2015 化學生物學handout Ch. 3-1

Section 3-1 National Tsing Hua University
CHEM5980
Organization of genomic DNA depends on the type of organism

• Genomic DNA appears in double helix to store information. However
depending on the type organism, these macromolecules were organized
differently.
• E. coli genomic DNA has both ends connected in cyclic form. Bacteria also
contains small cyclic DNA called plasmid.
• Human cells have their genomic DNA located in nucleus and mitochondria, in
which the mitochondrial DNA are cyclic as like E. coli and nuclear DNA are
divided into 23 chromosomes.
CHEM3100
DNA secondary structure: Double helix

• 3 double helix DNA structures have been identified
• The most stable one under physiological conditions is B-DNA
Minor groove
Major
groove
Rise per
turn
Rise per
residue Curr Prot Nucl Acid Chem 2009 A.1B
A-DNA B-DNA Z-DNA
Helical sense Right handed Right handed Left handed

Diameter ~26Å ~20Å ~18Å
Base pair / turn 11 10.5 12
Right hand helix
Helix rise / base 2.6Å 3.4Å 3.7Å
Diameter Base tilt normal to axis 20˚ 6˚ 7˚
CHEM3100
Nucleosides, nucleotides and nucleic acids

• Nucleic acids are polymers of ribose derivatives through diphosphate bonds
• Nucleotides, the monomer for nucleic acids, are composed with aromatic
bases, riboses (or it deoxy form) and phosphates
-
O- O- O-
O O O O
P P P Base
O
O O O
OH R
Nucleoside
Nucleotide
Nucleoside = Base + sugar

Nucleotide = Base + sugar + phosphate
Nucleic acid
© 2014 Pearson Education Inc.
CHEM3100
Nomenclatures
R R R R
R = OH adenosine guanosine cytidine uridine
R=H 2’-deoxyadenosine 2’-deoxyguanosine 2’-deoxycytidine thymidine

CHEM5980
DNA base and aromaticity

• Linear conjugation transmit
resonance while cross
conjugation impedes that.
• For heterocyclic compounds,
aromaticity often comes at the
price of charge separation.
• In such cases, the overall state of
the heterocyclic compounds also
depend on the environmental
conditions as the dielectric
constant governs the energy cost
for charge separation. Therefore
the resonance in vacuum and in
aqueous solution will be very
different.
CHEM5980
DNA under physiological conditions

• Nucleic acids are not acidic, and DNA bases are not basic. A paradox?
• pKa of phosphodiester is around 1~2, under physiological condition most of them
are deprotonated and no longer function as acid anymore.
• The pKa of the protonated bases are pretty small, showing these bases are very
weak bases.
• Ignore the diplomatic language and focus on the ionization state of DNA in
physiological condition. The DNA base are rarely protonated at pH 7.4.
CHEM3100
DNA and 2’-OH

• RNA is not stable due the presence of 2’-OH, which is also a nucleophilic catalyst for
RNA cleavage
• DNA is the media for storing genetic information and has to be very accurate.
Cleavage of DNA will be disastrous for cell; in contrast RNA are meant to degrade
after it served its purpose

CHEM5980
DNA under physiological conditions

• Apart from the formation of cyclic phosphodiester in the case of RNA, the 2’-OH
on ribose also affect the DNA stability in another way.
• Due to the induction effect from the 2’-OH, the cation on C-1 of ribose is
destabilized. Therefore 2’-OH of RNA prevent the possible SN1 ionization of the
base group. In contrast, DNA has no 2’-OH on ribose is 1000 time more susceptible
to base ionization.
CHEM5980
Base modifications on DNA

• Nucleic bases can be modified on DNA with enzymes or chemical reagents
• Some enzyme methylate nucleic bases in a site specific manner. S-Adenosyl methionine
is used as the source of methyl group.
• DNA methylation affects cytosine adenine
sequence recognition by DNA-(cytosine-5)- DNA-(cytosine-N4)- DNA-(adenine-specific)-
methyltransferase methyltransferase methyltransferase
endonucleases and
transcription factors.
These modification
results in the change of
expression and belongs S-Adenosyl methionine
to the field of epigenetics
• To detect cytosine 5-
methylation, bisulfite
addition can be used
to transform cytosine
to uracil. This process
does not alter 5-
methylcytosine and
the location of such
methylation can be
revealed
CHEM5980
Elementary forces in DNA

