A short RNA molecule was isolated that demonstrated a hyperchromic shift (see Chapter 10), indicating secondary structure. Its sequence was determined to be

     5'-AGGCGCCGACUCUACU-3'

Propose a two-dimensional model for this molecule.

Key Concepts

RNA Secondary Structure

RNA secondary structure refers to the local folded structures formed within a single RNA molecule due to base pairing interactions. These structures, such as hairpins and loops, are crucial for the molecule's stability and function. Understanding the sequence of nucleotides helps predict how the RNA will fold, which is essential for modeling its two-dimensional shape.

Hyperchromic Shift

A hyperchromic shift is an increase in the absorbance of UV light by nucleic acids, indicating a change in their structure, often associated with the denaturation or unfolding of double-stranded RNA. In the context of RNA, a hyperchromic shift suggests that the molecule has a stable secondary structure that can be disrupted, providing insights into its folding and interactions.

Two-Dimensional RNA Modeling

Two-dimensional RNA modeling involves creating a visual representation of the RNA molecule's secondary structure, illustrating how the nucleotides interact through base pairing. This model helps in understanding the spatial arrangement of the RNA, which is critical for predicting its biological function and interactions with other molecules, such as proteins or other RNA strands.