Q22  Rehan made a single stranded DNA with the following sequence 5’GGATCT3′. With which of the
following single strands will it form the weakest duplex?
1. 3’CCTAGA5′
2. 5’AGATCC3′
3. 5’AGAATT3′
4. 3’CCAAGA5′

 

Introduction to DNA Duplex Formation

DNA duplex formation is a fundamental process in molecular biology where two complementary single-stranded DNA molecules hybridize to form a double-stranded structure. The strength of duplex formation depends on the base-pairing between complementary nucleotides, governed by Watson-Crick pairing rules (A-T and G-C). Understanding duplex stability is essential for applications like PCR, sequencing, and gene expression analysis.

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Question Analysis

Rehan made a single-stranded DNA with the following sequence:

5′−GGATCT−3′

We need to identify which of the following single strands will form the weakest duplex with Rehan’s DNA strand:

1. 3′ – CCTAGA – 5′
2. 5′ – AGATCC – 3′
3. 5′ – AGAATT – 3′
4. 3′ – CCAAGA – 5′

Base Pairing Rules and Stability

The stability of a DNA duplex depends on the strength of the hydrogen bonding between nucleotides:

• G-C pairs form three hydrogen bonds – stronger and more stable.
• A-T pairs form two hydrogen bonds – weaker and less stable.

Key Factors Affecting DNA Duplex Stability:

 High GC content increases duplex stability.
 High AT content decreases duplex stability.
 Mismatched or non-complementary sequences reduce duplex stability.

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Step-by-Step Analysis

Option 1:

3′ – CCTAGA – 5′

• Fully complementary to the original sequence.
• High GC content = Strong binding

Option 2:

5′ – AGATCC – 3′

• Reverse complement of original sequence = Strong binding

Option 3:

5′ – AGAATT – 3′

• Non-complementary regions (TT mismatch) reduce stability = Weak binding

Option 4:

3′ – CCAAGA – 5′

• Non-complementary to the original sequence = Weak binding

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Correct Answer:

The weakest duplex will form with Option 3 – 5′ – AGAATT – 3′ because it has non-complementary regions and a low GC content, leading to reduced hydrogen bonding and weaker binding.

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Understanding Duplex Formation in Molecular Biology

• DNA duplex formation is essential for gene expression, replication, and repair.
• The stability of a duplex influences hybridization efficiency in PCR and sequencing.
• Stronger duplex formation enhances the accuracy of molecular techniques.

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Conclusion

The single-stranded DNA 5′ – AGAATT – 3′ forms the weakest duplex with Rehan’s DNA sequence due to low GC content and mismatched base pairs. Understanding DNA duplex formation and stability is critical for molecular biology experiments and genetic analysis.

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