Introduction to Bioorganic Chemistry and Chemical Biology 1

Answers to Chapter 3
(in-text & asterisked problems)

Answer 3.1
OH
-O P O
O
O O
5'
N NH

O
3'
O
-O P N O
O
O O N
NH
N
O NH2
dash/wedge -O P NH2
drawing O
O
O N N

O
O
-O P N NH2
O
O O N
5'
N
N
3'
O
pTGCAp -O P
O
The labor of drawing a simple tetranucleotide helps O
one to appreciate why we use a combination of
one-letter code and atom-numbering to discuss DNA.
Introduction to Bioorganic Chemistry and Chemical Biology | A3211
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.2
© www.garlandscience.com design by www.blink.biz

In the gas phase, the charge separation costs 83 kcal mol–1, which is much more costly
than the maximum benefit of aromaticity (35 kcal mol–1). However, in water, where the
dielectric constant is about 78, charge separation costs only 1.1 kcal mol–1, which is a
small compared with the energetic benefits conferred by aromaticity.
q1 q2
Energy = ke 4.0 Å
ε distance
9.0 x 109 J•m (1.6 x 10 -19 C)(1.6 x 10 -19 C) 1Å R N O
= + -
C2 1 × (4.0 Å) 10-10 m

= 5.8 x 10-19 J 1 kJ 6.0 x 1023 gas phase ε=1

× water (25 ° C) ε = 78
1000 J mol
= 35 kJ mol–1
or 83 kcal mol–1 (1 cal = 4.18 J) in gas phase ( ε = 1)

Energy = 1.1 kcal mol–1 in water at 25 °C ( ε = 78)

Introduction to Bioorganic Chemistry and Chemical Biology | A3212
It is important to recognize that the positive charge on nitrogen and negative charge on
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
oxygen is a Lewis structure formalism. In fact, the nitrogen atom has a partial negative
charge and most of the positive charge is distributed on the various hydrogen atoms.
Surprisingly, ab initio calculations HF/STO-3G predict a dipole moment of 4.8 Debye
units, not too different from the dipole moment predicted from a +1 charge and -1
charge separate by 4.0 Å (4.0 Debye units).
2 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3

Answer 3.3
- ..
O :O: most basic and most nucleophilic
amide
N N+

N +N
amidine .. -
N N: most basic and most nucleophilic

Introduction to Bioorganic Chemistry and Chemical Biology | A3213

Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.4
© www.garlandscience.com design by www.blink.biz

.. H A +
N .. NH + NH
O N NH2 O N NH2 O NH2
HO HO HO N
+
N N N N N
HO HO HO N

+ H : A-
O O O O OH
HO : OH2 HO + H HO

HO HO HO

: A-
.. H H
NH N N+ N
A H :N NH2 N NH2 NH2 HN NH2
H + H N
N N N N N N N N
Introduction to Bioorganic Chemistry and Chemical Biology | A3214
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.5
© www.garlandscience.com design by www.blink.biz

The major groove.

major
groove
H
N N H O R
N N H N
R
N N
O R

Introduction to Bioorganic Chemistry and Chemical Biology | A3215

Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.6
© www.garlandscience.com design by www.blink.biz

O NH2 NH2 NH2 NH2

NH N N NH
or
N N O N O
H
Introduction to Bioorganic Chemistry and Chemical Biology | A3216
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.7
© www.garlandscience.com design by www.blink.biz

Five possible 18-base probes (A–C) will have complete overlap with the 14-base
sequence. Probes A–C will have the highest GC content and therefore the highest Tm.
Probes D and E will have a slightly lower Tm.

target 5'-CGGGGGTGGCGCAGTGAGGAGG-3'
probe A 3'-GCCCCCACCGCGTCACTC -5' Tm = 4x2 + 14x4 °C = 64 °C
probe B 3'-CCCCCACCGCGTCACTCC-5' Tm = 4x2 + 14x4 °C = 64 °C
probe C 3'-CCCCACCGCGTCACTCCC -5' Tm = 4x2 + 14x4 °C = 64 °C
probe D 3'-CCCACCGCGTCACTCCCT -5' Tm = 5x2 + 13x4 °C = 62 °C
probe E 3'-CCACCGCGTCACTCCCTC -5' Tm = 5x2 + 13x4 °C = 62 °C
Introduction to Bioorganic Chemistry and Chemical Biology | A3217
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 3

Answer 3.8
415 = 1,073,741,824
416 = 4, 294,967,296
4 =
17
17,179,869,184
418 = 68,719,476,736
419 = 274,877,906,944
420 = 1,099,511,627,776
Introduction to Bioorganic Chemistry and Chemical Biology | A3218
There are 68 billion possible DNA sequences composed of 18 base pairs, over 20 times
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
more than the number of bases in the human genome. At most, a human-size genome
could contain only about 3  billion different 18  bp sequences. Thus, it is reasonably
unlikely that an 18-base sequence would be present in the human genome as a result
of random chance.

