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Patrick: An Introduction
to Medicinal Chemistry 5th Edition
Chapter 6

DRUG TARGETS
NUCLEIC ACIDS
DNA & RNA

Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.1 Primary Structure

5' end

3' End

Lecture 2
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.1 Primary Structure (sugars and bases)
5
HOCH2

Sugar
Deoxyribose

Nucleic acid bases

5 7
4 9

4 H
H
3
OH

H 1
H
2
H

NH2
N1

OH

N
H

HN1

H2N

Adenine

NH2

5 7
4 9

N3

N
H

Guanine

HN3

Cytosine

Purines

2 1

N
H

CH3

N
H

Thymine

Pyrimidines
Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.1 Primary Structure
Nucleosides = Sugar + nucleic acid base

NH2

O
N

N
HO
O
H

Deoxyadenosine

HO

N
O

HO

Deoxyguanosine

HO

HO

H
H

CH3

HN

H
HO

H2N
HO

NH2

HO

H
H

Deoxythymidine

Deoxycytidine

Lecture 2
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.1 Primary Structure
Building blocks Nucleotides (note the phosphates)
NH2

O
N

N
H2O3PO

N
H2N
H2O3PO

Deoxyadenosine
Monophosphate

HO

H
HO

Deoxyguanosine
Monophosphate

H2O3PO

H
HO

N
O

H2O3PO

H
HO

O
H

CH3

HN

O
H

NH2

O
N

Deoxythymidine
Monophosphate

Deoxycytidine
Monophosphate

Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.2 Secondary Structure - Double Helix
o
10A
G C
AT
Major
groove

TA
T A
G C
G C
TA
T A
T A

Minor
groove

AT
AT
T A
C

G
G C
TA
T A

G C
GC
GC
T A
A T
C G
TA
T A

o
34A

Notes:
Sugar phosphate backbone is ionized
Charge favours solubility with water
Nucleobases point inward
Base pairing rules: A-T or G-C
Purine pairs with pyrimidine
Base pairs are stacked (vdw interactions)
Chains are complementary & antiparallel

DNA DOUBLE HELIX

Lecture 2
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.2 Secondary Structure - Double Helix
Thymine
o
10A

Me
O

TA
T A
G C
G C

NH

O
O

5'

TA
T A
AT
AT
T A
C G
G C
TA
T A
G C
GC
GC
T A
A T
C G
TA
T A

DNA DOUBLE HELIX

o
34A

5'

O
P

3'

O
5'

N
NH2

3'

3'

O
O

O P

T A
Minor
groove

H2N

G C
AT
Major
groove

Adenine

HN

O P

3'

N
O

Cytosine

5'

H2N

Guanine

O P

O
O

Base Pairing
G-C base pairing involves 3 H-bonds
A-T base pairing involves 2 H-bonds
Lecture 2
Oxford University Press, 2013

DNA hybridization

Formation of the DNA duplex (hybridization) is rapid and spontaneous

under physiological conditions. The melting temperature (Tm) is the
temperature at which half of DNA is double-stranded and half is single
stranded. The process is reversible and cooperative.
Oxford University Press, 2013

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Structural Variation in DNA

For each monomeric unit, six of
the bonds rotate freely.
The limited rotation about bond 4
gives rise to ring pucker, in which
one of the atoms in the fivemembered furanose ring is out of
the plane described by the other
four.
This conformation is endo or exo,
depending on whether the atom is
displaced to the same side of the
plane as C-5 or to the opposite
side

Oxford University Press, 2013

Conformations of Ribose

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Conformations of Ribose
2 endo

3 endo
Oxford University Press, 2013

syn versus anti conformations

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Base Tautomerization

Keto and amino forms are preferred by 99.99% in nature.

Enol tautomers can lead to mutagenesis

Oxford University Press, 2013

stacking stabilizes the double helix

stacking of aromatic rings is

favorable in aqueous environments
to minimize hydrophobic effects
The energetic benefits of stacking
dependent on the sequence

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Snug fit

The oligosaccharide moiety of

calicheamicin binds the minor
groove of DNA
The trisulfide trigger (yellow) of
calicheamicin is readily
accessible to other thiols like
glutathione

Oxford University Press, 2013

Staining the nucleus of the cell

Hoechst 33258 is fluorescent when

bound to the minor grove of cells
When added to cells, Hoechst
accumulates in the nucleus and
can be observed by fluorescence
microscopy

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Nucleic acid helices adopt several forms

Double stranded DNA most often adopts a right-handed

B-form helix (seen above)
A-form is also right-handed, but has a shorter helical pitch and
is generally observed in RNA/RNA or RNA/DNA duplexes
Under some conditions DNA can adopt a left-handed Z-form
helix

