While we are waiting…

Have a think about, and/or chat to your neighbour about:

• What are the differences between DNA and RNA? (think back to first
year!)
• Function
• Structure
• Relationship between structure and function

Please add any questions you

have during the lecture and I will
try to address them in class.
As usual, please post on Ed if you
have any questions afterwards.
https://sydney.padlet.org/alice/BCMB2024
Lecture 18:
Nucleic Acid
Structure
Dr Alice Huang
Learning Outcomes
• Identify the main components of DNA and RNA with reference to
Chargaff's rules
• Describe the key covalent bonds in DNA and RNA; phosphodiester, N-
glycosidic
• Explain how the weak forces work to maintain the double helix: base
stacking (hydrophobic interactions, electronic interactions), base
pairing (hydrogen bonding), ionic interactions, van der Waal’s forces
• Describe the structural features that make DNA a very good store of
genetic information: two strands, deoxyribose, thymine
• Explain the importance of the major and minor grooves to gene
expression
• Identify the structural differences between DNA and RNA
 Molecular Biology Lectures
20-22. Copying
DNA: Prokaryotic
and Eukaryotic 23. The Eukaryotic Genome
19. Nucleic Replication, DNA
Synthesis in the Lab
Today Acid
Structure
24 & 25. Copying RNA: 26. Post-
Prokaryotic and transcriptional
Eukaryotic Transcription processing

27-29. Translation:
Prokaryotic and
Eukaryotic Translation,
Translational Regulation
30-32: Molecular
Techniques
How is DNA so good at storing information?

Paper (free version)

• Fur from woolly dog named Mutton that died in 1859, kept in
Smithsonian National Museum of Natural History
• Example of drawing on science and Indigenous Knowledge to improve
our understanding
Flow of Genetic Information

DNA RNA Protein

DNA RNA
Parts of Nucleic Acids: The Bases

Most common form

at physiological pH

Figure 8.2, Page 264

Chargaff’s Rules
• Erwin Chargaff was able to purify purines and pyrimidines
and quantify them from different organisms

Erwin Chargaff 1930

Varied between
organisms
Same for all

Chargaff, E., Lipshitz, R., and Green, C. (1952) Composition of the desoxypentose nucleic acids of four genera of
sea-urchin. J. Biol. Chem. 195, 155-160 (Paper)
Properties of the Bases

H bond donor
H bond acceptor

Difference between
thymine and uracil is
the methyl group

Adapted from Figure 8.2,

Page 264
Base Pairing

sugar sugar sugar sugar

Adapted from Figure 1.6, Page 5 and Figure 4.11, Page 118

What might lead to changes in protonation states?

Consequences?
Parts of Nucleic Acids:
Sugar

RNA: DNA:
• 1’: N-glycosidic bond attaches here
• 2’: OH for ribose, H for deoxyribose
• 3’: hydroxyl (OH)
• 5’: phosphate attaches here

Figure 4.2, Page 114

Sugar-Phosphate Backbone

Adapted from Figure 4.3, Page 115

 NH2

Putting it Together -
N
N

Adenine
O

5’ Phosphate -
O P O CH2
N
N

O H
O
H
N-glycosidic bond
NH2

H H

5’
O
-
OH N Cytosine
O P O
Phosphodiester bond
N O
Information
Backbone
O CH2
O
H H O

H H
N
O OH NH
- Guanine
O P O
N NH2
N
O CH2
O
H H O

Is this DNA or RNA? H

O OH
H
NH
Uracil
Explain your response.
-
O P O

3’ O CH2
O
N O

H H

3’ Hydroxyl H
OH OH
H
The Double Helix
What interactions are in the double helix?
• Hydrogen bonds
• Ionic interactions
• van der Waals interactions
• Hydrophobic interactions

How do we disrupt these?