Answer 3.9
This hairpin was selected from a library of oligonucleotides because it binds to the amino
acid arginine. Only the first six and last six nucleotides form contiguous Watson–Crick
base pairs. NMR studies of the hairpin•arginine complex (PDB 1DB6) revealed additional
interactions not shown in the answer below, a Watson–Crick base pair between G9 and
C16 as well as non-Watson–Crick interactions between other pairs of bases.
1
5'-CGACCA A
CG T
G
3'-GCTGGTC T
22 CG C

Introduction to Bioorganic Chemistry and Chemical Biology | A3219

Answer 3.10
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz

T TT G
hairpin 5'-GGG GATGG CAC T
3'-CCCGCTACC GTG A
GG
Introduction to Bioorganic Chemistry and Chemical Biology | A3220
Answer 3.11
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
B
.. good nuc
Ph Ph - Ph - Ph O
O
H H O- H O: H O: H H
N N H N H N N
R NH2 H N R N R N R N Ph
.. + H
N HO R N HO B H :N HO good L.G. H N HO HO
+ HN S
-O S -O S HO2C S HO2C S
2C 2C
Me
Me Me Me Me Me Me Me Me HO2C Me
Introduction to Bioorganic Chemistry and Chemical Biology | A3221
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.12 design by www.blink.biz
© www.garlandscience.com

The guanidine moiety of arginine is protonated at pH 7, and these protonated arginine
side chains confer a significant affinity for the phosphate backbone of DNA. The urea
group of citrulline, which is not protonated at neutral pH, would have a lower affinity for
an anionic phosphate diester. Deimination of histones would release the bound DNA,
making it accessible to transcription factors.

O O
O O
arginine H H - P O citrulline - P O
N+ O O O
H H
N N N N
H H H H
stable salt bridge with DNA less stable interaction DNA
Introduction to Bioorganic Chemistry and Chemical Biology | A3222
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
4 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3

Answer 3.13
DNA polymerase can only add to the 3ʹ end of a growing strand. The primer will be
identical to the 5ʹ end and complementary to the 3ʹ end.
5ʹ-CCATGCCTATGTTCATCGTGA-3ʹ
5ʹ-CCATGCCTATGTTCATCGTGAACACCAATGT……CTGGCCCCACTTACCTGCACCGCTGTTC-3ʹ
3ʹ-GTGAATGGACGTGGCGACAAG–5ʹ

Answer 3.14
O Ph
B: H H H
NHBz N NHBz N NH NHCH3
H3C + H3C
.. N - N: - N: N
CH3NH2
N O N O N O N O
R R R R
Introduction to Bioorganic Chemistry and Chemical Biology | A3224
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.15 design by www.blink.biz
© www.garlandscience.com

OR OR
H +
NC P
.. i-Pr NC P i-Pr OR i-Pr
O N O N H
NC P N H A

..
i-Pr i-Pr O
H i-Pr
.. N
N N N
N N -
N N
N N N N

H
i-Pr2N : OR OR
OR + i-Pr H
H NC P NC P
NC P N H O + N O N
O N N
N i-Pr N N N N
N
N N
Introduction to Bioorganic Chemistry and Chemical Biology | A3225
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.16 design by www.blink.biz
© www.garlandscience.com

-
B: H O OH :O OH OH
O
Gal O Gal O Gal O
O O O

OSO3Na OSO3Na
Introduction to Bioorganic Chemistry and Chemical Biology | A3226
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.17
© www.garlandscience.com design by www.blink.biz

The amount of inhibitor drug is increasing from lane 1 to lane 6. At the highest
concentration of drug, most of the plasmid DNA remains in the fully supercoiled state.
(Figure adapted from I. Larosche et al., J. Pharmacol. Exp. Ther. 321: 526–535, 2007.)

