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.
, Tertiary structure
Pseudoknot. 2 stems and 2 loops merged together.
Double-stranded helices in nucleic acids:
B-form helix general form of DNA.
RNA typically has a A-form helix.
Differences between helixes:
B-form wide and open major helix groove.
A-form helix, deep but narrow major groove and exposed
minor groove, bases are more exposed at the surface of the
helix.
Molecules interaction with DNA, major groove is more
important. Molecules interaction with RNA is more important
with the minor groove (higher accessibility).
The beta-form of DNA and the alpha-form of DNA are based
on the pucker on the sugar ribose. As DNA doesn't have a 2'-
OH, it can obtain both conformations. RNA does not have this
luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus
constraining the RNA to adopt the A-form.
Secondary structures of mRNA:
5’ – UTR and 3’- UTR both contain regulatory elements in the areas outside of the coded area . These
regulatory elements are binding sites for transcription factors and gene regulation. More secondary
structures in the untranslated areas of mRNAs.
There is more RNA secondary structure in the untranslated regions of mRNAs than in the coding
sequence. Influence on synthesizing in ribosomes. Regulatory elements in 5’- and 3’- UTRs of mRNAs.
Specific interactions are supported by secondary structures of RNA with regulatory elements.
Unusual base pairing in RNA
Watson-Crick (Normal base pairing)
G-C
A-U
Wobble (abnormal basepairing)
G-U
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.
, Tertiary structure
Pseudoknot. 2 stems and 2 loops merged together.
Double-stranded helices in nucleic acids:
B-form helix general form of DNA.
RNA typically has a A-form helix.
Differences between helixes:
B-form wide and open major helix groove.
A-form helix, deep but narrow major groove and exposed
minor groove, bases are more exposed at the surface of the
helix.
Molecules interaction with DNA, major groove is more
important. Molecules interaction with RNA is more important
with the minor groove (higher accessibility).
The beta-form of DNA and the alpha-form of DNA are based
on the pucker on the sugar ribose. As DNA doesn't have a 2'-
OH, it can obtain both conformations. RNA does not have this
luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus
constraining the RNA to adopt the A-form.
Secondary structures of mRNA:
5’ – UTR and 3’- UTR both contain regulatory elements in the areas outside of the coded area . These
regulatory elements are binding sites for transcription factors and gene regulation. More secondary
structures in the untranslated areas of mRNAs.
There is more RNA secondary structure in the untranslated regions of mRNAs than in the coding
sequence. Influence on synthesizing in ribosomes. Regulatory elements in 5’- and 3’- UTRs of mRNAs.
Specific interactions are supported by secondary structures of RNA with regulatory elements.
Unusual base pairing in RNA
Watson-Crick (Normal base pairing)
G-C
A-U
Wobble (abnormal basepairing)
G-U
