Acid Nucleic

Acid nucleic là polymer bao gồm các

mononucleotide liên kết với nhau qua liên kết
phosphodiester.

Chức năng của các nucleotide:

- Lưu trữ và truyền đạt thông tin di truyền
- Điều hoà
- Khác
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 Indicate the extensive presence of mitochondria with a tick ( ), intermediate presence (-) and

Bài tập khởi động

absence of mitochondria with a cross ( ). Match the key function(s) of mitochondria (a to d)

suited to the respective cells. (1.8 points)

Hãy
3. sắp xếp
Arrange the theo
order ofthứ tự tăng
the DNA dầnfrom
molecules nhiệt
lowestđộ tan của
to highest cácof DNA
in terms có
their melting
các trình tự sau
temperature (Tm). (0.9 points)

a. 5’-AAGTTCTCTGAA-3’

3’-TTCAAGAGACTT-5’

b. 5’-AGTCGTCAATGCGG-3’

3’-TCAGCAGTTACGCC-5’

c. 5’-GGACCTCTCAGG-3’

3’-CCTGGAGAGTCC-5’

IBO, 2014

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CÁC VẤN ĐỀ LIÊN QUAN
ĐẾN ACID NUCELIC?

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 Lưu trữ thông
tin di truyền Sao mã, phiên
Truyền đạt thông
mã
tin di truyền
Điều hoà

Sinh tổng hợp Khác

protein

Chức năng

Cấu trúc

Cấu tạo hóa học

Tổng hợp Acid nucleic Phân giải

Tandv 2017
Nucleoside và NucleoQde

Base
Nucleoside
Đường Nucleotide
Phosphate
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14 THÍ NGHIỆM CỦA GRIFFITH
Chapter 2 / The Molecular Nature of Genes

Strain of Strain of
Colony Colony

Cell type Effect Cell type Effect

– Capsule No capsule

Smooth (S) Live S Rough (R) Live R

strain strain

(a) (b)

Effect Effect
Live R strain

Heat-killed
S strain
Heat-killed
S strain

Live S and R strains

isolated from dead
(c) (d) mouse

Figure 2.2 Griffith’s transformation experiments. (a) Virulent strain S S. pneumoniae bacteria kill their host;
(b) avirulent strain R bacteria cannot infect successfully, so the mouse survives; (c) strain S bacteria that are
heat-killed can no longer infect; (d) a mixture of strain R and heat-killed strain S bacteria kills the mouse. The
Tan DV 2017
Weaver R, 2012
killed virulent (S) bacteria have transformed the avirulent (R) bacteria to virulent (S).
Base: Pyrimidine và Purine

Jan Koolman, 2005

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 Base nitrogen khác

Jan Koolman, 2005

Garret and Grisham

1999
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 Base Purine

Jan Koolman, 2005

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 Đường
Pentsose

Garre], and Grisham,

1999

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 Liên kết
Beta glycoside

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Garret,1996
Nucleotid/Nucleoside
Deoxyribonucleoside

Lehninger, 4th

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Nucleotid/Nucleoside
Deoxyribonucleoside
Lihnger, 4th

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Ribonucleoside

Lehninger, 4th
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 Ribonucleoside

Lihnger, 4th Tan DV 2017

Lehninger, 4th

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Nucleotid mang nang luong

Lehninger, 4th

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e production of second messengers inside the cell, ■ ATP is the central carrier of
hich in turn leads to adaptive changes in the cell interior O" cells. The presence of an ad
Nucleotide vòng
hapter 12). Often, the second messenger is Adenosinea nu- variety of enzyme cofactors
3!,5!-cyclic monophosphate
eotide (Fig. 8 – 39). One of the most common is (cyclic AMP; binding-energy
cAMP) requirement
■
5!
Cyclic AMP, formed from AT
5! O Guanine
CH2 catalyzed by adenylyl cyclas
O CH2 Adenine O
O messenger produced in resp
HotherH chemical signals.
H H
H H H H
3!
3!
O P O OH O P Key
O Terms
OH

O" O"
Terms in bold are defined in the g
Adenosine 3!,5!-cyclic monophosphate Guanosine 3!,5!-cyclic monophosphate
(cyclic AMP; cAMP) (cyclic
geneGMP; 271cGMP) ba
5!
ribosomal RNA ma
Lehninger et al,
O2008 CH2 Guanine O" O" (rRNA) 271 mi
O
messenger
5! RNA B-f
"O P O P O CH Guanine
H H 2
(mRNA)O 271 A-f
H H
O O transfer RNA Z-f
3! H H
O P O OH (tRNA) 271 pa
H H
nucleotide
3! 271 ha
O"
Lehninger, 4th
Guanosine 3!,5!-cyclic monophosphate
nucleosideO 272 OH cru
pyrimidine
A 272 trip
(cyclic GMP; cGMP) "O P O
Tan DV 2017 purine 272 Gt
" " O
deoxyribonucleotide 273 tra
 3!
O P O OH (t

Nucleotide khác O"

Guanosine 3!,5!-cyclic monophosphate
(cyclic GMP; cGMP)
nucle
nucle
pyrim
purin
O" O" deox

Guanosine 5’- "O P O P O

5!
CH2
O
Guanine ribon
phos
O O
diphosphate, H H
lin
H H 5! en
3! 3! en
3’diphosphate (ppGpp) ức "O
O
A
P O
OH
oligo
polyn

chế quá trình tổng hợp O

"O P O Furt
rRNA và tRNA, do đó làm O" Gene
Guanosine 5!-diphosphate,3!-diphosphate

giảm quá trình sinh tổng (guanosine tetraphosphate)