least most
inhibitor inhibitor
sample 1 2 3 4 5 6
relaxed

partially supercoiled

supercoiled

actual [inhibitor] (µM) ~0 5 10 20 50 100

Introduction to Bioorganic Chemistry and Chemical Biology | A3227
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 5

Answer 3.18
A 5'-5'- 5'- AACTGAATTTCAGGGGGATCCGCATGGCGT
AACTGAATTTCAGGGGGATCCGCATGGCGT
AACTGAATTTCAGGGGGATCCGCATGGCGT -3'-3' -3'
3'-3'- 3'-TTGACTTAAAGTCCCCCTAGGCGTACCGCA
TTGACTTAAAGTCCCCCTAGGCGTACCGCA
TTGACTTAAAGTCCCCCTAGGCGTACCGCA -5'-5' -5'

B Design and synthesize two oligonucleotides with BamHI overhangs on the ends.
These will hybridize to any site cut with BamHI.

5'-5'- 5'- AACTGAATTTCAGGGGGATCCGCATGGCGT

AACTGAATTTCAGGGGGATCCGCATGGCGT
AACTGAATTTCAGGGGGATCCGCATGGCGT -3'-3' -3'
3'-3'- 3'-TTGACTTAAAGTCCCCCTAGGCGTACCGCA
TTGACTTAAAGTCCCCCTAGGCGTACCGCA
TTGACTTAAAGTCCCCCTAGGCGTACCGCA -5'-5' -5'

BamH1 BamH1
BamH1
GATCCGCATGGCGT
GATCCGCATGGCGT
GATCCGCATGGCGT -3'-3' -3'
GCGTACCGCA
GCGTACCGCA
GCGTACCGCA -5'
-5'-5' design
design design and
and
5'- AACTGAATTTCAGGGG and
5'-5'- AACTGAATTTCAGGGG
AACTGAATTTCAGGGG synthesizesynthesize
synthesize
3'-3'- 3'- TTGACTTAAAGTCCCCCTAG
TTGACTTAAAGTCCCCCTAG
TTGACTTAAAGTCCCCCTAG
kinase
kinase kinase
pGATCCGCATGGGTTTCAAATCG
pGATCCGCATGGGTTTCAAATCG
pGATCCGCATGGGTTTCAAATCG
GCGTACCCTTTGTTTAGCCTAGp
GCGTACCCTTTGTTTAGCCTAGp
GCGTACCCTTTGTTTAGCCTAGp

5'-5'- 5'- AACTGAATTTCAGGGG

AACTGAATTTCAGGGG
AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG
GATCCGCATGGGTTTCAAATCG
GATCCGCATGGGTTTCAAATCG GATCCGCATGGCGT
GATCCGCATGGCGT
GATCCGCATGGCGT -3'-3' -3'
3'-3'- 3'-TTGACTTAAAGTCCCCCTAG
TTGACTTAAAGTCCCCCTAG
TTGACTTAAAGTCCCCCTAG GCGTACCCTTTGTTTAGCCTAG
GCGTACCCTTTGTTTAGCCTAG
GCGTACCCTTTGTTTAGCCTAG GCGTACCGCA
GCGTACCGCA
GCGTACCGCA -5'-5' -5'

T4T4
DNADNA T4 DNA
ligase
ligase ligase
Mg•ATP
Mg•ATP Mg•ATP

5'-5'- 5'- AACTGAATTTCAGGGG

AACTGAATTTCAGGGG
AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG
GATCCGCATGGGTTTCAAATCG
GATCCGCATGGGTTTCAAATCG GATCCGCATGGCGT
GATCCGCATGGCGT
GATCCGCATGGCGT -3'-3' -3'
3'-3'- 3'-TTGACTTAAAGTCCCCCTAG
TTGACTTAAAGTCCCCCTAG
TTGACTTAAAGTCCCCCTAG GCGTACCCTTTGTTTAGCCTAG
GCGTACCCTTTGTTTAGCCTAG
GCGTACCCTTTGTTTAGCCTAG GCGTACCGCA
GCGTACCGCA
GCGTACCGCA -5'-5' -5'