• DNA double helix structure is hold by many types of forces, however the
essential base pairing, which is responsible for complemented recognition, is
hold by the hydrogen bonds
• These hydrogen bonds have matching donor-acceptor combination and the 2
pairs of bases have comparable geometry that allows the stable and uniform
double helix structure.
CHEM5980
Tautomers of nucleic bases

• Like other imine or amide groups, tautomers of these functional groups exist.
• Tautomerism alters the hydrogen bond donor acceptor pattern and would
change the recognition between nucleic bases
H H
O O N
H H
N N N
N
N O N O N N
Thymine Uracil Adenine
• 5-bromouracil, mimic of thymine,

has more enol form tautomers
from equilibrium and this shift
would lead to significant error in
base pairing with guanine.
• 5-bromouridine readily
incorporates into DNA and cause
mutations beyond DNA repairing
system can fix.
CHEM5980
Roles of Hydrogen bonds beyond base pairing

• The nucleic bases have extra hetero atoms that are not involved in base pairing
• Some functional groups used for base pairing can be shared to initiate more
interactions.
• The above groups can initiate hydrogen

bonds specifically with other biomolecules ,
such as other nucleic base and proteins.
• Antibiotic chromomycin bind to double
helix in the minor groove, and transcription
factor Fos binds in the major groove.
CHEM5980
Hoogsteen base pair

• Hoogsteen found 1-methylthymine co-crystalize with 9-ethyladenine in different
manner comparing to Watson-Crick pairing . Similarly, protonated cytosine also
binds to guanine in such manner.
• Hoogsteen suggested there
are two edges for purine
one is for Watson-Crick
base pairing and the other
edge can be used for
pairing in the major groove.
• It is possible to fit another
strand of nucleic acid into Hoogsteen
major groove if purine are base pair
in the same strand Watson-Crick
• Hoogsteen interaction is base pair
important in DNA binding,

but it is found in RNA.
Extra section National Tsing Hua University
CHEM5980
The story of Iron: Bleomycin

• Bleomycin was discovered as antitumor antibiotic from Streptomyces verticillus.
• Bleomycin is a family of glycopeptide with several common moieties including
metal binding region, carbohydrate moiety, linker region and bithiazole tail.
• Bleomycin is used to treat Hodgkin's lymphoma, squamous cell carcinomas,
testicular cancer, and plantar warts.
• Bleomycin binds metal ion such as Fe (II), Cu (I) and Co (II) to be functional.
Metal
extraction
Curr Opin Chem Biol 2004,8, 175 PNAS 2000, 97, 13537
CHEM5980
The mechanism of Bleomycin

• After almost a half century of research, the detailed functions of all the Bleomycin
moieties are still not clear. But it is known that the antitumor activity come from
the cleavage of nucleic acid.
• Metal ion plays a essential role in the cleavage process. From the proposed
mechanism, oxidation metal-bleomycin complex allows the extraction hydrogen
from ribose C-4’ and then either break the nucleic acid backbone or lose the
nucleic base.
• Bleomycin binds to minor groove of DNA double helix and cleavage both
strands.
Nat Rev Cancer 2005, 5, 112

CHEM5980
DNA footprinting
• The mechanism of Bleomycin has demonstrate how can natural product cleavages
DNA. Based on the same strategy, chemical alternative could be made as tools.
• The design would require metal complex ligands, non-selective DNA binding moiety
and a linker connects two parts.
• This design cleavage DNA at all accessible location, therefore the location block
by other molecules can be detected. This strategy is called footprinting.
DNA binding moiety
Linker
Metal binding moiety
J Am Chem Soc 1982, 104, 313

CHEM5980
DNA affinity cleavage

• When the DNA cleaving metal complex conjugated to a sequence selective molecule,
the DNA double strand can be cleaved at designed location
Linker
DNA cleaving moiety
Distamycin:
Sequence specific
binding moiety
Tetrahedron 1984, 40, 457 Science 1987, 238, 645
CHEM5980
Recognition of DNA sequence by small molecules

