primer

Answer 3

true

Question 4

It is an extremely powerful technique that enables one to amplify fragments of DNA.

Answer 4

Polymerase Chain Reaction

Question 5

Give the 3 types of primers

Answer 5

1. Target-Specific Primers
2. Universal Primer
3. Degenerate Primers

Question 6

It is a type of primer that can anneal only to the templates from one species

Answer 6

Target-specific primer

Question 7

It is used when the DNA sequence is known. It also amplifies only the intended target and will not anneal to those areas other than the
target.

Answer 7

Target-specific primer

Question 8

the primers do not have matches to other targets.

Answer 8

Target-Specific Primers

Question 9

A type of primer that consists of a single sequence used for the amplification of a similar gene related to a specific genus.

Answer 9

Universal Primer

Question 10

This can amplify several targets

Answer 10

Universal Primers

Question 11

This gene is highly conserved across different species, and has very low evolution rate.

Answer 11

16srRNA

Question 12

This type of primer is a mix or series of primers in which some positions have several possible bases.

Answer 12

Degenerate Primers

Question 13

It is usually the ______ and ______ nucleotides are degenerate

Answer 13

Seventh and twelfth

Question 14

Most commonly used software in primer designing

Answer 14

Primer3 and primerBLAST

Question 15

A characteristics of a good primer that affects both its specificity and the annealing temperature

Answer 15

Primer Length

Question 16

optimal size of primer length

Answer 16

18-25 nucleotides

Question 17

Ideal primer should be?

Answer 17

50% to 60% GC

Question 18

It is the midpoint of temperature over which the DNA is denature

Answer 18

Melting temperature (Tm)

Question 19

It is critical in determining the Annealing Temperature (Ta)

Answer 19

Melting temperature (Tm)

Question 20

This range of melting temperature generally produce the best results

Answer 20

52-58°C

Question 21

True or False:
The annealing temperature should be 5°C lower than the Tm

Answer 21

True

Question 22

it contains different temperature gradients

Answer 22

Gradient PCR machine