C The sequence contains two BamHI sites. Any new overhangs on the ends could
hybridize within the oligonucleotide or between oligonucleotides.
GATCCTTTCATAAGTGGTGGGATCCCCATTCAATTG
GATCCTTTCATAAGTGGTGGGATCCCCATTCAATTG
GATCCTTTCATAAGTGGTGGGATCCCCATTCAATTG
GAAAGTATTCACCACCCTAGGGGTAAGTTAACCTAG
GAAAGTATTCACCACCCTAGGGGTAAGTTAACCTAG
GAAAGTATTCACCACCCTAGGGGTAAGTTAACCTAG
Introduction
Introduction Introduction
to Bioorganic
to Bioorganic to Bioorganic
Chemistry
Chemistry andandChemistry
Chemical
Chemical and Chemical
Biology
Biology Biology | A3228
| A3228
| A3228
VanVan Answer 3.19
Vranken
Vranken &Van Vranken
Weiss
& Weiss & Weiss | 978-0-8153-4214-4
| 978-0-8153-4214-4
| 978-0-8153-4214-4
© www.garlandscience.com
© www.garlandscience.com
© www.garlandscience.com design
design design by www.blink.biz
by www.blink.biz
by www.blink.biz
Enz
H2..
N Enz
O O F2 O O HN Enz
O HN
CF 3 .. C CF 2 .. CF 2
HN HN - F HN HN - CF 2
HN
O N O N S O N S O N S
O N
R S- R R R
..

Enz Enz Enz R

Enz
Introduction to Bioorganic Chemistry and Chemical Biology | A3229
Answer 3.20
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
..
O O :O O+
N N H N N
O: H A O H A OH2+ ..
- ..

-A
..

.. + H H H H - H A
+
NH2 N O N O N O N O
..

..

..

Gua Gua + N Gua N Gua N

A- .. H A .. + +
..

H N OH2
N OH Gua N N
..

N OH Gua N Gua N
Gua + N
O
O
O N :O -
HN N
N N HN
NH NH
H2N N N +
.. N N N
N N N R N N H
+ N N R
R R + 2

O O
N NH HN N

N N N N N
R H R
Introduction to Bioorganic Chemistry and Chemical Biology | A3230
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
6 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3

Answer 3.21

C6H13 C6H13 C6H13

..N +
N N
.. O
Nu
S C N N+
NH
fascicularin aziridinium ion N
N NH2
DNA
Introduction to Bioorganic Chemistry and Chemical Biology | A3231
Van Vranken & Weiss | 978-0-8153-4214-4
Answer 3.22
© www.garlandscience.com design by www.blink.biz

abstraction of the two H atoms is not concerted

• H H
abstract
H atom

• H H

H H H H
• abstract
H atom
+

• H H H H

Answer 3.23

H
uncialamycin
reducing
R intracellular H
O HN HO HN R
O environment HO OH
OH
OH H2O

O OH R = CH(OH)CH 3 HO OH

reduced Bergman
in the cell rearrangement

R R
HO HN HO HN
O HO

OH OH OH
S N1
HO OH
Introduction to Bioorganic Chemistry and Chemical Biology | A3232
HO OH
Van Vranken &to
Introduction Weiss | 978-0-8153-4214-4
Bioorganic Chemistry and Chemical Biology | A3233
www.garlandscience.com
Van
© design by www.blink.biz
Vranken & Weiss | 978-0-8153-4214-4
Answer 3.24
© www.garlandscience.com design by www.blink.biz

H
H
H
H H H • H
H H
H H H H
H
H H
H H H
•
H
H H H H H
H H H H H
H H H H +
•
H H
H H H
H H H
•
H H H H H
H
Introduction to Bioorganic Chemistry and Chemical Biology | A3234
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 7

*Answer 3.26

A The conformational depiction OH B Gua

below and the dash/wedge O
-O P
depiction to the right are O HO
O O O Ade
equally acceptable Thy O
-O P O
O O Cyt
O O
-O P -O P O
O O O Ade
O O Ade d( GACA) O
-O P O
"d" prefix means 2-deoxy
O HO
O
OH Thy -O P
O O
-O P O O O Thy
O O Ade
O
-O P O
O Thy O
O
O -O P
-O P O O
O O
O O Ade Ade
pTATA O
presence of Thy -O P O
suggests that this is DNA O HO HO

C Gua
O
HO
O Ura
OH O
-O P O
O O Cyt
OH O
-O P O
O O Ura
OH O
GUCU -O P O
presence of Ura
suggests that this is RNA O HO OH
Introduction to Bioorganic Chemistry and Chemical Biology | A3236
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
*Answer 3.27
CH3
H N
N N H N

N N H N
dR
N N
O dR
Introduction to Bioorganic Chemistry and Chemical Biology | A3237
Van Vranken & Weiss | 978-0-8153-4214-4
*Answer 3.30
© www.garlandscience.com design by www.blink.biz

A In PDB 1AIO, cisplatin forms a crosslink between the N7 atoms of guanine bases
(rendered in yellow).