(ppGpp)
Chan
recog
D

hợp protein ở vi khuẩn FIGURE 8–39 Three regulatory nucleotides. acid s

trong điều kiện thiết hụt Lehninger et al, 2008

các amino acid

Lehninger, 4th

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 Liên kết
Phosphodiester

Lehninger, 4th
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Thủy phân liên kết phosphodiester

Lehninger, 4th
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Liên kết hydrogen kiểu Watson-Crick

4
3
61

4
3 2
61
2
Lehninger, 4th

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Liên kết hydrogen kiểu Hoogsteen

4
3 4
3

6
7 1

7 1
6 7
16

1
6
7 6 1
7

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Acid Nucleic

Lehninger, 4th

Koolman,
et al 2005
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Acid Nucleic

Lehninger et al, 4th

Lodish et al, 5th

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Liên kết hydrogen kiểu Hoogsteen

Lehninger, et al, 4th

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Một số mô hình cấu trúc DNA:
Lehninger, 4th

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Lehninger, 4th
Mũ hóa nucleotide
trong mRNA

Giúp bảo vệ xâm

nhậm của vật
chất di truyền
lạ, và giúp
mRNA bám vào
rRNA

Lehninger, et al 4th
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 RNA vận chuyển

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RNA ribosome

Koolman, 2005
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Micro RNA

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• Interferemce RNA (1106)

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P. K. Gupta
• RNAi
(a)

Slicer-dependent Target mRNA

passenger ejection
siRNA duplex
3' 5' mRNA cleavage
Slicer-independent
passenger ejection
(high temperature) OR

MID
PIWI
N PAZ

Catalytically
active
Advanced Review
hAGO2 wires.wiley.com/rna

Slicer-independent Target mRNA

T
passenger ejection
AGO
MID CCR4–NOT
Nucleus Cytoplasm PIWI deanylase
Genome miRNA duplex
Microprocessor N PAZ
complex

miRNA(guide)

DGCR8 GW182 PABP

Passenger
Gene of miRNA
P PABP
P P
Dicer AAAAAA
Transcription Loading
Drosha P P P
Target mRNA
RISC
(b) 5' 3'
(AGO + guide)
primary Precursor miRNA
Translational
miRNA miRNA duplex repression
and
mRNA
Nakanishi, 2016
P
siRNA duplex deadenylation

F I G U R E 1 | Canonical biogenesis of miRNA in Tan DV

the human system.
Slicer-independent The2017
gene of a miRNA is transcribed into primary miRNA (pri-miRNA) and
passenger ejection
processed by the microprocessor, a complex of an(high
RNase III enzyme Drosha, and its binding partner DGCR8. The product, pre-miRNA, is
temperature)
• RNAi
Hsc70
PIWI

(b) MI
D Pri-RISC

Hsc70 I miRNA duplex

PIW
40
Hsp L1 Weak
N
interaction Hsc70
Strong
interaction 4 0
AGO folding Hsp
Nascent AGO Hsc70

TRP
P
TR
40 Hop
Hsp
TRP

PPIase
TRP
ATP
Hsc70 Hsc70
Hsc70

TRP
40 0
40 p9

TRP
Hsp Hsp Hs 4 0
Hsp Hop

Hop PPIase TRP

Hop EEVD motif
TRP
EEVD motif
Asymmetric complex Intermediate complex AGO•Hsc70•Hop complex
Hs
c7
Hsp40 0
p23

0
PPIase p9
TRP
P Hs
Hop

Pre-RISC pri-RISC
pre-RISC
p23

and
PPIase
TRP
ADP

Pre-RISC•Hsp90 complex
AGO•Hsp90 complex Nakanishi, 2016
F I G U R E 5 | Legend on next page
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Tạo dòng động vật có xương sống. Các gene mã hóa các protein GFP được
đưa vào các chủng cá ngựa khác nhau, tạo nên các màu khác nhau. Mỗi
một huỳnh quang khác nhau được quan sát dưới quang phổ ánh sáng tạo
nên sự biểu hiên có màu đặc trưng (đỏ, xanh vàng

Hình (Lehninger, 2008)

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Lehninger, 4th

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Lehninger, 2008 Tan DV 2017
 Chức năng của Nucleotide
• Tham gia vào thành phần của vật chất di truyền
• Nucleoside 5'-triphosphates mang năng lượng
• Base đóng vai trò là đơn vị nhận biết
• Cyclic nucleotides là chất truyền tín hiệu và
điều hòa trao đổi chất và tế bào
• Tha gia vào thành phần một số co-enzyme
• ATP Trung tâm trao đổi năng lượng
• GTP điều khiển tổng hợp protein
• CTP điều khiển tổng hợp lipid
• UTP điều khiển tổng hợp sarcharide
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 Cấu trúc bậc 3 của acid nucleic
Histone, topoisomerase, cohesin, condensin
Genes and Chromosomes

for every 10.5 bp. If one of these turns were re-

ed, there would be (84 bp)!7 ! 12.0 bp per turn,
er than the 10.5 found in B-DNA (Fig. 24–14b). This
deviation from the most stable DNA form, and the
cule is thermodynamically strained as a result.
erally, much of this strain would be accommodated (a) Lk = 1
oiling the axis of the DNA on itself to form a super-
(Fig. 24–14c; some of the strain in this 84 bp seg-
would simply become dispersed in the untwisted
cture of the larger DNA molecule). In principle,
train could also be accommodated by separating
wo DNA strands over a distance of about 10 bp
24–14d). In isolated closed-circular DNA, strain
duced by underwinding is generally accommodated
upercoiling rather than strand separation, because (b) Lk = 6
ng the axis of the DNA usually requires less energy
breaking the hydrogen bonds that stabilize paired FIGURE 24–15 Linking number, Lk. Here, as usual, each blue ribbon

s. Note, Cấu trúc that

however, genome của người of DNA in
the underwinding Lehninger
represents one strand et al, 2008
of a double-stranded DNA molecule. For the

makes separation of the DNA strands easier, facili- DV 2017 in (a), Lk = 1. For the molecule in (b), Lk = 6. One of the
Tanmolecule
strands in (b) is kept untwisted for illustrative purposes, to define
answer is not yet known in detail, but it is known that the chromatin fiber
is folded into a series of loops, and that these loops are further condensed

Cấu trúc bậc III

to produce the interphase chromosome; finally, this compact string of
loops is thought to undergo at least one more level of packing to form the
mitotic chromosome (Figure 5–24 and Figure 5–25).

