SUMMARY
RNA STRUCTURE AND FUNCTION
Abstract
Summary of lectures/ tutorials and papers of the course RNA Structure and Function.
NWI MOL107
Radboud University (RU)
Nijmegen
2022-2023
Kevin Booij
,Lecture 1: RNA structure and function
Key differences between RNA and DNA*
RNA DNA
Single stranded * Double stranded *
Ribose sugar * Deoxyribose sugar *
Unstable Stable
Often shorter than DNA Longer (base-pairs) than RNA
Uracil * Thymine *
Secondary structure A-helix Secondary structure B-helix
Primary, secondary, tertiary and quaternary Secondary structure of DNA strand, and helical
structure is tertiary
Structure tertiary structure: complexity of RNA structures are way more complex than those of
DNA. *
RNA can act as a catalyst DNA can not
RNA has an additional OH-group compared to DNA because of the ribose phosphate backbone.
Non-standard nucleotides:
Iosine is the most abundant non-standard nucleotide. Iosine, pseudodouridine, ribothymidine and
dihydrouridine are examples of non-standard nucleotides. All of these nucleotides are atypical and
related to the original nucleotides, but will result in another secondary or tertiary structure of the
RNA molecule.
Primary structure RNA:
Single stranded structure with a right-handed helical confirmation held together by H-bonds and
base-stacking interactions. RNA structure:
, Hydrolysis of RNA:
RNA is unstable under alkaline conditions (high pH!). RNA is used for a temporary function. After use,
it is destroyed or become dysfunctional. RNAses: s-RNase, RNase P, Dicer (microRNA production) and
RNA exomes.
Base-catalyzed hydrolysis of RNA:
High pH (alkaline). Lot of OH can bind to OH on nucleotide break bond between nucleotides in
RNA and thereby shorten it.
- RNA is unstable under alkaline conditions.
- Hydrolysis is also catalysed by enzymes (ribonuclease and RNase).
- RNase enzymes are abundant around us: - S-RNase in plants prevents inbreeding.
- RNase P is a ribozyme that processes tRNA precursors.
- Dicer is an enzyme that cleaves double-stranded RNA into oligonucleotides. This leads to protection
from viral genomes and RNA interference.
- RNA exosome is an ubiquitous complex of 3’- 5’ exoribonucleases.
- Phosphate backbone is broken down by hydrolysis and leads to departed bases which results in
dysfunction of the RNA.
RNA interference (RNAi) = A biological process in which RNA molecules are involved in sequence-
specific suppression of gene expression by double-stranded RNA, through translational or
transcriptional repression.
Exoribonuclease = Enzyme that degrades RNA by removing terminal nucleotides from either the 5'
end or the 3' end of the RNA molecule.
Oligonucleotides = Short DNA or RNA molecules
Secondary and tertiary structure of RNA:
Secondary structure
Hairpin loop < 6 bases in a loop
Stem-loop >6 bases in a loop. With a Double-helical stem region before the loop.
- Internal loop.
Asymmetric -> unequal number of non-base paired residues in both strands.
Symmetric -> equal number of non-base paired residues in both strands.
- Bulge.
Single nucleotide bulge.
Multiple nucleotide bulge.
RNA STRUCTURE AND FUNCTION
Abstract
Summary of lectures/ tutorials and papers of the course RNA Structure and Function.
NWI MOL107
Radboud University (RU)
Nijmegen
2022-2023
Kevin Booij
,Lecture 1: RNA structure and function
Key differences between RNA and DNA*
RNA DNA
Single stranded * Double stranded *
Ribose sugar * Deoxyribose sugar *
Unstable Stable
Often shorter than DNA Longer (base-pairs) than RNA
Uracil * Thymine *
Secondary structure A-helix Secondary structure B-helix
Primary, secondary, tertiary and quaternary Secondary structure of DNA strand, and helical
structure is tertiary
Structure tertiary structure: complexity of RNA structures are way more complex than those of
DNA. *
RNA can act as a catalyst DNA can not
RNA has an additional OH-group compared to DNA because of the ribose phosphate backbone.
Non-standard nucleotides:
Iosine is the most abundant non-standard nucleotide. Iosine, pseudodouridine, ribothymidine and
dihydrouridine are examples of non-standard nucleotides. All of these nucleotides are atypical and
related to the original nucleotides, but will result in another secondary or tertiary structure of the
RNA molecule.
Primary structure RNA:
Single stranded structure with a right-handed helical confirmation held together by H-bonds and
base-stacking interactions. RNA structure:
, Hydrolysis of RNA:
RNA is unstable under alkaline conditions (high pH!). RNA is used for a temporary function. After use,
it is destroyed or become dysfunctional. RNAses: s-RNase, RNase P, Dicer (microRNA production) and
RNA exomes.
Base-catalyzed hydrolysis of RNA:
High pH (alkaline). Lot of OH can bind to OH on nucleotide break bond between nucleotides in
RNA and thereby shorten it.
- RNA is unstable under alkaline conditions.
- Hydrolysis is also catalysed by enzymes (ribonuclease and RNase).
- RNase enzymes are abundant around us: - S-RNase in plants prevents inbreeding.
- RNase P is a ribozyme that processes tRNA precursors.
- Dicer is an enzyme that cleaves double-stranded RNA into oligonucleotides. This leads to protection
from viral genomes and RNA interference.
- RNA exosome is an ubiquitous complex of 3’- 5’ exoribonucleases.
- Phosphate backbone is broken down by hydrolysis and leads to departed bases which results in
dysfunction of the RNA.
RNA interference (RNAi) = A biological process in which RNA molecules are involved in sequence-
specific suppression of gene expression by double-stranded RNA, through translational or
transcriptional repression.
Exoribonuclease = Enzyme that degrades RNA by removing terminal nucleotides from either the 5'
end or the 3' end of the RNA molecule.
Oligonucleotides = Short DNA or RNA molecules
Secondary and tertiary structure of RNA:
Secondary structure
Hairpin loop < 6 bases in a loop
Stem-loop >6 bases in a loop. With a Double-helical stem region before the loop.
- Internal loop.
Asymmetric -> unequal number of non-base paired residues in both strands.
Symmetric -> equal number of non-base paired residues in both strands.
- Bulge.
Single nucleotide bulge.
Multiple nucleotide bulge.