Introduction to Bioorganic Chemistry and Chemical Biology | A3238

B The platinum
Van Vranken atom sits in the major groove.
& Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz

C The crosslink is intrastrand, between adjacent guanine bases.

8 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3

Answer 3.32
*A 3ʹ-AGCTTACGTAATAAGCA-5ʹ or
5ʹ-ACGAATAATGCATTCGA-3ʹ

*Answer 3.33
A The following secondary structures are expected for each oligonucleotide or pair of
oligonucleotides. The sites of oxidation are shown with arrows.

arrows highlight
sites of oxidation ssDNA 5'-CATGCGTTCCCGTG -3'

5'-CATGCGTTCCCGTG -3'
duplex formation 3'-GTGCGCAAGGGCAC -5' strand not analyzed

hairpin or 5'- AGTCTA G

5'- AGTCTA TAGACT -3'
duplex with mismatch bulge 3'- TCAGAT G or
3'- TCAGAT ATCTGA -5'
G

G
duplex with mismatch bulge 5'-ACGTCAG TGGCAT -3'
3'-TGCAGTC strand not analyzed
ACCCGTA -5'

hairpin or 5'- AGTCTAT G

G TGGGT
or 5'-AGTCTA TAGACT -3'
duplex with mismatch bulge 3'- TCAGATT G 3'-TCAGAT ATCTGA -5'
TGGGT

Introduction to Bioorganic Chemistry and Chemical Biology | A3239

Van Vranken & Weiss | 978-0-8153-4214-4
B On the basis
© www.garlandscience.com ofbythe
design structures, the susceptible bases seem to be guanidines that
www.blink.biz

are not protected by both base-pairing and π stacking. Therefore, Gs at the ends of
duplexes or in bulges or loops are susceptible.

*Answer 3.37

MeO
MeO MeO
MeO NO2 OH
hv
Ca2+ MeO N MeO N
H2O O O
N N or...
Ca R'
O O O O NH O N HO
-O CO2-
HO O O OH 2C
-O CO2-
2C

MeO * MeO MeO

OH
+ O- O-
MeO N
hv MeO N MeO N
O OH ..
O
H R'
R 2N N N
R' R 2N
Ca
O O O O
HO O O OH
Introduction to Bioorganic Chemistry and Chemical Biology | A3242
Van Vranken & Weiss | 978-0-8153-4214-4
*Answer 3.38
© www.garlandscience.com design by www.blink.biz

A
..
O O :O O+
N N H N N
O: H A O H A OH2+ ..
- ..

-A
..

.. + H H H H - H A
+
NH2 N O N O N O N O
..

..

..

Ph Ph + N Ph N Ph N

A- .. H A .. + +
..

H N OH2
N OH Ph N N
..

N OH Ph N Ph N
Ph + N
 N N H N N
O: H A O H A OH2+ ..
- ..

-A

..
.. + H H Introduction
H to Bioorganic Chemistry
H - H Aand Chemical Biology: Answers to Chapter 3 9
+
NH2 N O N O N O N O

..

..

..
Ph Ph + N Ph N Ph N

A- .. H A .. + +
..
H N OH2
N OH Ph N N

..
N OH Ph N Ph N
Ph + N

B
NH2 as in part A.

N O
DNA

H H
N2+ +N + OH OH O O
2 OH2 A + H A A-
OH2+

..
..

+
..

N :N- N N NH NH

..
N O N O N O N O N O N O
DNA DNA DNA DNA DNA DNA

C
NH2 O
adenine NaNO 2
N N HCl N NH
N N H2O N N
DNA DNA
O O
guanine NaNO 2
N NH HCl N NH
N N NH2 H2O N N O
DNA DNA H
Introduction to Bioorganic Chemistry and Chemical Biology | A3243
Van Vranken & Weiss | 978-0-8153-4214-4
*Answer 3.41
© www.garlandscience.com design by www.blink.biz

:
:

B :B
H - OH
N O :N O N O: H B N N N-
N
O 2N N O 2N N C N C + :N N+ N+
N N N N N NH C
H H NH C B: C
CH3 CH3 O 2N CH3 O 2N H H H H H H
H H
Introduction to Bioorganic Chemistry and Chemical Biology | A3246
Van Vranken & Weiss | 978-0-8153-4214-4
*Answer 3.42
© www.garlandscience.com design by www.blink.biz