QUESTION 5–2
short region of 2 nm
DNA double helix Assuming that the histone
octamer (shown in Figure 5–21)
forms a cylinder 9 nm in diameter
and 5 nm in height and that the
“beads-on-a-string” 11 nm human genome forms 32 million
form of chromatin nucleosomes, what volume of
the nucleus (6 m in diameter) is
occupied by histone octamers?
(Volume of a cylinder is r2h; volume
chromatin fiber of a sphere is 4/3 r3.) What fraction
of packed 30 nm
nucleosomes
of the total volume of the nucleus
do the histone octamers occupy?
How does this compare with the
volume of the nucleus occupied by
human DNA?
chromatin fiber
700 nm
folded into loops

centromere

entire
mitotic 1400 nm
chromosome Figure 5–24 DNA packing occurs on
several levels in chromosomes. This
NET RESULT: EACH DNA MOLECULE HAS BEEN schematic drawing shows some of the levels
PACKAGED INTO A MITOTIC CHROMOSOME THAT
IS 10,000-FOLD SHORTER THAN ITS FULLY
Albert at al, 2014
thought to give rise to the highly condensed
mitotic chromosome. The actual structures
EXTENDED LENGTH
are still uncertain.
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matin-remodeling complexes, the enzymes that modify
e tightly regulated. They are brought condensed
to particularchromatin
ECB4 e5.27/5.26
chro-
mainly by interactions with proteins that bind to specific
Cấu trúc bậc III ATP ADP

REPEATED ROUNDS OF
decondensed

(C)
ail NUCLEOSOME SLIDING
H2B tail
H3 histone modification state meaning
H3 tail

another indicates that the

M genes in that stretch of chromatin should be
heterochromatin
H4 tail formation,
expressed; still others indicate
K that the gene
nearby
silencing genes should be silenced
9
(Figure 5–27C).
H3 tail M Ac

Like the chromatin-remodeling

K K complexes, the enzymes that modify
gene expression
Ac 4 9
Ac Ac Ac M histone tails are tightly regulated. They are brought to particular chro-
M M M M P M P Ac ECB4 e5.27/5.26
matin regions
histone
H3 mainly by interactions with proteins that bind to specific
gene expression
K RK K RK S K S K
14 1718 23 26 2728 36 10 14
(A) (C)
pattern of modification of histone tails can dictate how H4 tail
a stretch of chromatin is treated by the cell.
wing showing the positions of the histone tails that extend from each H2B tail
nucleosome. (B) Each histone can be modified H3 histone modi
tachment of a number of different chemical groups,
H2A tail mainly to the tails. Histone H3,
H3fortail
example, can receive an acetyl
hyl group (M), or a phosphate group (P). The numbers denote the positions of the modified amino acids in the protein
mino acid designated by its one-letter code. Note that some positions, such as lysines (K) 9, 14, 23, and 27, can be
than one way. Moreover, lysines can be modified with either one, two, or three methyl groups (not shown). Note that
ns 135 amino acids, most of which H2A
are intail
its globular
ECB4 portion (green), and that most modifications are on its N-terminal
e5.28/5.27 M
ifferent combinations of histone tail modifications can confer a specific meaningH4 on tail
the stretch of chromatin on which
cated. Only a few of these “meanings” are known. K
H2B tail 9

H3 tail M Ac
(B)
K K
Ac Ac 4 9
M Ac Ac Ac M
M M P M M M M P M P
histone
H3 Albert at al, 2014
R K KS K RK K RK S K S
2 4 9 10 14 1718 23 26 2728 36 10
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 histone proteins. The modifications that direct the formation of the most
common type of heterochromatin, for example, include the methylation
of lysine 9 in histone H3 (see Figure 5–27). Once it has been established
heterochromatin can spread because these histone tail modifications
attract a set of heterochromatin-specific proteins, including histone-mod-
ifying enzymes, which then create the same histone tail modifications on

Cấu trúc bậc III

adjacent nucleosomes. These modifications in turn recruit more of the
heterochromatin-specific proteins, causing a wave of condensed chro-
matin to propagate along the chromosome. This heterochromatin wil
continue to spread until it encounters a barrier DNA sequence that stops
the propagation (Figure 5–29). In this manner, extended regions of het-
erochromatin can be established along the DNA.

hetero-
heterochromatin euchromatin heterochromatin euchromatin chromatin euchromatin heterochromatin

telomere centromere telomere

Figure 5–28 The structure of chromatin varies along a single interphase chromosome. As schematically indicated by different
colors (and the path of the DNA molecule represented by the central black line), heterochromatin and euchromatin each represent
a set of different chromatin structures with different degrees of condensation. Overall, heterochromatin is more condensed than
euchromatin.

