Your lab was asked to recommend the best treatment for the patient with a urinary tract infection.  Based on the sequencing results, the resistance that was observed against the β-lactam antibiotic amoxicillin likely results from the production of a β-lactamase, an enzyme that degrades β-lactams. However, it is still possible to use β-lactam antibiotics to treat infections caused by bacteria that produce β-lactamases. Some β-lactam antibiotics cannot be degraded very easily by β-lactamases. In addition, β-lactam antibiotics are often co-prescribed with β-lactamase inhibitors, drugs that interfere with β-lactamases and protect β-lactams. Therefore, to identify the best treatment for this bacterial infection, further characterization of the β-lactamase enzyme is needed.  A recombinant form of the β-lactamase can be produced in a lab strain of Escherichia coli. This enzyme can then be purified, and its activity and inhibition tested using in vitro enzyme assays.  To generate the recombinant β-lactamase, the gene for the β-lactamase must be cloned into an expression vector. This first step in this cloning experiment is to amplify the full gene sequence that encodes this enzyme using the polymerase chain reaction (PCR).  Now, design primers to amplify the gene that encodes for the β-lactamase. You should use a Tm calculator (preferably, http://tmcalculator.neb.com/ a free tool; with default settings) when designing these primers, and the Tm values for both primers should be close to 65 °C.  The nucleotide sequence of the gene is:  > resistance gene  ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATT  ATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGT  TGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTG  CTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAA  CGGGCGAACCAAGCATTTTTACCCGCATCTAGTGCGAAAATTCCC  AATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACAC  CAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGG  AATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTG  CCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATG  AGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCG  GGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCG  GCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAG  TTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATG  CTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGA  TACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGAT  GATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCG  GATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAA  CAGGAAAAAATTATTCCCTAG  What are the nucleotide sequences of your forward and reverse primers? Make sure to write out the nucleotide sequences from 5ʹ to 3ʹ, and make sure that your primers amplify the entire sequence shown above, including the start codon and the stop codon.

Basic Clinical Laboratory Techniques 6E
6th Edition
ISBN:9781133893943
Author:ESTRIDGE
Publisher:ESTRIDGE
Chapter6: Basic Clinical Chemistry
Section6.1: Introduction To Clinical Chemistry
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Your lab was asked to recommend the best treatment for the patient with a urinary tract infection. 

Based on the sequencing results, the resistance that was observed against the β-lactam antibiotic amoxicillin likely results from the production of a β-lactamase, an enzyme that degrades β-lactams. However, it is still possible to use β-lactam antibiotics to treat infections caused by bacteria that produce β-lactamases. Some β-lactam antibiotics cannot be degraded very easily by β-lactamases. In addition, β-lactam antibiotics are often co-prescribed with β-lactamase inhibitors, drugs that interfere with β-lactamases and protect β-lactams. Therefore, to identify the best treatment for this bacterial infection, further characterization of the β-lactamase enzyme is needed. 

A recombinant form of the β-lactamase can be produced in a lab strain of Escherichia coli. This enzyme can then be purified, and its activity and inhibition tested using in vitro enzyme assays. 

To generate the recombinant β-lactamase, the gene for the β-lactamase must be cloned into an expression vector. This first step in this cloning experiment is to amplify the full gene sequence that encodes this enzyme using the polymerase chain reaction (PCR). 

Now, design primers to amplify the gene that encodes for the β-lactamase. You should use a Tm calculator (preferably, http://tmcalculator.neb.com/ a free tool; with default settings) when designing these primers, and the Tm values for both primers should be close to 65 °C. 

The nucleotide sequence of the gene is: 

> resistance gene 
ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATT 
ATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGT 
TGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTG 
CTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAA 
CGGGCGAACCAAGCATTTTTACCCGCATCTAGTGCGAAAATTCCC 
AATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACAC 
CAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGG 
AATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTG 
CCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATG 
AGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCG 
GGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCG 
GCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAG 
TTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATG 
CTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGA 
TACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGAT 
GATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCG 
GATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAA 
CAGGAAAAAATTATTCCCTAG 

What are the nucleotide sequences of your forward and reverse primers? Make sure to write out the nucleotide sequences from 5ʹ to 3ʹ, and make sure that your primers amplify the entire sequence shown above, including the start codon and the stop codon. 

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