Bioinformatics Master Course II:
DNA/Protein structure-function analysis and prediction
Lecture 12:
DNA/RNA structure
Centre for Integrative Bioinformatics VU
Biological Functions of Nucleic
Acids
• DNA
transcription
mRNA
translation
Protein
tRNA (transfer RNA, adaptor in translation)
rRNA (ribosomal RNA, component of ribosome)
snRNA (small nuclear RNA, component of splicesome)
snoRNA (small nucleolar RNA, takes part in processing of rRNA)
RNase P (ribozyme, processes tRNA)
SRP RNA (RNA component of signal recognition particle)
……..
transcription + translation = expression
Eukaryotes have
spliced genes…
DNA makes RNA makes Protein
Some facts about human genes
•
•
•
•
•
•
Comprise about 3% of the genome
Average gene length: ~ 8,000 bp
Average of 5-6 exons/gene
Average exon length: ~200 bp
Average intron length: ~2,000 bp
~8% genes have a single exon
• Some exons can be as small as 1 or 3 bp.
• HUMFMR1S is a typical gene : 17 exons 40-60 bp
long, comprising 3% of a 67,000 bp gene
• The human factor VIII gene (whose mutations cause
hemophilia A) is spread over ~186,000 bp. It consists of
26 exons ranging in size from 69 to 3,106 bp, and its 25
introns range in size from 207 to 32,400 bp. The
complete gene comprises ~9 kb of exon and ~177 kb of
intron.
• The biggest human gene yet is for dystrophin. It has
>30 exons and is spread over 2.4 million bp.
Nucleic Acid Basics
• Nucleic Acids Are Polymers
• Each Monomer Consists of Three Moieties:
Nucleotide
A Base + A Ribose Sugar + A Phosphate
Nucleoside
• A Base Can be One of the Five Rings:
• Pyrimidines
• Purines
Nucleic Acid Basics
• Nucleic Acids Are Polymers
• Each Monomer Consists of Three Moieties:
Nucleotide
A Base + A Ribose Sugar + A Phosphate
Nucleoside
• A Base Can be One of the Five Rings:
•Pyrimidines and Purines Can Base-Pair (Watson-Crick Pairs)
Nucleic Acids As Heteropolymers
• Nucleosides, Nucleotides
• Single Stranded DNA
5’
3’
•A single stranded RNA will have OH
groups at the 2’ positions
•Note the directionality of DNA or RNA
Stability of base-pairing
• C-G base pairing is more stable than A-T (AU) base pairing
• 3rd codon position has freedom to evolve
(synonymous mutations)
• Species can therefore optimise their G-C
content (e.g. thermophiles are GC rich)
DNA compositional biases
• Base composition of genomes:
• E. coli: 25% A, 25% C, 25% G, 25% T
• P. falciparum (Malaria parasite): 82%A+T
• Translation initiation:
• ATG (AUG) is the near universal motif indicating
the start of translation in DNA coding sequence.
Genetic diseases
Cystic Fibrosis
• Known since very early on (“Celtic gene”)
• Inherited autosomal recessive condition (Chr. 7)
• Symptoms:
– Clogging and infection of lungs (early death)
– Intestinal obstruction
– Reduced fertility and (male) anatomical anomalies
• CF gene CFTR has 3-bp deletion leading to Del508
(Phe) in 1480 aa protein (epithelial Cl- channel) –
protein degraded in ER instead of inserted into cell
membrane
Structure Overview of Nucleic Acids
• Unlike three dimensional structures of proteins, DNA
molecules assume simple double helical structures
independent on their sequences. There are three kinds of
double helices that have been observed in DNA: type A,
type B, and type Z, which differ in their geometries. The
double helical structure is essential to the coding function
of DNA. Watson (biologist) and Crick (physicist) first
discovered the double helix structure in 1953 by X-ray
crystallography.
• RNA, on the other hand, can have as diverse structures as
proteins, as well as simple double helix of type A. The
ability of being both informational and diverse in structure
suggests that RNA was the prebiotic molecule that could
function in both replication and catalysis (The RNA
World Hypothesis). In fact, some viruses encode their
genetic materials by RNA (retrovirus)
Three Dimensional Structures of
Double Helices
A-DNA
Minor
Groove
Major
Groove
Forces That Stabilize Nucleic Acid
Double Helix
• There are two major forces that
contribute to stability of helix formation
– Hydrogen bonding in base-pairing
– Hydrophobic interactions in base stacking
5’
3’
3’
5’
Same strand stacking
cross-strand stacking
A-RNA
Types of DNA Double Helix
• Type A: major conformation of RNA, minor
conformation of DNA;
• Type B: major conformation of DNA;
• Type Z: minor conformation of DNA
3’
5’
3’
A
Narrow
tight
5’
5’
3’
3’
B
Wide
Less tight
5’
5’
3’
Z
3’ Left-handed 5’
Least tight
Secondary Structures of Nucleic
Acids
• DNA is primarily in
duplex form.
• RNA is normally
single stranded which
can have a diverse
form of secondary
structures other than
duplex.
Non-B-DNA secondary structures
•Cruciform
•Triple-helical H-DNA
•Slipped DNA
= Hoogsteen
basepair
Secondary Structures of Nucleic
Acids
More Secondary Structures
Pseudoknots:
• DNA is primarily in
duplex form.
• RNA is normally
single stranded which
can have a diverse
form of secondary
structures other than
duplex.
Source: Cornelis W. A. Pleij in Gesteland, R. F. and Atkins, J. F.
(1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.
rRNA Secondary Structure Based on Phylogenetic Data
3D Structures of RNA:
Transfer RNA Structures
Secondary Structure
of tRNA
Tertiary Structure
of tRNA
3D Structures of RNA:
Ribosomal RNA Structures
Secondary Structure
Of large ribosomal RNA
Tertiary Structure
Of large ribosome subunit
TyC Loop
Variable
loop
Anticodon
Stem
D Loop
Anticodon Loop
Ban et al., Science 289 (905-920), 2000
3D Structures of RNA:
Catalytic RNA
Secondary Structure
Of Self-splicing RNA
Tertiary Structure
Of Self-splicing RNA
Some structural rules:
•Base-pairing is stabilising
•Un-paired sections (loops)
destabilise
•3D conformation with
interactions makes up for this
Sense/antisense RNA
• antisense RNA blocks translation
through hybrisization with coding
strand
Sense/antisense peptides
•Have been therapeutically used
Sense/antisense proteins
•Does it make (anti)sense?