ECB4 e5.31/5.28

Albert at al, 2014

Tan DV 2017

Eukaryotic rRNA Processing
The rRNA genes in eukaryotes are repeated several hun-
dred times and clustered together in the nucleolus of the
cell. Their arrangement in amphibians has been especially
Nhân con trong (nucleolus) NST
well studied, and, as Figure 16.1a shows, they are sepa-
rated by regions called nontranscribed spacers (NTSs).
NTSs are distinguished from transcribed spacers, regions
rRNA gene NTS
(a)
(b)
Figure 16.1 Transcription of rRNA precursor genes. (a) Map of a
portion of the newt (amphibian) rRNA precursor gene cluster,
showing the alternating rRNA genes (orange) and nontranscribed
Robert F. Weaver,
spacers (NTS, green). (b) Electron micrograph of part of a newt
2012
C.A. Thomas, Electron microscopic visualization of transcription. Cold Spring
nucleolus, showing rRNA precursor transcripts (T) being synthesized
in a “tree” pattern on the tandemly duplicated rRNA precursor
of transcription from the lengths of the transcripts within a
given gene; the shorter RNAs are at the beginning of the
gene and the longer ones are at the end.
We have seen that mRNA precursors frequently require
splicing but no other trimming. On the other hand, rRNAs
and tRNAs first appear as precursors that sometimes need
splicing, but they also have excess nucleotides at their ends,
or even between regions that will become separate mature
rRNA gene NTS
1 µm
genes (G). At the base of each transcript is an RNA polymerase I, not
visible in this picture. The genes are separated by nontranscribed
spacer DNA (NTS). (Source: (b) O.L. Miller, Jr., B.R. Beatty, B.A. Hamkalo, and
Harbor. Symposia on Quantitative Biology 35 (1970) p. 506.)
Tan DV 2017
 Cấu trúc Nucleosome wea25324_ch13_355-393.indd Page 361 12/3/10 8:56 PM user-f469 /

(a)

(a)

(c)

Figure 13.3 Crystal structure of a nucleosomal core particle.

Richmond and colleagues crystallized a core particle composed of a
146-bp DNA and cloned core histones, then determined its crystal
structure. (a) Two views of the core particle, seen face-on 110
(left)Åand
edge-on (right). The DNA on the outside is rendered in tan and
green. The core histones are rendered as follows: H2A, yellow; H2B,
red; H3, purple; and H4, green. Note the H3 tail (arrow) extending
through a cleft between the minor grooves of the two adjacent turns
of the DNA around the core particle. (b) Half of the core particle,
showing 73 bp of DNA plus at least one molecule each of the core
histones. (c) Core particle with DNA removed. (Sources: (a–b) Luger, K.,
A.W. Mäder, R.K. Richmond, D.F. Sargent, and T.J. Richmond, Crystal structure
Figurecore
of the nucleosome 13.6particle
The solenoid model of
at 2.8 Å Resolution. chromatin
Nature folding.
389 (18 Sep 1997) A string of (b)
f. 1, p. 252.nucleosomes coils into
Copyright © Macmillan a hollow
Magazines tube,
Ltd. or solenoid.
(c) Rhodes, Each nucleosome
D., Chromatin
is represented
structure: The nucleosome coreby all
a blue cylinder
wrapped with 389
up. Nature DNA(18(pink) coiled around it.
Sep 1997)
(b) f. 2, p. 233.For simplicity,
Copyright the solenoid
© Macmillan is Ltd.)
Magazines drawn with six nucleosomes per
turn and the nucleosomes parallel to the solenoid axis.
Source: Adapted from Widom, J. and A. Klug. Structure of the 300 Å chromatin
filament: X-ray diffraction from oriented samples. Cell 43:210, 1985.

Robert F. Weaver, 2012

linker DNA outside the nucleosome, and this linker DNA core histones. Because the tails are relatively unstructured,
is digested by the nuclease. To resolve
the crystal structure doesthis
not long-standing
include most ofcontroversy,
their length. higher-
Figure 13.3 depicts the core nucleosome structure deter- resolution structural data were needed.
The tails are especially evident with the DNA removed Finally,inin 2005, Figure 13.7 Stru
mined by Richmond and colleagues. We can see the DNA panel c. The tails of H2B and H3 pass out of the core particle by re-
Richmond and colleagues achieved a breakthrough tetranucleosome
through porting
a cleft the x-rayfrom
crystal
twostructure
adjacentofDNA
a tetranucleosome, conformation co
winding almost twice around the core histones. We can also formed minor Tan DV 2017DNA around the
see the H3–H4 tetramer near the top and the two H2A–H2B or string of four nucleosomes. The resolution of this
grooves (see the long purple tail at the top of the left part of struc-
x-ray crystallogr
dimers near the bottom. This arrangement is particularly ture was not very high, only 9 Å, but it was
panel a). One of the H4 tails is exposed to the side of thegood enough
Cấu trúc NST trong các kì phân bào
Published online: September 4, 2017
The EMBO Journal Structural dynamics during the cell cycle Christopher Barrington et al

A Figure 1. Chromosome structures and SMC

proteins during the cell cycle.
Active (A) Schematic representations of chromosome
AC structure during the cell cycle. TADs on a section of
compartment
a chromosome are indicated as shaded areas in
* Repressive
TADs RC active (AC) or repressive (RC) compartments,
compartment separated by the dotted line. Cohesin is shown in
AC
purple and replication machinery in orange on the
RC DNA. In G1, TADs are insulated from one another
and occupy distinct nuclear space and
compartments. During S-phase, DNA is replicated
at specific times, from early to late replicating
* domains indicated by proportion of replicated DNA
in the TAD. TAD insulation is maintained, albeit to a
Nuclear compartments Cohesin
lesser extent, but compartmentalisation increases.
Replication Once in M-phase, the chromatin is highly
machinery compacted with TAD structure barely identifiable
and abundant very-long-range contacts emerge
between distant TADs (e.g. compare the
relationship between the orange and turquoise
TADs marked with stars in the zoom-out of
AC G1-phase to the M-phase). (B) Comparison of the
G1
structure of mitotic chromosomes in yeast (for
simplicity, only individual sister chromatids are
RC shown). Saccharomyces cerevisiae chromosome
*
* arms are compacted by cohesin compared to
M S Schizosaccharomyces pombe where condensin is
required. The rDNA locus of S. cerevisiae is brought
into proximity of the centromere by condensin,
which is not required at other loci.