• Distamycin is known for sequence-
specific binding to DNA at minor
groove, is it possible to change the
specificity by modify distamycin?
• Distamycin has repeated pyrrole units
seems to fit each base pair
• Introduction of 3-hydroxypyrrole and
H imidazole provide selectivity to
specific sequence.
Distamycin
Nature 1998, 391, 468

CHEM5980
G-quadruplex
• G-quadruplex is a specialized DNA structure that can be formed in G-rich unpaired
DNA. This special structure can be formed with Hoogsteen pairing among four
guanines.
• Cation such as potassium resides between layers formed by four guanines and help
stabilizing the structure.
• The function of G-quadruplex is not totally clear, but it may involve in transcription
control and the inhibition of telomerase action. Telomere is region at the end of
chromosome that has repeating sequence of GGTTAG to maintain chromosome
from deterioration.
• Telomerase add short sequence to T T
A A
T T
telomere to prevent shortening
through aging. But this process is GM G
G G
related to most cancers. G M
G
Formation of G-quadruplex in G M
G
telomeres has been shown to G G
G G
decrease the activity of the T A
enzyme telomerase and may be a T
promising target of drug discovery.
CHEM5980
Unnatural nucleic base pairs

• The four natural nucleic base uses the number of hydrogen bonds and donor/acceptor
pattern for recognition. Is it possible to create artificial nucleic base pairs?
• By changing the location of carbonyl and amine groups, iso-C and iso-G were created
as a matching pair. The hydrogen bonds pattern seem fits perfectly.
• Although iso-C/iso-G pair are accepted by ribosomal machinery, there are
fundamental problems: relocating carbonyl group on G cause the loss of aromaticity.
To compensate, iso-G has larger extent on its enol form, whose hydrogen bond
pattern matches thymine. In addition, 2-amino group of iso-C is more susceptable to
hydrolysis.
O N
G
HN N
R
N
H2N
CHEM5980
Unnatural nucleic base pairs

• It is possible to design complementary nucleic base without hydrogen bonds.
Although hydrogen bonds are essential for base pair recognition, this
recognition is not necessary for every pair.
• DNA polymerase can selectively incorporate these base pairs based on steric
complement demand rather than hydrogen bonds.
• Following are several nucleic bases that “pairs” without help from hydrogen
bonds,
CHEM5980
Design of unnatural nucleic base

• To design an unnatural nucleic base, the steric factors must be taken into account.
The size and geometry of the base have to fit the natural DNA double helix.
Curr Prot Nucl Acid Chem 2009, 1.4.1

• The interactions between the matching bases in a pair can be classified into several
categories:
Alternating hydrogen bond pattern pairs
Expanded base pairs
Non-hydrogen-bonding pairs
Stacking base pairs
Mimic bases for probing DNA damage
Covalent base pair analogs
Degenerate bases
• Useful book:
http://onlinelibrary.wiley.com/book/10.1002/0471142700/toc
CHEM5980
Purine-pyrimidine-like unnatural nucleic base

• Use three-hydrogen-bond pattern from C and
G pair, there are 6 combinations. Current only
one (and half) pair is used by natural base.
• K and X nucleotide was synthesized and used
with DNA polymerase to incorporate this
unnatural pair into DNA.
N
κ O N R
H H
N
H
N N
H X
N N O
H
N
R H
C-1’ epimerization Nature 1990, 343, 33

problem Curr Prot Nucl Acid Chem 2009, 1.4.1
CHEM5980
Purine-pyrimidine-like unnatural nucleic base

• Bases with 4 hydrogen bonds have been studied. The additional bonding is supposed to
provide stronger interaction.
• Interestingly, short DNA destabilized when one base pair of this type incorporated to
the middle of a DNA. However, when the insertion expanded to three tandem pairs,
the DNA become more stabilized. This type of base pair extend the distance between
paired deoxyriboses and cost some energy that gained from extra hydrogen bonds.
• Self-complement base pairs have also been studied

CHEM5980
Expanded unnatural nucleic base

• Natural nucleic bases can be expanded by fused aromatic rings or acetylene spacer.
This base expansion increases the diameter of DNA double helix.
• Due to the significant difference to natural nucleic base, these bases and unlikely
to be recognized by enzymes and DNA binding proteins.
C-glycosides
J Am Chem Soc 2004, 126, 11826 J Am Chem Soc 2008, 130, 8762
CHEM5980
Non-hydrogen-bonding unnatural nucleic base

