Selecting Primers for DNA Amplification

Selecting Primers for DNA Amplification

 

Choose the pair of primers that will allow amplification of the DNA sequence both two given structures the DNA ?
5’GACCTGTGGAAGC…………..CATACGGGATTGA3′
3’CTGGACACCTTCG……………GTATGCCCTAACT5′
1. 5’GACCTGTGGAAGC3′
2. 5’CTGGACACCTTCG3′
3. 5’CATACGGGATTGA3′
4. 5’TCAATCCCGTATG3′

(a) 1 and 2
(b) 1 and 3
(c) 1 and 4
(d) 2 and 3

The correct answer is (c) 1 and 4.


Correct Answer: (c) 1 and 4

Explanation:

To successfully amplify a DNA sequence using PCR (Polymerase Chain Reaction), the following conditions must be met:

  1. Primers must be complementary to the flanking sequences of the target DNA.
  2. One primer should bind to the 5′ to 3′ strand of the target DNA, and the other should bind to the 3′ to 5′ strand.
  3. DNA synthesis occurs in the 5′ to 3′ direction, so the primers should be oriented toward each other.

Given DNA Sequence:

5’GACCTGTGGAAGC…………..CATACGGGATTGA3′
3’CTGGACACCTTCG……………GTATGCCCTAACT5′


Primer Pair Selection:

  1. Primer 1: 5'GACCTGTGGAAGC3' → Matches the 5′ end of the sense strand → Acts as the forward primer.
  2. Primer 4: 5'TCAATCCCGTATG3' → Reverse complement of the antisense strand at the 3′ end → Acts as the reverse primer.

Why Other Options Are Incorrect:

Option Explanation Correct/Incorrect
(a) 1 and 2 Both primers are oriented in the same direction → No amplification. ❌ Incorrect
(b) 1 and 3 Primer 3 is in the wrong orientation for binding to the template strand. ❌ Incorrect
(c) 1 and 4 Correct orientation and complementarity for DNA amplification. ✅ Correct
(d) 2 and 3 Primer 2 is oriented in the wrong direction. ❌ Incorrect

How PCR Works with the Correct Primers:

  1. Denaturation: Double-stranded DNA is heated to separate the strands.
  2. Annealing:
    • Primer 1 binds to the 5′ end of the sense strand.
    • Primer 4 binds to the 3′ end of the antisense strand.
  3. Extension: DNA polymerase extends both primers, synthesizing complementary DNA strands.

Primer Orientation and Complementarity:

Primer Sequence Binding Strand Function
Primer 1 5’GACCTGTGGAAGC3′ Sense strand (5′ → 3′) Forward Primer
Primer 4 5’TCAATCCCGTATG3′ Antisense strand (3′ → 5′) Reverse Primer

Applications of PCR-Based Amplification:

1. Molecular Cloning

  • Amplify target genes for insertion into plasmids.

2. Mutation Analysis

  • Detect and analyze genetic mutations.

3. Pathogen Detection

  • Identify bacteria and viruses using gene-specific primers.

4. Genetic Fingerprinting

  • Amplify and analyze variable DNA regions for forensic studies.

Summary:

  • The correct primer pair for successful amplification of the DNA sequence is Primer 1 and Primer 4.
  • Primer 1 binds to the 5′ end of the sense strand, and Primer 4 binds to the 3′ end of the antisense strand — enabling successful PCR amplification.
89 Comments
  • shivani meena
    March 16, 2025

    done

  • Akshay mahawar
    March 17, 2025

    Done 👍

    • Shobha sharma
      August 30, 2025

      Option c
      1 and 4

  • Suman bhakar
    March 20, 2025

    Done

  • Parul
    March 23, 2025

    Done sir

  • Ujjwal
    March 26, 2025

    Done sir

  • Anita Choudhary
    April 19, 2025

    Done

  • Roopal Sharma
    August 23, 2025

    There are two types of primers forward primer and reverse primer . Primer 1 and 4 are correct set of primer

    • Varsha Tatla
      August 24, 2025

      Easily clear

  • Diksha Chhipa
    August 23, 2025

    5prime seq is always same of dna seq nd 3 prime primer seq is complementary to 3prime

  • Khushi Pareek
    August 23, 2025

    1&4

    • Mahima Sharma
      August 24, 2025

      1 and 4th

  • Neha Yadav
    August 24, 2025

    Primer that are allow amplification of dna sequence are : 1 5′ GACCTGTGGAAGC 3′ ( Primer 1 always same as a 5′ sed of dna )
    2. 3′ GTATGCCCTAACT 5′ ( Read always 5′ to 3′ and its always complementary sequence of 3′ prime dna sequence )

  • Soniya Shekhawat
    August 24, 2025

    Forward primer binds at 5’to 3′ and reverse primer binds at 3’to 5’so `1 and 4 is correct option.