Oxford University Press, 2013

DNA Polymorphism

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Oxford University Press, 2013

DNA polymerases are right handed

DNA polymerases adopt a conserved right handed model

Exonuclease domain (green), the template DNA strand (orange)
and the growing DNA strand (red).
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DNA replication

DNA synthesis is a primer extension process

that occurs in the 5 to 3 direction
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.2 Secondary Structure - Double Helix
Replication

New
DNA
chains

Template

DNA
Double Helix

New
DNA
chains

Template

Replication
Lecture 2

DNA
Daughter helices
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.2 Secondary Structure - Double Helix
Template Copying (by a DNA polymerase)

5'

Template
chain

X
A

Template
chain

5'

T
C

3'

5'
Growing
chain

3'

5'

Template
chain
A

3'

X-

3'

3'

5'

5'
Growing
chain

Growing
chain

Approach of dNTP

3'

Base pairing

Enzyme-catalysed
primer-extension

Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.2 Secondary Structure - Double Helix
Mechanism

O
O

P
O

O P O

Me

NH
O

OH

NH2

P
O

N
O

HN

OH

P
O

O P O

H2N

H2N

O
O
O P O

O
O P O

Template

Growing chain
Lecture 2
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.2 Secondary Structure - Double Helix
Replication

O
O

P
O

O P O

Me

NH
O

H2N

OH

P
NH2

O P O
O

N
O

N
O

Chemical Bond
Formation

HN

Displace
Pyrophosphate

O
O

H2N

O
O
O P O

O
O P O

Template

Growing chain
Lecture 2
Oxford University Press, 2013

Polymerase Chain Reaction (PCR)

Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.3 Tertiary Structure
Notes:
Double helix coils into a 3D shape - supercoiling
Double helix has to unravel during replication
Unravelling leads to strain
Relieved by enzyme-catalysed cutting and repair of DNA chain
Quinolone and fluoroquinolone antibacterial agents inhibit this enzyme

Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.4 Action of topoisomerase II
Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr

5'

3'

3'

DNA

5'

Tyrosine residues in the enzyme are involved in the chain breaking process

Lecture 2
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.4 Action of topoisomerase II
Relieves the strain in the DNA helix by temporarily cleaving the DNA
chain and crossing an intact strand through the broken strand

Topo II

Tyr
5'

3'

3'

Tyr

DNA

5'

Topo II

Tyrosine residues in the enzyme are involved in the chain breaking process
The tyr residues form covalent bonds to DNA

Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.4 Action of topoisomerase II

Topo II

Tyr

Tyr

DNA

Topo II

The enzyme pulls the chains apart to create a gap

Lecture 2
Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.4 Action of topoisomerase II
3

Topo II

Tyr
5'

3'

3'

5'

Tyr
Topo II

The intact strand of DNA is passed through the gap

Lecture 2
Oxford University Press, 2013

1. DEOXYRIBONUCLEIC ACID (DNA)

1.4 Action of topoisomerase II

Topo II

Tyr
5'

3'

3'

5'

The break is resealed

Lecture 2

32

Oxford University Press, 2013

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1. DEOXYRIBONUCLEIC ACID (DNA)

1.4 Action of topoisomerase II
Mechanism of chain cutting
5'

Base

5'

Base

O
H

HO

TopoII

Tyr

HO
H

O
O P
O O

O P
O O

Base

O
H

Base

O
H

H
H

TopoII
Tyr

3'

3'

Lecture 2
Oxford University Press, 2013

2. RIBONUCLEIC ACID (RNA)

2.1 Primary structure
Similar to DNA with the following exceptions
Ribose is used instead of deoxyribose
Uracil is used rather than thymine

O
HOCH2 O
H

OH

HN

OH

OH

Ribose

N
H

Uracil

Lecture 2
Oxford University Press, 2013

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2. RIBONUCLEIC ACID (RNA)

2.2 Secondary structure
Notes
RNA is single stranded
Some regions of helical secondary structure exist due to
base pairing within the same strand (see t-RNA)
Adenine pairs to uracil; guanine pairs to cytosine

Lecture 2
Oxford University Press, 2013

2. RIBONUCLEIC ACID (RNA)

2.3 Tertiary structure
Three types of RNA are involved in protein synthesis:
Messenger RNA (mRNA)
Contains the genetic code for protein synthesis
Transfer RNA (tRNA)
The adapter unit linking the triplet code to specific amino acids
Ribosomal RNA (rRNA)
RNA in the ribosome that catalyzes peptide-bond formation