• Key feature of these type of base pair is to fill up the space within DNA double
strands
• Melting temperature of these pairs have demonstrated the pairing between these
pairs are better than pairing with natural bases.
Contributed from Kool group
J Am Chem Soc 2008, 130, 2336

CHEM5980
Stacking unnatural nucleic base
• Nucleic bases with aromatic groups

tend to stack together.
• To allow stacking interaction between
double helixes, the bases need to be
extended to overlap with the their
parts.
• Analogs of biphenyl are used for this
type of unnatural base pair.

CHEM5980
Mimic to probe DNA damage

• One type of DNA damage is the removal of nucleic base, other damages include
alkylation to nucleic base
• The complement base of the damaged DNA can be use for selectively pairing at the
site of DNA damage.
• Pyrene nucleic base has been developed to pair to nucleotide with missing base
moiety; Naphthalene-based analogs have been tested to locate benzyl-
deoxyguanosine
Lost of nucleic base Alkylation of nucleic base
Probe for the damage Probe for the damage

CHEM5980
Metal-mediated base pair

• Coordination of metal ions have also been used for nucleic base pairing
• Square planar and linear planar complex have developed
• Rather than biological functions, this type of nucleic base are suitable for material
science and nanotechnology.

CHEM5980
Covalent base pair

• Reversible covalent bond provides possible pairing for nucleic bases, but
relatively rare.
• Disulfide bond have been exploited for this type of base pairing

CHEM5980
Creating organism with unnatural nucleic bases
• Unnatural base pair d5SICS and dNaM were used

• Endogenous polymerase recognize unnatural
nucleotide triphosphate (UNT).
• Problems with generation of UNT in cell, use
nucleotide triphosphate transporter instead.
• Deletion of periplasmic phosphatase to prevent
dephosphorylation of imported UNT.
• Engineering to focus on polymerase I instead of
Polymerase III
• Unnatural base pair not efficiently removed by
DNA repairing pathways.
Nature 2014, 509, 385
CHEM5980
“Nucleic acids” with unnatural backbones

O
N
• DNA recognition comes from the

NH
N N NH2
matching Watson-Crick base pair.

O
O NH2
Is it possible to replace the O

N
N
O-
deoxyribose-phosphodiester
O P N N
O
O
backbone to change the

NH2
N
O N
properties of DNA? O P
O
O-
N N
• Libraries of the scaffolds were O
created to change the location to O

O
P O-
present nucleic bases. O
• To see how the artificial

backbone resembles DNA, one N
O
can simply test Tm of the

NH
N N NH2
unnatural nucleic acid–DNA/RNA NH2
hybrid. N
N
• A series of peptide-based
N N
backbone were tested in the

NH2
N
N
format of H-GTAGATCACT-NH2. N N
Scaffold
library
Chem Soc Rev 1997, 73
CHEM5980
Peptide nucleic acid

• Peptide nucleic acid (PNA) has repeated N-(2-
aminoethyl)glycine backbone to mimic DNA.
• PNA was designed to be able to arrange
6 bonds
geometrically to the way DNA is. As DNA, the 3 bonds
number of bonds on the backbone that
separate each nucleic base is 6. Moreover,
the number of bonds from nucleic base to
the backbone is 3 for both PNA and DNA. 6 bonds
• One essential feature of PNA is that
phosphodiester group in DNA was replaced 3 bonds
by amide bonds, which has no charge in the
physiological conditions.
• Without the negative charged
phosphodiester group, there is no charge
repulsion between PNA and DNA when DNA
formed hybrid. Therefore PNA-DNA
interaction is stronger than that in duplex
PNA
DNA.
Chem Soc Rev 1997, 73
CHEM5980
Peptide nucleic acid

• General stabilities (Tm) of nucleic acids in the same sequence: PNA-PNA > PNA-RNA >
PNA-DNA ( > RNA-DNA > DNA-DNA )
• Interestingly, PNA-NA hybridize in both parallel and more stable anti-parallel manner.
Tm difference between these two orientations is around 1~2 ˚C.
• For such strong interaction, PNA are promising for antisense drug. It also forms
strong Hoogsteen (PNA)2-DNA triplex.
• Pure PNA duplex has very wide helix diameter at 28 Å.
PNA-DNA duplex PNA-PNA duplex
Science 1995, 270, 1838

