The shotgun sequencing method is used to generate the following sequences: Fragment 1: ATGCT, Fragment 2: AGCATGC, Fragment 3: TGCTGCA. a ATGCTAGCATGCTGCTGCA b TGCTGCAATGCT c ATGC d AGCATGCTGCA

The underlined regions in the following sequence indicate the annealing sites of two primers to be used in a polymerase chain reaction. 5’CCGGTGCTGCAATGCTTTTTAGACGGCTTGCTGTCCGCCTTATCCACATGACTCTCGGCA ACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGAAT TGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCATTCGGCC GAGGGCACGCCTGCCTGGGCGTCACGCAAAACACGCTCCCAACCCCCCTCATCGGGGAG CGGGATGCGGCATGTGGCTTTCCGTCACGCAAGTGGCGGTGGGCCGAAGATATGGCTGC CGGCGTGGTGGGCGTCATCGCTTTGTATCGTGCCGGACACAGCG 3’

Which of the following primer pairs should be used to amplify this sequence of DNA? Explain your answer. (2 points)

A. 5’ CCGGTGCTGCAATGCTTTTTA 3’ and 5’ TGTATCGTGCCGGACACAGCG 3’

B. 5’ CCGGTGCTGCAATGCTTTTTA 3’ and 5’GCGACACAGGCCGTGCTATGT 3’

C. 5’ ATTTTTCGTAACGTCGTGGCC 3’ and 5’ TGTATCGTGCCGGACACAGCG 3’

D. 5’ CGCTGTGTCCGGCACGATACA 3’and 5’ CCGGTGCTGCAATGCTTTTTA 3’

How can I change this nucleotide sequence?

----TAGCCCTCAAGCAGCTGCAaTGCTAGCTACG—

I need the change of “a” to “G” with what I learned in regulatory RNA.

And what is the cellular mechanism to be used for such substitution?

Please answer the following genetics question:

1.) The following is a partial coding sequence (only 360 bp) of the “high affinity nitrate transporter” protein in wheat. Design both (a) forward and (b) reverse primer (each 20 bp long) that are capable of amplifying the entire 360 bp segment.

ATGGAGGTGCAGGCCGGCTCTCATGCCGACGCCGCGGCGAGCAAGTTCACGCTGCCGGTGGACTCCGAGCACAAGGCCAAGTCCTTCAGGCTCTTCTCCTTCGCCAACCCCCACATGCGCACCTTTCACCTCTCGTGGATCTCCTTCTTCACCTGCTTCGTCTCCACCTTTGCTGCGGCGCCCCTCGTGCCCATCATCCGCGACAACCTCAACCTTGCCAAGGCTGACATCGGCAATGCCGGTGTCGCGTCCGTGTCTGGGTCCATCTTCTCCAGGCTGGCCATGGGCGCTATCTGTGACTTGCTTGGCCCACGGTATGGTTGTGCCTTCCTCGTCATGCTCTCGGCACCGACCGTCTTC

2.) The following represents a 600 bp portion of the coding sequence of the “high affinity nitrate transporter” protein in wheat. Two primers as shown in the table are used in a successful PCR.

a. What DNA fragment size should we expect from this primer pair and this template?

TGCTGCGGCGCCCCTCGTGCCCATCATCCGCGACAACCTCAACCTTGCCAAGGCTGACATCGGCAATGCCGGTGTCGCGTCCGTGTCTGGGTCCATCTTCTCCAGGCTGGCCATGGGCGCTATCTGTGACTTGCTTGGCCCACGGTATGGTTGTGCCTTCCTCGTCATGCTCTCGGCACCGACCGTCTTCTGCATGGCCGTCATCGATGATGCCTCAGGGTACATCGCCGTCCGGTTCCTCATTGGCTTCTCCCTCGCCACCTTCGTGTCATGCCAATACTGGATGAGCACCATGTTCAATAGCAAGATCATTGGCACGGTCAATGGCTTGGCTGCAGGCTGGGGCAACATGGGTGGCGGCGCCACGCAGCTCATCATGCCGCTTGTCTTCCACGCAATCCAGAAGTGTGGCGCCACGCCCTTCGTGGCATGGCGTATTGCCTACTTCGTGCCGGGAATGATGCACATCGTGATGGGCTTGCTGGTCCTCACCATGGGGCAAGATCTCCCTGACGGGAACCTTGCGAGCCTCCARAAGAAGGGAGACATGGCCAAGGACAAGTTCTCCAAGGTCCTTTGGGGCGCYGTCACCAACTACCG

b. What is your explanation if—besides the true DNA fragment—we also see other DNA fragments as a result of this PCR reaction (For instance, we see bands at 500 bp and 2300 bp)?