2: base pairing

What are alternative base pairs in folded RNA structures?

Alternative base pairs in folded RNA structures are base-pairing interactions that do not have the same geometry as standard base pairs, often serving as recognition elements.

What is a key characteristic of base pairing in alternative base pairs?

Alternative base pairs often contain one hydrogen bond and may involve water-mediated base-base interactions.

What is the most common alternative base pair in RNA?

The G-U wobble base pair is the most common alternative base pair in RNA.

What makes G-U wobble base pairs functionally significant?

G-U wobble base pairs have chemical and structural properties that make them well-suited for binding RNA molecules, proteins, or other ligands.

Where are G-U wobble base pairs commonly found?

• In the acceptor stem of tRNA, helping it load the correct amino acid.

• In catalytic RNA molecules involved in RNA self-splicing.

What are Hoogsteen base pairs?

• Hoogsteen base pairs are an example of alternative base pairing that involves hydrogen bonds between a base paired as in standard Watson-Crick pairing and the major groove edge of another base.

How are Hoogsteen base pairs formed?

They are formed when a single-stranded piece of DNA or RNA enters the major groove of a double-stranded nucleic acid and forms hydrogen bonds with one of the strands in the double helix, potentially leading to the formation of a triple helix.

What are post-transcriptional modifications in RNA and DNA?

• Post-transcriptional modifications include:

  • Various modifications of RNA bases.

  • Methylation of the 2’-OH group in the ribose sugar of RNA.

  • Methylation of the cytosine base in DNA, forming CpG islands.