Primer Design Exercise PCR primers must be complementary and anti-parallel to your sequence of interest. Two primers are used, one for each strand of DNA. Design primers 18-22 nt long to amplify the segment of DNA below. Indicate the 5' and 3' ends of your primers. For the sake of simplicity, only the coding strand of the DNA is shown below. The segment indicated as --- represents an internal sequence, 500 nt long. 5' A C A T G A G G G C T T G A C T G C T G C---G G T A T C C T A C G G T A A A G C T A T 3' Forward Primer : Reverse Primer :
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We need to design two primers: one for the forward strand (coding strand) and one for the reverse strand (template strand). The primers should be complementary and anti-parallel to the target sequence. Show more…
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3. Primer Design You are analyzing the region of DNA shown below to determine how many AATG repeats are present. To do so, you must amplify the entire region of AATG repeats. Design primers of 16 bases each so they anneal outside the region of interest. More than one primer pair is possible, but just give one. 5′-ACTGGCACAGAACAGGCACTTAGGAATGAATGAATGAATGAATGAATGAATGACCTGTGTGGTTCCCAGTTCCTCC-3′ 3′-TGACCGTGTCTTGTCCGTGAATCCTTACTTACTTACTTACTTACTTACTTACTGGACACACCAAGGGTCAAGGAGG-5′ a. Primer 1: Primer 2: b. Highlight the repeats in yellow. c. How many repeats of the AATG sequence are there? 4. PCR Product size You use the primers below in a PCR with the DNA in question 3 above. 5'-CTGGCACAGAACAGGCACTT -3' and 3'-ACACACCAAGGGTCAAGGAG -5' a. How long (in base pairs) will the PCR product be? b. How long would the PCR product be if there were 5 repeats? What about if there were 10 repeats?
Josee P.
Design PCR primers 15-20 nucleotides (nt) long to amplify the segment of DNA below. Indicate the 5' and 3' ends of your primers. For the sake of simplicity, only the coding strand of the DNA is shown below. The segment indicated as ------ represents an internal sequence, 300 nt long: 5' GAGAACATTAGGACGAGTACACT-----TGTATCCTCATAGTATCTCAGTATGT 3' Forward Primer: Reverse Primer:
Nibaal K.
Choose two primers that can be used to PCR-amplify the bold portion of the DNA segment shown below (no more and no less). All primer sequences are in the 5'-> 3' direction. 5'-ATGTGTGATCTAAACGTAGCCGGATACGTATACTCGCATTAGTAAACTGT-3' 3'-TACACACTAGATTTGCATCGGCCTATGCATATGAGCGTAATCATTTGACA-5' primer #1: AAATCTA primer #2: ATCTAAA primer #3: GTAATCA primer #4: TGATTAC primer #5: ACTAATG primer #6: CATTAGT primer #7: TAGATTT primer #8: TTTAGAT primer #9: ATGTGTG primer #10: GTGTGTA primer #11: TACACAC primer #12: CACACAT primer #13: AAACTGT primer #14: TGTCAAA primer #15: TTTGACA primer #16: ACAGTTT
Madhur L.
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