CHEM5980
Locked and unlocked nucleic acids (LNA & UNA)

• Ribose/deoxyribose is the basic building block for the nucleic acid backbone,
modification on the sugar may directly lead to change in nucleic acid structures
• Furanose ring in equilibrates between C2’-endo and C3’-endo conformations with
a ~2kcal/mol barrier.
• The C2’-endo conformation gives B-form helix structure while C3’-endo gives A-
form. The fact that deoxyribose favors C2’-endo and ribose favors the C3’-endo
explains why DNA duplex are in B-form.
• By bridge the furanose ring the conformational change can be “locked” as the
strain can be also “unlocked” by dissecting the furanose ring.
Chem Soc Rev 2011, 40, 5680

CHEM5980
Hybridization of LNA and UNA

• Incorporation of LNA into oligonucleotides increases the stability of duplex. Single
LNA increases Tm by 2~10˚C.
• LNA stabilizes complement RNA more than DNA.
• In the case of mismatch, LNA/DNA hybrid destabilized hybrid as much as DNA
duplex. Therefore LNA is not only a better oligonucleotide binder but also retain
the selectivity for hybridization.
• LNA forms very stable LNA duplex
and has much greater Tm than
corresponding DNA duplex.
• In contrast to LNA, UNA reduce the
stability when incorporated into DNA
or RNA duplex.
• In the case of mismatch, UNA
destabilize duplex more than DNA or
RNA. Therefore UNA help
discriminate the mismatches.
DNA-DNA RNA-RNA LNA-LNA
Chem Soc Rev 2011, 40, 5680 Nucleic Acids Res 2010, 38, 6729
CHEM5980
Syntheses of LNA and UNA

• Unlike nucleic acids, LNA and UNA can only be made by chemical synthesis.
• While the synthesis of UNA monomer is quite straightforward, LNA monomer
takes many more steps to make. These monomers are further made into building
blocks, which are compatible with nucleic acid solid phase synthesis.
HO
MsO nucleic base
O 1. MsCl, Py OAc
O TMSOTf
HO O
OBn O 2. TFA then MsO
OBn OAc TMS TMS
Ac2O, Py O N
1. NaOBz
MsO B MsO B 2. Pd(OH)2, HO B
O NaOH O HCOONH4 O
3. NH4OH
MsO O O
OBn OAc OH
OBn
LNA
DMTO B 1. NaIO4 DMTO B

O then NaBH4 O
2. BzCl
OH OH OH OBz
UNA
Chem Soc Rev 2011, 40, 5680

CHEM5980
Applications of LNA
• Unlike other nucleic acid backbone mimics, LNA is promising candidate for
biotechnological applications.
• In addition to the previous introduction, LNA has two features that make it
attractive: 1. enhance cellular uptake with an unclear mechanism
2. increased nuclease resistance
• LNA applications include:
1. Antisense activity (next chapter)
2. Improve siRNA performance (next chapter)
3. Splice switching (next chapter)
4. Antigene function
5. As primers or probes
6. As molecular beacons
7. As aptamers (next chapter)
Adv Genetics 2013, 82, 47

CHEM5980
LNA alters mRNA splicing

• Splicing is removal of a segment mRNA before it become mature (next chapter)
• The splicing is controlled tightly by the pre-mRNA sequence, LNA can alter the way
pre-mRNA splices by binding to specific sequence.

CHEM5980
Antigene function of LNA

• The antigene oligonucleotides blocks RNA
polymerase action to inhibit transcription.
There are three major ways for antigene
oligonucleotide to function:
1. Triplex formation: binds to DNA duplex major
groove via Hoogsteen or reverse Hoogsteen
interactions
2. Double strand invasion: displace one strand
in existing DNA duplex and form Watson-
Crick pair with the complement strand.
3. Clamp-type binding : combination of the two
types above. It replace one strand DNA with
Watson-Crick pair and a flexible linker allows
the Hoogsteen triplex at the same location to
“clamp” the target gene.
• Other minor types of antigene LNA design are
also possible.