A With a calculator: 430 = 1,152,921,504,606,847,000 = 1.2 × 1018

Even better, work this without a calculator using the approximation 410 ≈ 106: [410]3 =
[106]3 = 1018
B
5'-GGGAGAATTCCCAGACC-3'
5'-GGGAGAATTCCCAGACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGAGGGAAATTCTCCC-3'
3'-GACTCCCTTTAAGAGGG-5'
5'-GGGAGAATTTCCCTCAG-3'
C
AC GT
5'-GGGATCGAA A
3'-CCCTAGCTT G
CC GC

Arg
D
H H H H H
+ NH2 + NH2 Arg + NH2
N N N N N N
 5'-GGGAGAATTTCCCTCAG-3'
C
AC GT
5'-GGGATCGAA
10 A Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3
Introduction to
3'-CCCTAGCTT G
CC GC

Arg
D
H H H H H
+ NH2 + NH2 + NH2
N N N N Arg N N
H H H H H
N N or N N or N N
H H H H H
O N O N O N
dC dC dC
Arg
Introduction to Bioorganic Chemistry and Chemical Biology | A3248
*Answer 3.44
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz

Me OH Me OH Me OH
Me Me Me
Me Me Me
OH OH +H O OH
HO HO.. 2
O : SR OH SR OH SR
- H A

DNA: Me Me
OH OH
Me DNA
Me

Me + OH Me OH
OH SR OH SR

*Answer 3.48

Hto Bioorganic
Introduction H Chemistry and Chemical Biology | A3251
N | 978-0-8153-4214-4
Van Vranken & Weiss H H
© www.garlandscience.com design by www.blink.biz N
N N N N
N N
.. N N
DNA +
DNA
H
N
HN N R HN N O
O
O O N
H O HO H
+
Introduction to Bioorganic Chemistry and Chemical Biology | A3255
Van Vranken & Weiss | 978-0-8153-4214-4
*Answer 3.51
© www.garlandscience.com design by www.blink.biz

B
 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 11

*Answer 3.54
O
Introduction to Bioorganic Chemistry and Chemical OMe
Biology | A3258
NHCO2Me
Van Vranken & Weiss | 978-0-8153-4214-4
HO
© www.garlandscience.com Sby www.blink.biz
design NHEt

O O O

O OH
aromatic N can
by-product Me S intercalate
Me O between
base pairs
HN

OH
Introduction to Bioorganic Chemistry and Chemical Biology | A3261
*Answer 3.57
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz

5ʹ-TCCTNNAGGA-3ʹ
head (H)
A The oligosaccharide
OH is asymmetric with a head (H), a tail (T), a left-hand side and a
right-hand
MeO side.Me
head (H)
O
HO OH
O MeO Me
MeO I
O
HO
left- MeO O
Me right-
hand MeOhand I
side S O side
HO left- MeMeO Me right-
hand hand
O
side S O side
O HO Me
HN
HO Me O

O O
O O HN
O HO Me
EtHN O
OMe O O
tail (T) O
EtHN
OMe
tail (T)
B Because the minor groove is also asymmetric, the 3ʹ end is different from the 5ʹ end.
Therefore the oligosaccharide will bind in a preferred orientation.
5' 3'
| |

T A
H 5'| 3'
C G |

C GT H A
T T AC G
|
3'
C
|
5'
G
T T A
| |
3' 5'
 C G
T T A
12 |
Introduction to Bioorganic Chemistry and Chemical |
Biology: Answers to Chapter 3
3' 5'

C If you link the oligosaccharide tail to tail, each half still wants to bind with the origi-
nal orientation.

5' 3'
| |

T A
H
C G
C G
T T A
N O
N
N N
A T T
G C
G C
A| H T
|
3' 5'

*Answer 3.58 Chemistry and Chemical Biology | A3264

Introduction to Bioorganic
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz
para-benzyne enediyne
+ intermediate - .. precursor
- Cl :

NC NC
- .. - Cl : + NC
O O O O
O O
OH OH OH
HO
HO HO OH
OH OH
O
O O
Introduction to Bioorganic Chemistry and Chemical Biology | A3265
Van Vranken & Weiss | 978-0-8153-4214-4
© www.garlandscience.com design by www.blink.biz