12. Which of the following mRNA molecules would form the most stable stem-loop
structure?
a. 5’…GGCUU……UUCGG…3′
b. 5’…GGCUU……AAGCC…3′
c. 5’…GGCUU……GGCUU…3′
d. 5’…GGCUU……CCGAA…3′
Most Stable mRNA Stem-Loop: CSIR NET Question Solved
Option B forms the most stable mRNA stem-loop structure among the choices. Stability depends on Watson-Crick base pairing in the stem, with GC pairs (3 hydrogen bonds) far stronger than AU pairs (2 hydrogen bonds); mismatches or non-canonical pairs destabilize it.
Option Analysis
Each option has 5′ GGCUU paired against the 3′ sequence in a hairpin stem.
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Option A (5’…GGCUU……UUCGG…3′): Forms G-U, G-U, C-C, U-U, U-G pairs. Zero Watson-Crick matches; all mismatches make it highly unstable.
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Option B (5’…GGCUU……AAGCC…3′): Perfectly complementary: G-C, G-C, C-G, U-A, U-A. Three GC pairs provide maximum stability.
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Option C (5’…GGCUU……GGCUU…3′): Self-complementary but yields G-U, G-U, C-C, U-G, U-G. No Watson-Crick pairs; unstable due to wobble/mismatches.
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Option D (5’…GGCUU……CCGAA…3′): Partial pairing: G-A, G-A, C-G, U-C, U-C. Only one GC pair; four mismatches reduce stability.
In CSIR NET Life Sciences preparation, understanding the most stable mRNA stem-loop structure is crucial for molecular biology questions on RNA secondary structure and stability. Stem-loops (hairpins) regulate mRNA degradation, translation, and gene expression, with stability driven by stem base pairing. This guide solves a classic MCQ while explaining factors like GC content for exam success.
Stem-Loop Basics
RNA stem-loops feature a double-stranded stem from complementary inverted repeats and a single-stranded loop. Stability increases with:
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More base pairs in the stem.
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GC pairs over AU (3 vs. 2 H-bonds).
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Strong closing base pairs near the loop.
Loops of 4-7 nt are optimal; mismatches (bulges) destabilize.
Detailed Option Breakdown
| Option | Sequence Pairing (5′-3′) | WC Pairs | GC Pairs | Stability |
|---|---|---|---|---|
| A | G-U, G-U, C-C, U-U, U-G | 0/5 | 0 | Lowest |
| B | G-C, G-C, C-G, U-A, U-A | 5/5 | 3 | Highest |
| C | G-U, G-U, C-C, U-G, U-G | 0/5 | 0 | Low |
| D | G-A, G-A, C-G, U-C, U-C | 1/5 | 1 | Moderate |
Option B wins due to perfect complementarity and high GC content, mimicking stable natural hairpins like UUCG tetraloops.
Exam Tips
Practice predicting pairings manually or via tools like mfold. Focus on CSIR NET topics: RNA structure affects half-life (e.g., histone mRNA 3′ stem-loop). Revise thermodynamics: ΔG favors GC-rich stems.