Figure 4.10, Page 118

Interactions in Double Helix:
Hydrogen Bonds
• Hydrogen bonds between complementary bases
• 2 between adenine and thymine, 3 between guanine and cytosine
(stronger)

sugar sugar sugar sugar

Adapted from Figure 1.6, Page 5 and Figure 4.11, Page 118
 Interactions in Double Helix:
Ionic Interactions
• Recall: backbone is full of negatively charged
phosphates
• Repulsive!
• Against interactions that favour base pairing
• Result: Twist
Hydrophobic Interactions
• Recall: bases have an aromatic ring
Hydrophobic
structure
• Hydrophobic and wants to stay
away from water

Hydrophilic

Figure 4.10, Page 118

Interactions in Double Helix:
Base Stacking
• van der Waals radius of C is 1.7 Å
• Distance between bases are 3.4 Å
• Leads to attraction via van der
Waals interactions

• Result: base stacking, favouring

formation of double helix

Figure 4.12, Page 119

 Bases All Absorb at 260 nm
At 260 nm:
• [DNA] of 50 ng/μL gives absorbance of 1 What’s different? Why
• [RNA] of 40 ng/μL gives absorbance of 1 might RNA absorb more?

Spectrum of plasmid DNA from practical Spectrum of one of my RNA samples

Hyperchromic Effect
• Due to base stacking, double-stranded nucleic acid absorb less at
260 nm

Figure 4.21, Page 124

Menti: DNA Spectrophotometry
Which of the following information can you obtain from an absorbance
spectrum?
A. Concentration of DNA
B. Purity or presence of contaminants
C. Distinguish intact from partially degraded DNA or nucleotides
D. Sequence
E. Source of nucleic acid, e.g., human, E. coli

There may be more than one answer.

Think about why.
Spot the Imposter

Source

Figure 8.13c, Page 271

 Other Structural Features:
Major and Minor Grooves

Major Groove

sugar sugar sugar sugar

Minor Groove

Adapted from Figure 1.6, Page 5 and Figure 4.11, Page 118
 Other Structural Features:
Major and Minor Grooves
Binding of zinc finger transcription Binding of DAPI (DNA dye) to the
factor to the major groove minor groove

Figure by Richard Wheeler

Figure by Thomas Splettstoesser

DAPI stained nuclei in blue
Figure from Wikipedia
Example:
Protein Interactions with Major Groove

Major Groove

Minor Groove N-glycosidic bonds

Adapted from Figure 28.10, Page 1061 (Lehninger)

 X-ray Diffraction of DNA Crystal
(interpreting this is not assessable!)

Stacked bases

Sodium deoxyribose nucleate from calf thymus, Structure B,

Rosalind Franklin Photo 51, taken by Rosalind E. Franklin and R.G. Gosling.
 Storing Information in DNA
• Backbone outside is hydrophilic
(sugars) and negatively charged
(phosphates)
• Information is buried inside and
is hydrophobic (bases)
• Between the bases are more
polar groups (recall: H-bonds)
• DNA is double stranded – Information in here
backup

Figure 4.10, Page 118

What might be some challenges of a molecule trying to access this information?

 DNA vs RNA for Long Term Storage
Agarose gel of RNA. Some
degradation in the last lane
indicated by the smeared
bands.
Note: this is after isolating
RNA from cells, and
potentially contaminating it
with ribonuclease during
the process

Paper

Cartoon by Sketching
Paper (free version) Science
 Impact of Differences in DNA and RNA on
Information Storage

The 2’ position of the sugar

Presence or absence of OH

Use of uracil vs thymine

Presence or absence of CH3

Figure 8.2, Page 264

Stability:
Attacking the 2’ Hydroxyl on Ribose

-
δ+

Figure 8.8, Page 268

Stability:
Attacking the 2’ Hydroxyl on Ribose

Figure 8.8, Page 268

A Sign of Mutation:
Cytosine Deamination → Uracil

+ H2O + NH3

• Estimated to occur spontaneously 100-500 times per cell, per day

• Corruption in the code!
• Uracil is recognised and removed from DNA by base excision repair
(no need to know the details of this process for this unit of study)
• This would not be recognised if uracil was normally present in DNA
RNA Stability
RNA stability inside a cell varies (Giselle’s lectures)
• What roles do RNA play in our cells?
• Do we want it to have the stability of DNA?