different organisations. While the genome

of S. cerevisiae is divided between 12 chro-
mosomes, whereas S. pombe has three.
The authors combined genetic ablation
with Hi-C analysis of genome structure on
B Christopher Barrington et al, 2017 populations of cells from individual cell
S. cerevisiae
Condensin
S. pombe
Tan DV 2017
cycle phases, taking advantage of genetic
dependent and chemical methods to arrest the cells at
loop particular stages.
SAF-A Regulates Interphase Chromosome Structure
through Oligomerization with Chromatin-
Cấu trúc NST
Associated RNAs
Graphical Abstract Authors
Ryu-Suke Nozawa, Lora Boteva,
Dinesh C. Soares, ..., Rory R. Duncan,
Sutherland K. Maciver, Nick Gilbert

Correspondence
nick.gilbert@ed.ac.uk

In Brief
A scaffolding protein interacts with
chromatin-associated RNAs to regulate
human interphase chromatin structures in
a transcription-dependent manner.

Highlights
d SAF-A remodels interphase chromosome structure
Ryu-Suke Nozawa et al, 2017
d Transcription regulates SAF-A oligomerization with caRNAs

d SAF-A and caRNAs interact to form a chromatin mesh

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d Chromatin structure affects genome stability
Cấu trúc bậc III của acid nucleic
24

Nick

Relaxed DNA
Lk " 200
strand ∆Lk " !2
break
(b) Lk undefined

∆Lk " !2 Negative

supercoils
Lk " 198
(a) Lk " 200 " Lk0

FIGURE 24–17 Negative and positive sup

molecule of Figure 24–16a, underwindin
ical turns (Lk " 198 or 202) will produc
coiling, respectively. Note that the D
(c) Lk = 198 directions in the two cases.

BatesFIGURE
A.D &24–16
, Maxwell A, 2005
Linking number applied to closed-circular DNA mole-
Lehninger et al, 2008 Tan in
cules. A 2,100 bp circular DNA is shown DVthree
2017forms: (a) relaxed, WORKED EXAMPLE 24–1
Lk " 200; (b) relaxed with a nick (break) in one strand, Lk undefined;
 Cấu trúc bậc III của acid nucleic
24.2 DNA Supercoiling 957

Nick

Relaxed DNA
Lk " 200
∆Lk " !2 ∆Lk " %2
d

Negative Positive
supercoils supercoils
Lk " 198 Lk " 202

FIGURE 24–17 Negative and positive supercoils. For the relaxed DNA
molecule of Figure 24–16a, underwinding or overwinding by two hel-
Batesical
A.Dturns
& , Maxwell
(Lk et A,
198
" al, 2005
or 202) will produce negative or positive super-
Lehninger 2008 Tan DV 2017
coiling, respectively. Note that the DNA axis twists in opposite
 interconversions can be achieved by type II topoisomerases but not by type I
enzymes, unless one of the circles already contains a break in one strand (4).

Cấu trúc bậc III của acid nucleic

More recently topoisomerases have been further subdivided into type IA and B,
and type IIA and B.

Relaxation

Knotting/
unknotting

(+) (–)

Duplex
+
formation

Figure 5.1 Reactions of

type I topoisomerases
Bates A.D & , Maxwell A, 2005 Catenation/decatenation (redrawn from ref. 48).
Tan DV 2017
 of both strands (Figure 5.2). Perhaps the best illustration of this distinction
is the catenation and decatenation of double-stranded DNA circles. These

Cấu trúc bậc 3 của acid nucleic

interconversions can be achieved by type II topoisomerases but not by type I
enzymes, unless one of the circles already contains a break in one strand (4).
More recently topoisomerases have been further subdivided into type IA and B,
and type IIA and B.

Relaxation

Knotting/
unknotting

(+) (–)

Duplex
+
formation

Figure 5.1 Reactions of

type I topoisomerases
Bates A.D & , Maxwell A, 2005 Catenation/decatenation (redrawn from ref. 48).

Tan DV 2017
 Topoisomerase
13
DNA TOPOISOMERASE: THE KEY ENZYME THAT REGULATES DNA SUPER STRUcrURE

Type I topoisomerase

I
tOEoryote)
---
(pro

topo I

---
topoI
---
(euliaryote) (euUryote)

---
topoID

reverse reverse

negative
---
gyrase

relax
---
gyrase

positive
supercoils supercoils
DNA DNA

- ---
gyrase gyrase

--- ---
topo IV topo IV

---
topo II
---
topo II

---
topo VI
---
topo VI

Type II topoisomerase
Fig. 1

bacterial type I enzyme. Kato S. & Kikuchi A., 1998

REVERSE GYRASE -Tan

THEDVNEW
2017TOPOISOMERASE
There is controversy over whether or not prokaryotes should be divided into two separate
III) generally relax DNA by removing negative super- Eukaryotic cells also have type I and type II topoiso-
coils (increasing Lk). The way in which bacterial type I merases. The type I enzymes are topoisomerases I and III;
topoisomerases change linking number is illustrated in the single type II enzyme has two isoforms in vertebrates

Topoisomerase I ở vi khuẩn
Figure 24–21. A bacterial type II enzyme, called either
topoisomerase II or DNA gyrase, can introduce negative
called II! and II". Most of the type II enzymes, including
a DNA gyrase in archaea, are related and define a family

(a)
O
O Active-site Tyr attacks phosphodiester
CH2 O Base
CH2 O Base bond of one DNA strand, cleaving it
5! 3! and creating covalent 5!-phospho-
DNA binding tyrosyl protein-DNA linkage.

