Primer Design Using Primer3 Software
18 Questions
0 Views

Choose a study mode

Play Quiz
Study Flashcards
Spaced Repetition
Chat to lesson

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What is the optimal amplicon size for the product size range?

  • ~120 bp (correct)
  • 70-200 bp, 80-150 bp
  • 70-200 bp
  • 80-150 bp
  • What is the acceptable range for primer size according to the text?

  • 15-25 bp
  • 16-24 bp
  • 18-28 bp (correct)
  • 20-30 bp
  • What is the optimal primer Tm (melting temperature) value mentioned in the text?

  • 60°C (correct)
  • 63°C
  • 59°C
  • 57°C
  • What is the maximum allowable Tm difference between the forward and reverse primers according to the text?

    <p>3°C</p> Signup and view all the answers

    What is the optimal GC% (guanine-cytosine content) range for primers mentioned in the text?

    <p>50-60%</p> Signup and view all the answers

    What is the recommended setting for 'Max 3' Self complementarity'?

    <p>0</p> Signup and view all the answers

    What is the primary purpose of the Primer3 software?

    <p>To design primers for PCR amplification</p> Signup and view all the answers

    Which database is mentioned in the text for retrieving rat gene sequences?

    <p>Rat Genome Database (RGD)</p> Signup and view all the answers

    What is the recommended approach for providing the target sequence to Primer3?

    <p>Save the sequence as a text file and upload it to Primer3</p> Signup and view all the answers

    Which species are supported by the Rat Genome Database (RGD) according to the text?

    <p>Rat, Mouse, Human, and Chinchilla</p> Signup and view all the answers

    What is the purpose of copying the nucleotide sequence from the Rat Genome Database to the NCBI GenBank?

    <p>To obtain additional annotations and features</p> Signup and view all the answers

    Which of the following steps is not mentioned in the text for primer design using Primer3?

    <p>Adjusting parameters for primer design in the Primer3 interface</p> Signup and view all the answers

    What should be avoided in the 3' end of a primer to prevent primer-dimer formation?

    <p>Repeated runs of 3 or more Cs or Gs</p> Signup and view all the answers

    Why is it mentioned to increase the primer setting by 1 if no primers are returned?

    <p>To get primers</p> Signup and view all the answers

    Which action should be taken after selecting the primers for testing?

    <p>Running BLAST and checking for Query coverage</p> Signup and view all the answers

    What could promoting mispriming at C or C-rich sequences potentially result in?

    <p>Primer-dimer formation</p> Signup and view all the answers

    Why is it important to check the E-value after running BLAST on the primers?

    <p>To assess the accuracy of the primer sequence alignment</p> Signup and view all the answers

    What should be done if there are no results after setting the value to 1 during primer selection?

    <p>Increase the value by an increment of 1</p> Signup and view all the answers

    More Like This

    Mastering Primer Design
    5 questions

    Mastering Primer Design

    CourteousEpiphany avatar
    CourteousEpiphany
    PCR Primer Design and Thermodynamics
    24 questions
    Use Quizgecko on...
    Browser
    Browser