Although we don’t have an RNA genome, some viruses do

• Some examples are coronaviruses and influenza viruses
• What might be some consequences of having an RNA genome?
Advances in Molecular Biology:
Working with RNA
• ~130 year old Tasmanian tiger skin and muscle preserved at room
temperature in museum
• RNA isolated and analysed!

Paper Tasmanian tigers in Washington D.C. National Zoo (Source)

What you have learnt
• Similarities and differences between DNA and RNA, and what this
means for function:
• Both have backbone with covalent bonds: phosphodiester bonds
in sugar-phosphate backbone, N-glycosidic between base (“N”)
and sugar (“glycosidic”)
• Mostly same bases: Except uracil in RNA, thymine in DNA
• Different sugars: 2’ OH in RNA but H in DNA (“deoxy”)
• Different roles: DNA needs to last, RNA only when needed
• Features of double helix:
• Various weak forces contribute to formation of the double helix
• Proteins and molecules can interact with major or minor grooves
Extra Resources
Textbook References
• Lehninger Principles of Biochemistry, Nelson et al.
• Chapter 8: structure and chemistry of nucleic acids.
• Biochemistry, Berg et al.
• Chapter 1: covers a lot of chemistry in the context of biochemistry, including
more detail about the forces holding the double helix together. Helpful for
anyone who wants to brush up on the chemistry.
• Chapter 4: more specifically about the structure of DNA.
• Chapter 29: for those interested, recognition of uracil in DNA and how it is
repaired are described here. Details about repair is beyond the scope of this
unit.
Other
• Dr NucleicAlice is an AI tutor that is available 24/7 for lectures 17 to
22
 Molecular Biology Lectures
Next Three Lectures 20-22. Copying
DNA: Prokaryotic
and Eukaryotic 23. The Eukaryotic Genome
19. Nucleic Replication, DNA
Synthesis in the Lab
Today Acid
Structure
24 & 25. Copying RNA: 26. Post-
Prokaryotic and transcriptional
Eukaryotic Transcription processing

27-29. Translation:
Prokaryotic and
Eukaryotic Translation,
Translational Regulation
30-32: Molecular
Techniques
To Prepare for Next Three Lectures:
Copying DNA
• Where is the information stored in the DNA molecule
• What needs to occur to access this information?
• How are nucleotides joined together?
• Describe the direction of the two DNA strands.
 Some practice questions
Please discuss on Ed if you need help (or if we don’t get to these
during the lecture)!
Prompt: Why is DNA more stable than RNA
Response:
DNA is more stable than RNA due to several reasons:
• Deoxyribose Sugar: DNA contains deoxyribose sugar, which has one less
oxygen-containing hydroxyl group than the ribose sugar in RNA. This makes
DNA less reactive and more resistant to hydrolysis.
• Double-Stranded Structure: DNA is double-stranded, which provides
additional stability. The two strands of DNA form a double helix, whereas
RNA is typically single-stranded.
• Thymine vs Uracil: DNA uses thymine as one of its bases, while RNA uses
uracil. Thymine is more stable than uracil, which contributes to the overall
stability of DNA.
• Length: DNA molecules are generally longer than RNA molecules. Longer
polymers are more stable.
• Enzymatic Repair: DNA is located in the nucleus where enzymes can repair
any damage. There are no comparable enzymes to repair RNA damage.
These factors make DNA a more stable molecule, which is crucial for its role in
storing genetic information.
AI generated the following MCQ for me:
What holds the two strands of the DNA double helix together?
A. Hydrogen bonds
B. Ionic bonds
C. Covalent bonds
D. Van der Waals forces

The answer and explanation it gave me:

The two strands of a DNA molecule are held together by hydrogen bonds
between the nitrogen bases on opposite strands[1][2]. Hydrogen bonds
occur between the two strands and involve a base[3][4], forming a double
helix structure[5].

Comment on the answer and explanation provided.