CHEM5980
LNA molecular beacon

• Molecular beacon is a stem-loop structure that
is used for DNA detection. It has a fluorophore
attached to one end and a quencher molecular
to the other.
Molecular
• In the presence of target DNA, the molecular beacon
beacon complement with the target and opens
up the stem-loop structure. The change in
conformation separate the fluorophore and Target DNA
quencher and result in fluorescence emission.
• The skeleton of molecular beacon can be made
with DNA. But in cell-based experiments, the
DNA tends to degrade or binds to protein to give
false positive signals.
• LNA based skeleton avoids degradation by
cellular enzymes and enhance the selectivity to
target DNA with its better discrimination on
target sequence. Detection
CHEM5980
Aromatic π stacking of DNA
• DNA double helix is stabilized by π stacking of the

base pairs
• π stacking is more favorable for guanine rather than
smaller adenine
• DNA conductivity was a controversial issue in
research. Such property can turn DNA into
molecular wire for materials science and electronics.
π stacking from the base pairs has been suggest to
contribute to the conductivity.
• π stacking allows the charge to be transfers for at
least few nanometers through tunneling.
Modifications on DNA molecules have been
performed to enhance the conductivity
CHEM5980
Intercalation between DNA base pairs

• The sugar-phosphodiester backbone can twist to allow the intercalation of
aromatic molecules through π stacking. This process alters DNA structure and
lead to functional change.
• Intercalation of DNA can leads inhibition of transcription, replication and DNA
repair processes, which makes intercalators potent mutagens.
• A number of anti-tumor natural products
target DNA by inhibit DNA replication
Ditercalinium-DNA complex
PNAS 1991, 88, 2422

CHEM5980
DNA double-strand folding

• The association of complement DNA into duplex is called hybridization.
• The stability of duplex DNA can be characterized by melting temperature (Tm).
• Tm is defined as the temperature where half of the DNA is single strand and the
other half in double strand.
• This melting temperature can be measured by ultraviolet absorption at 260nm,
where the unfolded and folded DNA has distinct absorption.
• Some dyes, such as SYBR Green I, having enhanced fluorescence when binds to
double strand DNA can be used for sensitive quantification of double strand DNA.
CHEM5980
DNA double-strand folding

• DNA duplex with high G-C content are more stable than those with high A-T
content due to more hydrogen bonds.
• Wallace rule has been proposed to estimate the melting temperature of short
oligonucleotide
• In the presence of mismatches, DNA can still form

duplexes. However, these mismatches decrease Tm
by several degrees.
• When a nucleotide is added into duplex DNA, a
bulge is formed and significantly reduces Tm.
CHEM5980
Why 5-member-ring sugar? (page 90)

• Why did nature picked furanose ring (ribose) instead
of pyranose as the backbone for nucleic acid?
• One would expect the furanose give more stable
duplex structure. But it does not.
• When different pyranoses have been tested as the
nucleic acid skeletons, the pyranoses give higher Tm
than RNA.
• This can be understood as the pyranose ring are
much more rigid than furanose ring.
• It seem like the nature picked a duplex structure that
is possible to unwind when necessary
during expression and duplication.
vs
pyran ring furan ring
CHEM5980
Complementarity and DNA self assembly

• When the one strand of DNA is
longer than its complement strand,
the unpaired hanging region (sticky
end) is able to pair with its
complementary sticky end.
• The resulted DNA molecules has no
covalent connection until DNA ligase
repair the nick site by forming
phosphodiester bonds.
• This strategy allows the insertion of
designed oligonucleotide into DNA
molecule of interest. This technology
is the foundation of modern DNA
recombination.
CHEM5980
DNA self assembly leads to DNA nanotechnology

• Homologous recombination is a natural way to exchange information
between two similar or identical DNA
• One specialized structure found during this process is Holliday junction
• Holliday junction connect between 4 strands of DNA
• This specialized structure provide a
building block for making nanomaterial
DNA CLEAVAGE
AND INVASION
PNAS 2000, 97, 3971

CHEM5980

• Holliday junction is natural existing DNA structure. Is it possible to exploit its
well defined structure for other purpose?
• DNA is known for recognition and self assembly properties. With proper design
in sequence, special shaped DNA can be produced.
• By extending four contributing DNA strands with complementary sequence of
alternative strands, Holliday junction can be connected together to a plane.
• Holliday junction can be used as building block to construct nanostructures.
Holliday junction
CHEM5980

