Nucleic Acid Structures Overview

Study Notes

This lecture covers the structures of DNA and RNA, outlining their differences and the diverse types of RNA and their functional relationships.

DNA is a double helix composed of two antiparallel polynucleotide strands.
The strands are held together by hydrogen bonds.
The bases are paired, with adenine pairing with thymine and guanine with cytosine.
The sugar-phosphate backbone forms the outside of the double helix.
The helix is 20 Å wide, with one nucleotide every 3.4 Å (0.34 nm). There are 10 nucleotides per turn of the helix.
Key models show pyrimidine: pyrimidine pairings are < 20 Å. Purine: purine pairings give a helix > 20 Å. Pyrimidine: purine pairings form a double helix of about 20 Å.
DNA is highly stable due to the stacking arrangement of bases and the presence of counter-ions to shield the negative charges.

RNA, unlike DNA, is typically a single-stranded molecule.
The extra hydroxyl group on the ribose sugar in RNA prevents stable double-helix formation.
RNA can adopt secondary structures like hairpins, stem-loops and tertiary structures such as pseudoknot.
Some RNA types have different conformations, like non-canonical base pairings and non-Watson-Crick bonding; these structures widen the major groove and enhance accessibility to ligands or proteins.
There are at least seven types of RNA.
Ribosomal RNA (rRNA) is a structural and enzymatic component of ribosomes (80% of total cellular RNA).
Messenger RNA (mRNA) carries genetic information from DNA to the cytoplasm for protein synthesis.
Transfer RNA (tRNA) acts as an adapter molecule, carrying amino acids to ribosomes during translation (5% of total RNA).
Small nuclear RNA (snRNA), signal recognition particle RNA (SRP RNA),microRNA (miRNA), piwi-interacting RNA (piRNA), and short interfering RNA (siRNA) are involved in various cellular processes, including pre-mRNA processing, protein synthesis regulation, and gene silencing.

The process of supercoiling is essential to allow DNA to be stored efficiently but also allows access to the genetic information necessary for transcription and replication.
The negative supercoiling is more energetically favorable in most organisms, helping maintain the structure and accessibility for protein production.

X-ray diffraction was instrumental in determining the 3D structure of DNA, which was crucial to the development of models of DNA and the discovery of the double helix.
Rosalind Franklin using X-ray diffraction significantly contribute to the discovery of DNA structure.
Chargaff's Rules state that the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine in a genome.