  • Santosh Saini
    August 24, 2025

    5’GACCTGTGGAAGC3′ , 5’TCAATCCCGTATG3′ SO primer 1st and 4th would be perfect, so option C is correct

  • Mohd juber Ali
    August 24, 2025

    Option (c) 1 &4
    5′ end primer same
    3′ end ka complementary use krte h (direction 5′ to 3′ )

  • Aafreen Khan
    August 24, 2025

    Primers must be complementary to the sequences of the target DNA.
    Primer 1 is 5’GACCTGTGGAAGC3′
    Primer 2 is 5’TCAATCCCGTATG3′

  • Priya dhakad
    August 24, 2025

    Primer 1 is 5’GACCTGTGGAAGC3′ Sense strand (5′ → 3′)
    Primer 4 5’TCAATCCCGTATG3′ Antisense strand (3′ → 5′) so option c is correct

    • Asha Gurzzar
      August 30, 2025

      Option c is correct because primer must be complementary of the target dna sequence

  • HIMANI FAUJDAR
    August 24, 2025

    Ans correct answer is 1 and 4 Two types of primer which is forward and reverse primer
    Primer 1 -Same as 5’end sequence
    Primer 2- complimentary to the 3′ end and read as 5′-3′ end.

  • Anurag Giri
    August 24, 2025

    5’ end primer directly used and 3’ end strand complimaetry use as primer so
    5’GACCTGTGGAAGC3′ And 5’TCAATCCCGTATG3

  • Sakshi yadav
    August 24, 2025

    Option c primer 1 5’GACCTGTGGAAGC3′
    Primer 2 is 5’TCAATCCCGTATG3′

  • Rakesh Dhaka
    August 24, 2025

    5′ end us ase same and 3′ end complimentary use karte h so ans is . option 3

  • Avni
    August 24, 2025

    Primer 1 : 5’GACCTGTGGAAGC3′ → Sense strand (5′ → 3′)
    Primer 2 : 5’TCAATCCCGTATG3′ → Antisense strand (3′ → 5′)

  • Arushi Saini
    August 24, 2025

    5’ end directly used as a primer and another is complimentory to the DNA strand

  • Mansukh Kapoor
    August 24, 2025

    The correct answer is option 3rd (1st and 4th)
    P1 is the same as the 5′
    P2 is the complementary of the 3′

  • karishma don
    August 24, 2025

    ans is 1 and 4 as 1 is forward primer and 4 is reverse primer of 1st dna

  • Khushi Agarwal
    August 24, 2025

    1,4 is correct here
    On 5′ same sequence use a primer and on 3′ complementary to sequence

  • Surbhi Rajawat
    August 24, 2025

    Answer is D because for primer designing from DNA strand. We take the 5 prime end sequence as it as. And for the next primer we take complimentary sequence of 3 prime end

  • Aakanksha Sharma
    August 24, 2025

    Option C 1&4

  • Dharmpal Swami
    August 24, 2025

    For amplification of dna two primers are required
    First obtain by 5’end of target dna
    Second obtain by 3’end of complementary dna sequences

    • Niti Tanwar
      August 24, 2025

      1,4 right answer
      5′ per same sequence
      3′ per complementary sequence

  • Yashika Choudhary
    August 24, 2025

    Primer5 to 3 synthesis

  • Dipti Sharma
    August 24, 2025

    Correct answer is c 1 and 4 bcz
    One primer at 5′ end is directly used as primer and the other at 3′ end must be complementary.

  • Priyanka Choudhary
    August 24, 2025

    Correct answer is option c, because of this
    P1 is the same as the 5′
    P2 is the complementary of the 3′

  • Aman Choudhary
    August 24, 2025

    Option C is correct
    5′ end primer is directly use and the other 3′ end primer is complementary

  • Payal Gaur
    August 24, 2025

    1 and 4

  • Sneha Kumawat
    August 24, 2025

    5’GACCTGTGGAAGC3′ ( PRIMER 1 always same as 5 ‘end of primer
    3’GTATGCCCTAACT5′ ( Read always 5’to3′ and it’s always complementary sequence.of 3’prime dna sequence. (5’TCAATCCCGTATG 3’)

  • Karishma
    August 24, 2025

    1 and 4 is right answer .. 5 prime end nueotide is use as a primer.. and 3 prime end ka complimantry sequence .. primer ki trh use hota h

  • Karishma
    August 24, 2025

    1 and 4 is right answer

  • Shrddha Modi
    August 24, 2025

    Option a

  • Sheikh Aleen
    August 24, 2025

    Option C -Primer 1 binds to the 5′ end of the sense strand and Primer 4 binds to the 3′ end of the antisense strand.

  • Divya rani
    August 24, 2025

    C is the answer because we take 5′ end sequence as it is as 1st primer and for 2nd primer we take complementary sequence of the 3′ end but read it in the 5′-3′ direction.

  • AKANKSHA RAJPUT
    August 24, 2025

    1,4 is correct here
    On 5′ same sequence use a primer and on 3′ complementary to sequence

  • Heena
    August 24, 2025

    There are two primers used ,one of which is forward primer i.e used as it is and other is reverse primer that’s complementary to 3’end

  • Heena Mahlawat
    August 24, 2025

    1 and 4

  • Tanvi Panwar
    August 24, 2025

    Option C is correct that is 1 and 4. First primer is Designed directly by 5’end sequence and second primer is complimentary to the 3’end sequence.

