Basic Primer Design Flashcards
The ? end of a primer should be GC-rich
Select one:
3’
5’
3’
Sequence complementarity within a single primer could result in:
Select one:
- Primer annealing to non-specific locations
* Primer degradation
- Primer dimer formation
- A shift in primer annealing temperature
Primer dimer formation
A sequence of DNA is six nucleotides in length - statistically, based on a random distribution of As, Ts, Cs, and Gs, the probe is likely to find a complementary sequence once in every ? number of nucleotides along a random sequence of nucleotides:
Select one:
24
4096
1296
256
4096
Here is a target sequence in single strand format (the sequence is, of course, double-stranded). What is the sequence of the 18 nt Reverse Primer written in the 5’ to 3’ direction?
5’
atccgtcgaacgagtcgatcggactgagtcgatcgtagatcacacatggctagafctagagacttacgttatatccgtgttaagat‹
tagatogacgagtcgatcgtagatcacacatggctagafctagagacttacgttatatccgtgttaagatgagtcgatcggactgag
cgttatatccgtgttaagatgtgaccagctgcgatcgtagcgatcgagttcgagacctagatcgacgagtcgatcgtagatcacac
3’
Select one:
*agetgagcaagctgecta
atgcaatatacagtatgg
ccatactgtatattgcat
ggtatgacatataacgta
ggtatgacatataacgta
The annealing temperature for primers is set a degree or so below the Tm values
Select one:
True
* False
true
Why does the GC content of a particular DNA molecule affect the melting of the two strands?
Select one:
* Because G and C base-pairing requires three hydrogen bonds and a higher temperature is required to “melt” the DNA.
* The nucleotide content of a DNA molecule is not important to know for biotechnology and molecular biology research.
* The percentage of As and Ts in the molecule is more important to melting temperature than the percentage of Gs and Cs.
* None of the above.
* The G and C bond only requires two hydrogen bonds, thus requiring a lower temperature to “melt” the DNA
Because G and C base-pairing requires three hydrogen bonds and a higher temperature is required to “melt” the DNA
Desirable traits of the forward and reverse primers include all of the following the following EXCEPT:
Select one:
Inability to self-hybridize
- Inability to hybridize with each other
* Inability to anneal anywhere but the target region
* Have similar Tm values
* All of the above are desirable
Inability to anneal anywhere but the target region
Primers should avoid complementarity with stretches of? sequences:
Select one:
* Heteropolymer
* Homopolymer
homopolymer
The annealing temperature of the forward and the reverse primer must be:
Select one:
* At least 5°C distinct from each other
* Highly variable
* Identical
* Similar
similar
Regions containing repeat sequences should be avoided when designing primers
Select one:
* True
*False
True
The Tm value for the following sequence 5’-
GCTTACTCCTCGACTTCCCATATTAGC-3’ is
Select one:
61.70
62.92
63.74
65.86
62.92
