Molecular Biology
CHM6640/7640
Lecture #2
“Structure of DNA and RNA”
Presented by Joanna Klapacz
For Dr. Ashok S. Bhagwat
Thursday January 10, 2008
Nucleic Acids:
• 2 major types: DNA and RNA
• Molecular repositories of genetic information in cells
• Variety of other roles in cellular metabolism:
• energy currency of metabolic transactions
• messengers in signaling pathways
• components of enzyme cofactors
1. Nucleotides are the building blocks/polymers of nucleic acids.
2. Nucleotides are composed of three parts:
•
Nitrogen containing base
•
Pentose sugar moiety
•
Phosphate group
3. Nucleoside is composed of base + sugar.
Solution Confirmations of Ribose Sugar Moiety
Remember the numbering!
1’
5’
2’
1’
4’
3’
3’
4’
5’
2’
Ribonucleotide
Found in Ribonucleic Acids (RNA)
D-ribose
Deoxyribonucleotide
Found in Deoxyribonucleic Acids (DNA)
H
D-deoxyribose
Two Parent Nitrogenous Bases
Remember the numbering!
Bases Found in Nucleic Acids
Nucleotides in RNA
Nucleotides in DNA
Nucleoside can have more than one phosphate groups
or TTP
Rotation Between
Seven Bonds is
Observed in
Nucleic Acids
C1’
GLYCOSYL
BOND
Conformation of Purines
with Respect to Attached Sugar
Only the anti- configuration is found in DNA
Structures of Adenosine Monophosphates
Found in DNA and RNA:
Default
or 2’-H
or 2’-H
Found in RNA only:
RNA is Chemically Less Stable
pH >11
Naturally occurring base modifications
in nucleic acids
Practice drawing:
8-oxoguanosine
2,6-diaminopurine
etc etc
DNA
RNA
Covalent backbones of
nucleic acids consist of
alternating phosphate
and sugar residues.
Schematic Representation of DNA Sequence
Hydrogen –Bonding of Base Pairs
Keto and Amino Groups in Bases Can
Undergo Rearrangements.
OH
O
HN
C
N
keto
C
enol
NH2
NH
HN
N C
amino
>10,000
C
imino
:
1
Resonance Structure of Bases
Predominant Forms
Could Lead to
Base Mispairing
Keto- and Amino groups in bases can undergo rearrangements.
Chemical Properties of Nucleic Acids
If pH is <4 or >10 in solution, the base pairs are disrupted because of
protonation/deprotonation of keto and amino groups.
Site Affected
pKa
Adenylate N1
Guanylate N1
Cytidylate N3
Thymidylate N3
Adenylate N7
Guanylate N7
3.9
10.0
4.5
10.5
2.4
2.4
B-Form DNA
• Defined by Watson-Crick
base pairing.
• Most stable structure of
DNA under physiological
conditions.
Schematic
Representation of DNA
(b) Stick Model
(c) Space-Filling Model
Comparison of A and B Form DNA
dsRNA
or
DNA:RNA
double-stranded
(ds) DNA
Specialized Structure in Nucleic Acids
: read identically either forwards or backwards
Regions of DNA with inverted repeats that are
self-complementary.
Hairpin Structures Formed in DNA and
RNA from a Single Nucleic Acid Strand
Cruciform Structures Formed in DNA and
RNA from both Strands of Nucleic Acids
RNA Can Adopt Complex Structures
Transfer-RNA (tRNA)
Tertiary (3D) Structure
Secondary Structure
tRNA Contains
Modified Bases
1
1-Methyladenine
DNA Damaging Agents
Hoeijmakers. Nature. 2001. 411:366-74.
Certain
chronic or
metabolic
diseases
CH3
Cell cycle
arrest
CELL DEATH
Alkylating Agents
Occur Ubiquitously
and Cause DNA
Damage
Mutation
DNA REPAIR
DISEASE
Alkylating
Agents
Endogenous
Environmental
Bi-functional/
Cross-Linking
SN1 Alkylating Agent
Man-made
SN2 Agent
Model
SN1 Alkylating
Agents
Monofunctional
Bifunctional
* Alkylating Agents used
clinically as chemotherapeutics
DNA Methylating Agents Induce More than a
Dozen Different Lesions in DNA
Filled Arrows: SN1
Empty Arrows: SN1 and SN2
Other targets
• phosphotriesters
• deoxyribose
Wyatt and Pittman. 2006. Chem. Res. Toxicol. 19:1580-94
O6-methylguanine is Mutagenic
H
N H
N
O
N
N
H N
N
dR
N
H N
O
dR
H
Cytosine
Guanine
CH3
H3C
O
O
N H
N
N
N
N
N
dR
O
Thymine
dR
H N
H
O6-methylguanine
3-methyladenine is a Toxic Lesion that Inhibits
DNA Polymerases
3meA also rapidly depurinates
7-methyl Adduct Causes Rapid Base Loss
H
Free Base
+
OH
Abasic (AP) site in DNA