Some examples of DNA nanotechnology:
Nat Nanotech 2011, 6, 763

CHEM5980
Nature 2006, 440, 297

CHEM5980
Nano Putians
J Org Chem 2003, 68, 8750

CHEM5980
Nano Putians
J Org Chem 2003, 68, 8750

CHEM5980
Nano Putians
J Org Chem 2003, 68, 8750

CHEM5980
close
open
Nature 2009, 459, 73

CHEM5980
Science 2011, 332, 342

CHEM5980

• The obstacle of DNA nanotechnology:
1. High cost of DNA
2. High error rate of self-assembly
• The potential use of DNA nanotechnology:

1. Biophysics: The concept of DNA nanotechnology came from the scaffolds to
support protein for crystallography for structural studies. This is still an
attractive field of research.
2. Biomimetic systems: Using DNA as material to mimic natural macromolecular
machines. Artificial nanopores may be useful in controlling the diffusion of
macromolecules, which involves new DNA sequencing technology.
3. Energy transfer and photonics: DNA nanotechnology allows both fine spatial
control to angstrom level and self-assembly into large structural molecule,
these properties are suitable to develop light harvesting apparatus or
photonic wire.
4. Diagnostics and therapeutics: Effective nano drug-carrier can be made with
DNA molecule. For example, DNA box can be used to store drug, which can be
released upon reaching target cells. The surface of such container can be
modified for cell recognition.
Nat Nanotech 2011, 6, 763

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Section 3-1 National Tsing Hua University

Organization of genomic DNA depends on the type of organism

DNA secondary structure: Double helix

Helical sense Right handed Right handed Left handed

Nucleosides, nucleotides and nucleic acids

Nucleoside = Base + sugar

R=H 2’-deoxyadenosine 2’-deoxyguanosine 2’-deoxycytidine thymidine

© 2014 Pearson Education Inc.

DNA base and aromaticity

DNA under physiological conditions

DNA and 2’-OH

© 2014 Pearson Education Inc.

DNA under physiological conditions

Base modifications on DNA

Elementary forces in DNA

Tautomers of nucleic bases

Thymine Uracil Adenine

• 5-bromouracil, mimic of thymine,

Roles of Hydrogen bonds beyond base pairing

• The above groups can initiate hydrogen

Hoogsteen base pair

important in DNA binding,

The story of Iron: Bleomycin

The mechanism of Bleomycin

Nat Rev Cancer 2005, 5, 112

DNA binding moiety

Metal binding moiety

J Am Chem Soc 1982, 104, 313

DNA affinity cleavage

Recognition of DNA sequence by small molecules

Nature 1998, 391, 468

Unnatural nucleic base pairs

Unnatural nucleic base pairs

Design of unnatural nucleic base

Curr Prot Nucl Acid Chem 2009, 1.4.1

Purine-pyrimidine-like unnatural nucleic base

C-1’ epimerization Nature 1990, 343, 33

Purine-pyrimidine-like unnatural nucleic base

• Self-complement base pairs have also been studied

Curr Prot Nucl Acid Chem 2009, 1.4.1

Expanded unnatural nucleic base

Non-hydrogen-bonding unnatural nucleic base

Contributed from Kool group

J Am Chem Soc 2008, 130, 2336

Stacking unnatural nucleic base

• Nucleic bases with aromatic groups

Curr Prot Nucl Acid Chem 2009, 1.4.1

Mimic to probe DNA damage

Probe for the damage Probe for the damage

Curr Prot Nucl Acid Chem 2009, 1.4.1

Metal-mediated base pair

Curr Prot Nucl Acid Chem 2009, 1.4.1

Covalent base pair

Curr Prot Nucl Acid Chem 2009, 1.4.1

Creating organism with unnatural nucleic bases

• Unnatural base pair d5SICS and dNaM were used

“Nucleic acids” with unnatural backbones

• DNA recognition comes from the

matching Watson-Crick base pair.

Is it possible to replace the O

backbone to change the

• Libraries of the scaffolds were O

created to change the location to O

present nucleic bases. O