  • Neelam Sharma
    August 24, 2025

    1 and 4

  • Simran Saini
    August 24, 2025

    1 and 4.
    5’GACCTGTGGAAGC3′
    5’TCAATCCCGTATG3′

  • MOHIT AKHAND
    August 24, 2025

    Done sir ✅

  • anjani sharma
    August 24, 2025

    Answer c
    5′ is used directly as primer while 3′ end is used complementary

  • Ayush Dubey
    August 24, 2025

    1 and 4.

  • Sakshi Kanwar
    August 24, 2025

    1 and 4
    As 1st primer will be same as 5′ end and act as the forward primer.
    And 2nd primer will be complementary to 3′ end as the reverse primer.

  • Bhawna Choudhary
    August 24, 2025

    Correct answer is 1 nd 4 bcz
    One primer at 5′ end is directly used as primer and the second at 3′ end must be complementary to seq.

  • Priyanka Verma
    August 24, 2025

    correct answer is 1 and 4
    First primer is Designed directly by 5’end sequence and second primer is complimentary to the 3’end sequence.

  • Bharti Yadav
    August 24, 2025

    1 and 4 is correct
    5’ same sequence directly use as primer
    3′ should be complimentary sequence

  • Minal Sethi
    August 24, 2025

    1 and 4
    1 is the forward primer of first sequence and 4th is the reverse primer of first sequence

  • Priti khandal
    August 25, 2025

    1 and 4 is right
    5 ‘ same sequence directly use as a primer and 3’ complimentary sequence

  • shruti sharma
    August 25, 2025

    1 and 4
    5 prime use directly use as sequence
    3 should be complementary

  • Divya Mandhania
    August 25, 2025

    Option c primer 1 5’GACCTGTGGAAGC3′
    Primer 2 is 5’TCAATCCCGTATG3′

  • Mitali saini
    August 25, 2025

    The correct answer is (c) 1 and 4.

  • Vanshika Sharma
    August 25, 2025

    Ans is c bcz 1 and 4 is work as forward and reverse primers

  • Surendra Doodi
    August 25, 2025

    5 prime end direct use as primer and 3 prime end complimentary sequence use as primer

  • Bhavana kankhedia
    August 26, 2025

    1 and 4

  • Bhavana kankhedia
    August 26, 2025

    1 and 4 is right answer

  • Nilofar Khan
    August 26, 2025

    Correct answer is c
    1.5’GACCTGTGGAAGC3′
    4. 5’TCAATCCCGTATG3′

  • Manisha
    August 26, 2025

    Forward and backward primers are used

  • Devika
    August 26, 2025

    1and 4 is correct Best Institute for CSIR NET Life Science Coaching – Let’s Talk Academy”

  • Rishita
    August 26, 2025

    Done

  • Mohini
    August 27, 2025

    C) 1 and 4

  • Neeraj Sharma
    August 28, 2025

    Option C is correct

  • Kanica Sunwalka
    August 28, 2025

    5’end used as a primer
    3’end ka complementary krdo and read it as 5′-3′

  • Kajal
    August 28, 2025

    Option c is correct answer as 5end directly work as primer and 3rd end is complementary

  • Anisha Beniwal
    August 28, 2025

    Option C is correct

  • Muskan singodiya
    August 28, 2025

    Option c
    1 and 4

  • Deepika sheoran
    August 28, 2025

    1 &4 is correct
    5′ same sequence directly use as primer.
    3′ should be complimentary sequence.

  • Sumit Chhimpa
    August 29, 2025

    In PCR for primer designing… We directly use 5 ‘ end as a primer.. & 3′ end is complimentory & read 5′ to 3’

  • Bhavana kankhedia
    August 29, 2025

    1 and 4 is correct.

  • Parul Yadav
    August 29, 2025

    Forward Primer – Matches the 5’end of the sense strand.
    Reverse Primer – Reverse complementary of the antisense strand at the 3’end.

  • Khushi Singh
    August 30, 2025

    C is correct

  • Yashika Choudhary
    August 30, 2025

    Complementary

  • Sonam Saini
    August 30, 2025

    5 prime and wale sequence ko as it is sakte hain 3 prime wale and ko complementary ke roop mein lete Hain use 5 prime to 3 prime read Kiya jata hai so right answer is one and three

    • Aartii sharma
      August 31, 2025

      Option c

  • Priyanka
    August 31, 2025

    Primer 4 binds to the 3′ end of the antisense strand

  • Kirti Agarwal
    August 31, 2025

    Opt c

  • Kajal
    August 31, 2025

    Correct Answer is (c) 1 and 4

  • Aartii sharma
    August 31, 2025

    1 and 4

  • Konika Naval
    September 1, 2025

    1 and 4

  • Muskan Yadav
    September 5, 2025

    The correct answer is (c) 1 and 4

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