–
OH
O O
1 H 2
Tyr O –O P O Tyr O P O
Tyr

:
O O
3! 5! CH2 O Base CH2 O Base
Closed
conformation

O O

(b) Enzyme changes to open

conformation; unbroken
5!3! DNA strand passes through 5!3!
break in first strand.

3
3! 3!

Open
conformation
3! 5! 3!5!

(c)
O Tan DV 2017 O
Lehninger
O
2008
Enzyme in closed conforma- O
CH Base CH Base
 (b) Enzyme changes to open
conformation; unbroken
5!3! DNA strand passes through 5!3!
break in first strand.

Topoisomerase I ở vi khuẩn
3! 3!

Open
conformation
3! 5! 3!5!

(c)
O O
CH2 O Base Enzyme in closed conforma- CH2 O Base
tion; liberated 3!-OH attacks
5!-phosphotyrosyl protein-
DNA linkage to religate 5! 3!
cleaved DNA strand.
OH O
:

– P
O– O O
4
Tyr O P O Tyr O O
H CH2 O Base
H+ O
CH2 O Base
3! 5!
5
O

O DNA is released, or
new cycle begins.

MECHANISM FIGURE 24–21 Bacterial type I topoisomerases alter link- strand is cleaved. (b) The enzyme changes to its open conformation
ing number. A proposed reaction sequence for the bacterial topoiso- and the other DNA strand moves through the break in the first strand
merase I is illustrated. The enzyme has closed and open conformations. (c) In the closed conformation, the DNA strand is religated.
(a) A DNA molecule binds to the closed conformation and one DNA

Tan DV 2017
 Topoisomerase I E. coli
5.3 STRUCTURES AND MECHANISMS OF TOPOISOMERASES 133

5!
3!

Figure 5.5 A proposed mechanism for E. coli topoisomerase I. The enzyme binds DNA and
cleaves one strand forming a 5′ -phosphotyrosine linkage (black circle). The complementary strand
is passed through the gap and into the central cavity of the enzyme. Resealing of the nick and
release of the passed strand changes the linking number by ±1, resulting in relaxation of the
DNA. If the initial cleavage is opposite a nick or gap in a duplex circle, then passage of another
duplex segment could lead to a catenation or knotting reaction.

‘cap’ lobe

DNA (end on)

5!

3!

‘catalytic’ lobe side view

Figure 5.6 A proposed mechanism for human topoisomerase I. The enzyme binds duplex DNA
and cleaves one strand forming a 3′ -phosphotyrosine linkage (black circle). The free 5′ -OH can
then rotate (controlled rotation) before the break is resealed, resulting in DNA relaxation.

Tan DV 2017
IA enzyme (Table 5.1). An important feature ofBates A.D & of
the structure , Maxwell A, 2005
this fragment
Topoisomerase type IIA ở Eucaryote
960 Genes and Chromosomes

called type IIA. Arch

topoisomerase VI, wh
The eukaryotic type
DNA (introduce neg
2 both positive and neg

N-gate FIGURE 24–22 Proposed

1 3 ber by eukaryotic type
C-gate
enzyme binds one DNA
below the bound DNA a
second segment of the s
N-gate, and 3 is trapp
5 4 cleaved (the chemistry is
second DNA segment is
DNA is religated, and the
C-gate. Two ATPs are bo
likely that one is hydroly
step 4 . Additional deta
reaction remain to be wo
Lehninger et al, 2008

Cần thuỷ phân 2ATP cho quá trình này

B O X 2 4 –1 M ETanDDVI 2017
CINE Curing Disease by Inhibiting To
 Topoisomerase type II
5.3 STRUCTURES AND MECHANISMS OF TOPOISOMERASES 135

(+)

2 × ATP (–)

(top view) (+) (–)

Figure 5.8 A proposed mechanism for E. coli DNA gyrase. Gyrase operates by a similar mech-
anism to topoisomerase II (Figure 5.7) except that the G segment is wrapped around the enzyme
(as illustrated in the figure) so as to present the T segment to the DNA gate. This wrap strongly
favours intramolecular strand passage and leads to the enzyme’s ability to introduce negat-
ive supercoils into DNA. The asterix represents ATP. (Reproduced from ref. 53 with permission;
copyright (2004) National Academy of Sciences, USA.)

Reverse
Bates A.D &gyrase, which
, Maxwell is a type IA enzyme, may act via a mechanism that is
A, 2005
distinct from those of the more conventional
Tan DV 2017 (DNA-relaxing) type I enzymes.
The enzyme contains a helicase-like domain and a type IA topoisomerase
134
Topoisomerase type II
DNA TOPOISOMERASES

T segment

G segment

+ATP

Figure 5.7 A proposed

mechanism for yeast
topoisomerase II. –ADP, Pi
A segment of DNA (the G
segment) is bound to the
enzyme in the vicinity of the
active-site tyrosines (black
circles). Cleavage of
the G segment (to yield
5′ -phosphotyrosine
linkages) allows passage
of a second DNA segment
(the T segment) through
the G segment.
The T segment is captured
by ATP-dependent
dimerization of the
N-terminal (ATPase)
domains of the enzyme, G segment
which form a ‘clamp’.
The T segment exits from
the bottom of the enzyme
as shown. ATP hydrolysis
T segment
releases the clamp and
allows the enzyme to reset.

