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DNA Secondary Structure

Predicting secondary structures that are formed from transcribed DNA is important in various molecular biology techniques, including siRNA design and cloning optimization. Paste your sequence below and receive a graphical output of predicted secondary structures. Free energy minimization is used to determine interactions between base pairs, highlighting potential stem and loop formations.

Secondary Structure Predictor Crash Course in Secondary Structure

Formation of secondary structures in RNA

We can examine the activity of cellular components based on various levels of organization. The primary structure of nucleic acids or proteins is the basic sequence of nucleotides or amino acids, respectively. DNA’s primary structure is the list of the ATGC sequence. Based on the interactions between nearby components, the molecule will form its most stable, lowest free energy conformation. For DNA, this secondary structure results from two long strands of complementary nucleotides winding around each other, forming a double helix. These two strands and their resultant secondary structure have a high level of stability.

However, once transcribed, RNA is formed as a single strand of nucleotides. This form is less stable, and nucleotides will seek to form hydrogen bonds with complementary nucleotides: A with U, C with G, and G with U. Without a complementary strand like that found in DNA, the single RNA strand will fold on itself into a lower-energy conformation. This can form a variety of different structures (Figure 1).

Single-stranded mRNA can fold on itself to form secondary structures.

Figure 1. Single-stranded mRNA can fold on itself to form secondary structures.

The secondary structures that are formed greatly influence the function of the RNA. Whether coding or non-coding, RNA structure plays an important role in gene function and regulation. Determining this structure can greatly help with experimental design and troubleshooting. Our secondary structure tool provides a graphical layout of the lowest-free energy conformation of the RNA strand.

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