Lecture 2
Oxford University Press, 2013

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2. RIBONUCLEIC ACID (RNA)

3'p
end
A
C
C
A
C
C
U
G
C
U
C

2.3 Tertiary structure

5'p
end
G
G
G
C
G
U
U U A
G A UG
G
A G G C C
UH2
C G C G mGU
G
C
U C C G G
C
G
T PsC
A G C G C m2G
G UH2
UH
C
G
A G 2
U
A
C
G
C
G
C
G
Ps
U
U
mI
I
C
G

Base Pairing

mI
I
UH2
T
Ps
mG
m2G

AMINO
ACID

Methylinosine
Inosine
Dihydrouridine
Ribothymidine
Pseudouridine
Methylguanosine
Dimethylguanosine

Yeast alanine-tRNA

ANTICODON

Anticodon - contains 3 bases that are specific for the attached amino acid
- base pairs to the complementary sequence on the mRNA strand
Lecture 2
Oxford University Press, 2013

ICG

2. RIBONUCLEIC ACID (RNA)

2.4 Transcription
The copying of a segment of DNA which codes for a specific protein

mRNA
G
T
A
T
C
T
G
T
C
C
C
T
T
A

DNA double helix

G
T
A
T
C
T
G
T
C
C
C
T
T
A

C
A
T
A
G
A
C
A
G
G
G
A
A
T

DNA unravelled
to reveal gene

G
U
A
U
C
U
G
U
C
C
C
U
U
A

C
A
T
A
G
A
C
A
G
G
G
A
A
T

G
U
A
U
C
U
G
U
C
C
C
U
U
A

mRNA

Transcription

Lecture 2
Oxford University Press, 2013

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2. RIBONUCLEIC ACID (RNA)

2.6 Modifications of mRNA prior to translation

Exon

Intron

Excised segment

Exon

Splicing

mRNA

Processed mRNA

Transcription

Translation

Notes:
Modifications can occur where a middle section (intron) is excised
End regions (exons) are then spliced together
Splicing requires an RNA/protein complex called a spliceosome
The RNA in spliceosome is called small nuclear RNA (snRNA)
snRNAs align the target mRNA by base pairing to it
splicing occurs in the nucleus
RNA is exported to the cytoplasm for translation
Lecture 2

39

Oxford University Press, 2013

2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis
Growing
protein chain

His

Ribosome
60S

mRNA

P-site A-site
GCU GCA
CGA CAU GUC
40S

Lecture 2
Oxford University Press, 2013

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2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis
Protein chain
transferred

OH

His

Ribosome
60S
P-site A-site
GCU GCA
CGA CAU GUC

mRNA

40S

Lecture 2
Oxford University Press, 2013

2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis
OH

Protein chain
transferred

His
GCU
Ribosome
60S

mRNA

P-site A-site
GCA
CGA CAU GUC
40S

Lecture 2
Oxford University Press, 2013

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2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis
Protein chain
transferred

His

Ribosome
60S

mRNA

P-site A-site
GCA
CGA CAU GUC
40S

Lecture 2
Oxford University Press, 2013

2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis
Protein chain
transferred

His

Val

tRNA

Ribosome
60S

mRNA

P-site A-site
GCA CAG
CGA CAU GUC
40S
Translocation

Lecture 2
Oxford University Press, 2013

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2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis (amide bond formation)
PEPTIDE
NH2

NH

R' C H
O C

R C H
O C
HO
H
H
Adenine

HO
H
H

O
H H OH
O

Adenine

O P O
O

O
H
O

t RNA
Transfer of
growing peptide
chain to next
amino acid

OH

O P O
O

PEPTIDE

t RNA

R C H
O C

NH

NH
HO
H
H
Adenine

R' C H
O C

OH
H H
O

HO
H
H

OH
P O
O

Adenine

O
H
O

t RNA

Lecture 2

H
OH
O

P O
O

t RNA

Oxford University Press, 2013

2. RIBONUCLEIC ACID (RNA)

2.5 Translation - protein synthesis

mRNA

Overview
Ribosome

Amino acid
tRNA

DNA
mRNA

Translation

Transcription
Nucleus

Protein

Lecture 2
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Recombinant DNA Technology

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DNA
Engineering

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Multiple
Cloning Site

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DNA Ligase (mechanism)

To rejoin DNA, ligase enzymes first attach to an adenosly monophosphate that is

attacked by the 5 phosphate, which is then attacked by the 3 OH on the other
side of the nick
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Recombinant Protein Expression

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Polyacrylamide Gel
Electrophoresis (PAGE)

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SDS PAGE
Analysis

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