Tan DV 2017
the members of this group for which we have structural information is human Bates A.D & , Maxwell A, 2005
topoisomerase I (Figure 5.4). The structure of a 70 kDa fragment of the human
dimeric, forming a V-shaped complex that is thought to ever, wrapping of the DNA about condensin may
be tied together through the protein’s hinge domains contribute to DNA condensation. The cohesins and

Protein duy trì cấu trúc NST (SMC)

(Fig. 24–34b, c). One N and one C domain come to- condensins are essential in orchestrating the many
gether to form a complete ATP-hydrolytic site at each changes in chromosome structure during the eukary-
free end of the V. otic cell cycle (Fig. 24–35).
Lehninger et al, 2008

(a) N Hinge C

Coiled coil Coiled coil

(b) (c)

ATP

ATP

50 nm

(d) Cohesin Condensin (e)

ADP + Pi
Smc1 Smc3 Smc2 Smc4

ATP
ATP ATP

Kleisin

FIGURE 24–34 Structure of SMC proteins. (a) The five domains of the
SMC primary structure. N and C denote the amino-terminal and
a. 5 domain của SMC; b. cấu trúc xoắn của các SMC, d. cohesin cấu tạo từ CMS1 và 3
carboxyl-terminal domains. (b) Each polypeptide is folded so that the
e. Condensin được cấu tạo từ CMS2 và 4
two coiled-coil domains wrap around each other and the N and C
domains come together to form a complete ATP-binding site. Two
polypeptides are linked at the hinge region to form the dimeric
Tan
V-shaped SMC molecule. (c) Electron micrograph of SMC proteins
from Bacillus subtilis. (d) Cohesins are made up of pairs of Smc1 and
Smc3 proteins, and condensins consist of Smc2-Smc4 pairs. These
eukaryotic SMC proteins are bound by kleisin and some additional
regulatory proteins (not shown). (e) ATP hydrolysis may serve to open
and close the ATPase domain ends of the SMC protein dimer, which
DV 2017
remain linked by kleisin (and other proteins not shown).
 970 Cấu trúc DNA trong các phase phân bào
Genes and Chromosomes

Anaphase
G1 S G2 Prophase Metaphase G1
Telophase
Replication

Chromo-
some Cohesin

Condensin
Centro-
mere
+ + +
separase

FIGURE 24–35 Model for the roles of cohesins and condensins during the chromatids in a condensed state. During anaphase, an activity
the eukaryotic cell cycle. Cohesins are loaded onto the chromosomes called separase removes the cohesin links. Once the chromatids sepa-
during the G1 phase, tethering the sister chromatids together during rate, the condensins begin to unload and the daughter chromosomes
replication. With the onset of mitosis, condensins bind and maintain return to an uncondensed state.
Lehninger et al, 2008
Bacterial DNA Is Also Highly Organized Tan DV 2017
 bp on FIGURE 24–36 E. coli nucleoids. The DNA of these cells is stained with
a dye that fluoresces when exposed to UV light. The light area defines
r chro-
ed; for
nly the
Cấu trúc nucleoid ở E.coli
the nucleoid. Note that some cells have replicated their DNA but have
not yet undergone cell division and hence have multiple nucleoids.

ains do
ies are
coordi-
es not
e local
ryotes.
e best-
called
sociate
histone
uctural
ct a re-
forma-
hort as FIGURE 24–37 Looped domains of the E. coli chromosome. Each do-
divide main is about 10,000 bp in length. The domains are not static, but move
greater along the DNA aset
Lehninger replication
al, 2008 proceeds. Barriers at the boundaries of
and/or the domains, of unknown composition,
Tan DV 2017 prevent the relaxation of
lism in
 Epigenetic, Euchromatin and consensus
sequence
• Information that is passed from one generation to the next— to
daughter cells at cell division or from parent to offspring—but
is not encoded in DNA sequences is referred to as epigenetic
information. Much of it is in the form of covalent modification
of histones and/or the placement of histone variants in
chromosomes.
• The chromatin regions where active gene expression
(transcription) is occurring tend to be partially decondensed and
are called euchromatin .
• Consensus sequence: common structural motifs: TATA.
• The TATA box is the assembly point for the RNA polymerase II
(Pol II) transcription complex.
Tan DV 2017
 Bài tập
Để xác định trình tự (****)trên đầu tận sợi của DNA đơn,
người ta thiết kế mồi RNA có trình tự 5’-AGAGCU-3’ được
đánh dấu phóng xạ để xác định độ dài RNA được tổng hợp khi
sử dụng RNA polimerase.

5’- **** AGAGAGCTCTGGAA****-3’

Bằng điện di người ta xác định

được các RNA được tổng hợp có Cho biết thí nghiệm này cho phép xác
khối lượng như sau: định trình tự nuclotide ở vị trí nào
của sợi đơn DNA trên?
**********U Hãy xác định trình tự đó.
***********G
************A
*************G
Tan DV 2017
 Di truyền ngoại gene
310
Epigenetic R. L. P. Adams

-CG -CGCGCG CG CG- DNA in which 3 of CGs are

-GC - GCGC - GC GC- symmetrically methylated
Replication

-CG -CCGG CG -CG - -CG CGCG- CG CG

-GC GCGC GC GC- -GC GCGC GC GC -
Hemimethylated DNA just after replication

IA second round
Maintenance of replication
methylation in the absence
of methylation

-CG-CGCG-CG -CG - -CG - CGCG - CG- CG- Unmethylated

-GC - GCGC- GC-GC - -GC- GCGC' GC- GC- duplex
Original pattern re-established
--CGCGCGCG CG- .

