Non-Canonical Structures

What are Non-Canonical Structures?

Non-canonical structures are alternative structures that DNA and RNA molecules can adopt in addition to the canonical double-helix structure of DNA and the single-stranded structure of RNA. Non-canonical structures of DNA/RNA increase the complexity and diversity of nucleic acid functions in biological processes. These non-canonical structures arise from the ability of nucleic acids to form specific interactions between nucleotide bases. These interactions can give rise to a variety of structural motifs that play important roles in biological processes such as gene expression, DNA replication, and RNA processing.

Fig. 1 Structure of B-DNA and non-B-DNA. (Bansal et al., 2022)

Non-canonical Structures of DNA and RNA

• Non-canonical Structures of DNA

1. Four-stranded Structures

A four-stranded structure is a structure formed by two pairs of intertwined DNA double helices. In a four-stranded structure, the two pairs of DNA strands are interconnected by hydrogen bonds to form a stable four-stranded body.

2. Hairpin Structure

A hairpin structure is a non-canonical structure formed by a part of a DNA strand. In a hairpin structure, a segment of the DNA strand forms a stable hairpin shape through internal hydrogen bonding, rather than being bound in pairs as in a double helix structure.

3. Occlusion Structure

A bitewing structure is a structure in which two parts of a DNA strand are connected to each other through internal hydrogen bonds to form a stable structure.

4. G-quadruplex

A G-quadruplex is a non-canonical structure formed by the guanine (G) bases of a DNA strand. In a G-quadruplex, multiple guanine bases are interconnected by hydrogen bonds and coordination of metal ions to form a stable quadruplex structure.

• Non-canonical Structures of RNA

1. Hairpin Structure

A hairpin structure is a non-canonical structure formed by partial sequences of an RNA strand. In a hairpin structure, one section of the RNA strand forms a stable double-stranded structure through internal base pairing, while the other section becomes a single-stranded structure.

2. Internal Loop Structure

An internal loop structure is a structure formed by the presence of unpaired nucleotides between two double-stranded segments of an RNA chain.

3. Bulge Structure

A bulge structure is the presence of unpaired nucleotides or mismatched base pairs in the double-stranded structure of RNA.

4. Pseudoknot

A pseudoknot is a complex RNA structure in which one region of the RNA strand forms a base pair with another region downstream to form a tertiary structure.

5. G-quadruplex

Similar to DNA, RNA can also form a G-quadruplex structure.

How to Study the Function of Non-canonical Structures of DNA/RNA?

• Bioinformatics Tools

The use of computerized methods, such as sequence analysis and structure prediction software, can be used to identify potential non-canonical structures in DNA/RNA sequences and predict their stability and potential biological function.

• Chemical and Enzyme Probes

Chemical and enzymatic probes can be used to selectively cut or modify nucleic acid structures, providing information about their location and stability. For example, dimethyl sulfate (DMS) can be used to probe RNA structures by methylating exposed adenine and cytosine residues.

• Nucleic Acid Footprinting

Nucleic acid footprinting methods can be used to determine the location and stability of nucleic acid structures by monitoring their protection from enzymatic cleavage.

• Biophysical Techniques

Biophysical techniques can be used to determine the three-dimensional structure of nucleic acids and their stability under different conditions.

• Functional Assays

Functional assays can be used to determine the biological function of non-canonical structures of DNA/RNA. For example, reporter gene assays can be used to measure the effect of non-canonical structures on gene expression, while gel shift assays and immunoprecipitation assays can be used to determine the binding affinity of nucleic acid structures to proteins or other molecules.

Advantages of DNA/RNA Non-canonical Structures

Functional Diversity - Non-canonical structures can provide functional diversity for nucleic acids by allowing them to interact with proteins, small molecules or other nucleic acids in unique ways.

Structural Stability - Some non-standard structures are more stable than canonical double helix or single stranded RNA structures, making them more resistant to nuclease degradation or thermal denaturation. This is advantageous in environments where nucleic acids are exposed to harsh conditions, such as in the cytoplasm or extracellular space.

Interaction Specificity - Non-standard structures can exhibit sequence-specific interactions with proteins or other molecules, allowing them to selectively bind or recognize specific targets.

Evolutionary Conservation - Some non-standard structures are highly conserved across species, suggesting that they have important biological functions.

Therapeutic Potential - Small molecules or therapeutic oligonucleotides can target non-standard structures, providing opportunities to develop novel therapies for diseases such as cancer and viral infections.

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