'De novo' -GC GCGC-GC -GC-

methylation

Maintenance
-CG-CGCG CG -CG- methylation
-GC-GCGC GC GC-
Change in pattern of methylation
-CG CGCG-CG -CG-
-GC-GCGCGC -GC-
Fig. 1. Maintenance and 'de novo' methylation
AdamDNA
The figure represents a stretch of vertebrate RLP,with1990
five CG dinucleotide pairs, three of which are methylated on both
strands. On replication two hemimethylated duplexes are produced. Maintenance methylation (on the left) will restore the
parental pattern of methylation. If, however, a second round of replication intervenes prior to methylation (right) then an
unmethylated molecule is produced. A 'de novo' methylaseTan
will DV methyl groups to CG dinucleotides previously unmethylated
add 2017
on both strands (bottom left). * represents a methyl group.
 Di truyền ngoại gene
Cho phép một tế bào chỉ biểu hiện số gene

h]ps://www.youtube.com/watch?v=urNJVFLcg5U

Tan DV 2017
ences and Cutting Enzyme giới hạn
complementarity between the ends created by EcoRI
(pronounced Eeko R-1 or Echo R-1):
Restriction
↓
59---GAATTC---39 ---G39 59AATTC--- complementarity be
Table 4.1 Recognition
→ Sequences and
+ Cutting
39---CTTAAG---59 ---CTTAA59
Sites of Selected Restriction 39G--- (pronounced Eeko R
on Sequence*
↑ Endonucleases
↓
T
59---GAATTC---39
TCC Note
Enzymealso that EcoRIRecognition
produces Sequence*
4-base overhangs that 39---CTTAAG---59
TCT protrude from the 59-ends of the fragments. PstI cuts at the ↑
AluI AG↓CT
GAT 39-ends of its recognition sequence, so it leaves 39-overhangs. Note also that E
BamHI G↓GATCC
TTC SmaI cuts in the middle of its sequence, so it produces blunt protrude from the 59
BglII A↓GATCT
ends with no overhangs. 39-ends of its recognit
C ClaI AT↓CGAT
Restriction
EcoRI
enzymes can make staggered cuts because
G↓AATTC SmaI cuts in the midd
↓ Pu A C
the sequences
HaeIII they recognize
GG↓C usually
C display twofold ends with no overha
CTT Restriction enzym
symmetry.
HindII That is, they areG identical
T Py ↓ Pu Aafter
C rotating them
G 180 degrees. the sequences they
HindIII For example,A imagine
↓ A G C T Tinverting the EcoRI
C↓C symmetry. That is, t
recognition
HpaII sequence just described:
C↓CGG 180 degrees. For ex
C KpnI GGTAC↓C recognition sequence
A↓G MboI ↓ ↓GATC
59---GAATTC---39
↓CG PstI CTGCA↓G
39---CTTAAG---59
GAC PvuI CGAT↓CG
↑
GGG SalI G↓TCGAC
see it will still look Cthe
SmaI
You can ↓ G Gafter
C Csame G the inversion. In
GGG You can see it will sti
XmaI C ↓ C C G G G
a way, these sequences read the same forward and
GCCGC Weaver
a way,R, 2012
these seque
NotI Thus, EcoRI cuts
backward. ↓ G G C Cthe
G Cbetween G CG and the A in
backward. Thus, Eco
is presented, but restriction the top strand
*Only one (onwritten
DNA strand, the 59→39
left),left and between the GAA and the the top strand (on t
as illustrated in the text for EcoRI. Tan DV 2017 to right is presented, but restriction
by an arrow.
A inendonucleases
the bottom actuallystrand (on the
cut double-stranded DNAright),
as illustratedas
The cutting site for each enzyme is represented by an arrow.
shown
in the by the
text for EcoRI.
A in the bottom str
 5
BÀI TẬP Cell-, molecular- and microbiology

The following schematic shows a stage of cell division for an eukaryotic diploid cell.

1. Quá trình phiên mã gene mã

hoá Histone diễn ra mạnh
trong giai đoạn phân bào này
đúng không? Tai sao?
2. Đột biến mất chức năng của
protein vận động ảnh hưởng
đến quá trình phân bào như
Indicate if each of the following statements is truethế nào?
or not.
A. The schematic may represent a stage of mitosis.
IBO-2013
B. The schematic may represent a stage of meiosis II.
C. The cell would have failed to reach this stage if microtubular motor proteins were inhibited.
D. Transcription of histone genes peaks during this stage.
A. False B. True C. True D. False

Tan DV 2017
Original commentary
Correct answers
 BÀI TẬP
Bạn sẽ phải chèn gene PhoQ (hình dưới) vào một plasmid sử
dụng enzyme giới hạn NcoI (CCATGG) và EcoRI (GAATTC).
Để thực hiện được việc này, ban cần thiết kế mồi một phần
trình tự 561 nucleotide như sau:
IBO 2014
BALI, INDONESIA

5’-ATGCGACAGTTCATCACCGA…...GCGGGACCGGACTGGGGTAA-3’
3. You plan to insert the gene PhoQ from Tobibacterium sp into a pl
artificial promotor followed by a restriction site for NcoI (CCATGG
EcoRI (GAATTC).

Vì sao phải sử dụng 2 enzyme giới hạn? Promoter NcoI

EcoRI
Hãy xác định trình tự mồi PhoQ.
Plasmid vector

To conduct this experiment you are required to design forward (the se

(antisense strand) primers. Part of the 561 nucleotide long coding seq

IBO-2014
5’-ATGCGACAGTTCATCACCGA... ______....GCGGGACCGGAC

Indicate if each of the following statements is true or false.

A. The use of two different restriction sites avoids wrong orientatio
B. A possible forward primer for amplification and insertion of Pho
Tan DV 2017 following sequence: 5’ – GATCCCATGGATGCGACAGTTC –
C. A possible reverse primer for amplification and insertion of PhoQ
 BÀI TẬP
5’-***GAATTC***-3’ 5’-***G AATTC***-3’
3’-***CTTAAG ***-5’ 3’-***CTTAA G ***-5’

5’-***CCATGG***-3’ 5’ AATTC***-***G
5’-***GGTACC***-3’ G ***-***CTTAA-5’

IBO-2014

Tan DV 2017