4.1 DNA Structure

Two DNA strands intertwine to form a double helix. Each strand has a backbone

composed of phosphates and sugars to which the bases are attached. The bases

form the core of the double helix, while the sugar–phosphate backbones are on

the outside. The two grooves between the backbones are called the major and

minor groove based on their sizes. Most protein–DNA contacts are made in the

major grove, because the minor groove is too narrow.

The DNA backbone is assembled from repeating deoxyribose sugar units

that are linked through phosphate groups. Each phosphate carries a negative

charge, making the entire DNA backbone highly charged and polar.

A cyclic base is attached to each sugar. The bases are planar and extend out

perpendicular to the path of the backbone. Pyrimidine bases are composed of

one ring and purine bases of two rings. Adjacent bases are aligned so that their

planar rings stack on top of one another. Base stacking contributes significantly

to the stability of the double helix.

In a double helix, each base on one strand is paired to a base on the other

strand that lies in the same plane. In these base pairing interactions, guanine

always pairs with cytosine, and thymine with adenine.

A GC pair is stabilized by three hydrogen bonds formed between amino and

carbonyl groups that project from the bases.

In contrast, an AT pair is stabilized by two hydrogen bonds.

The specificity of base pairing ensures that the two strands are complementary.1

教科書4.1.1

Figure 5-3 Molecular Biology of the Cell (© Garland Science 2008)

三リン酸（高エネルギー化合物）↓

マイナス電荷同志の反発に注目！

2

教科書4.2.2

4.2.3DNA合成のルール

鋳型ストランド

プライマーストランド

ピロリン酸

（DNA合成酵素の触媒中心に）

入ってきているヌクレオチド三リン酸体

頭（５’）からおしり（３’）に向かって合成され、逆はない。

Figure 5-4 Molecular Biology of the Cell (© Garland Science 2008)

3

教科書4.2.2DNA合成酵素（ポリメラーゼ）：

手のひらと親指と指でDNAをつかんで、重合反応を触媒している感じ

手： DNA合成酵素をデフォルメしている。

5.1 DNA Polymerase

DNA polymerase faithfully replicates DNA by using the nucleotide sequence of

the template strand, colored yellow, to select each new nucleotide to be added

to the 3’ end of a growing strand, colored gray. In this animation, the different

domains of DNA polymerase are colored differently.

Before a nucleotide can be incorporated into DNA at the 3’ end of the growing

strand, the blue finger domain of the polymerase moves inward to correctly

position the nucleoside triphosphate. A pyrophosphate group is released when

each nucleotide is added.

In this view, the details of nucleotide selection at the active site are shown

with the incoming nucleoside triphosphate and the template nucleotide in light

blue. The growing strand is green, and the template strand is red. When the finger

domain moves inward, the nucleoside triphosphate is tested for its ability to

form a proper base pair with the template nucleotide.

When a base pair forms, the active site residues catalyze the covalent addition

of the new nucleotide to the 3’ hydroxyl group on the growing strand, and

the entire process repeats at speeds up to 500 nucleotides per second.

On rare occasions, approximately once every 10,000 nucleotide additions,

the polymerase makes an error and incorporates a nucleotide that does not form

a proper base pair onto the end of the growing strand. When this occurs, the

polymerase changes conformation, and transfers the end of the growing strand

to a second active site on the polymerase, where the erroneous, added

nucleotide is removed. The polymerase then flips back to its original conformation,

allowing polymerization to continue.

As a result, such a self-correcting DNA polymerase will make a mistake only

about once every 107 to 108 nucleotide pairs.

4

教科書4.2.2

-4.2.4

Figure 5-7 Molecular Biology of the Cell (© Garland Science 2008)

Helicase(青色の蛋白質）によってほどかれた鋳型DNA

アニメーション時に、右下にほどかれる。

アニメーション時に、「右下」に伸びる鎖

アニメーション時に、「右上」にほどかれる鋳型DNA

アニメーション時に、上のほうから「逆向き」に合成

難しいので、アニメーション「5.4 Replication I」を見ながら理解ください。

5

教科書4.2.3

と図4.3DNAの不連続合成と岡崎断片

岡崎断片

5.4 Replication I

Using computer animation based on molecular research, we are able to picture

how DNA is replicated in living cells. You are looking at an assembly line of

amazing miniature biochemical machines that are pulling apart the DNA double

helix and cranking out a copy of each strand. The DNA to be copied enters

the production line from bottom left. The whirling blue molecular machine is

called a helicase. It spins the DNA as fast as a jet engine as it unwinds the double

helix into two strands. One strand is copied continuously and can be seen

spooling off to the right. Things are not so simple for the other strand because

it must be copied backwards. It is drawn out repeatedly in loops, and copied

one section at a time. The end result is two new DNA molecules.

元DNA

DNAをほぐす酵素（helicase）

6

教科書4.2.3

と図4.3

Figure 5-9 Molecular Biology of the Cell (© Garland Science 2008)

P: 合成酵素部E: 分解酵素部

7

教科書4.2.4

校正重合中

AT,GCペア以外のものを間違えて重合させてしまったら校正機能が働き、分解してもう一度重合反応しなおす。

鋳型DNA

複製途中のDNA

DNA合成酵素は複製エラーに対応可能な分子装置になっている。

Figure 5-19b,c Molecular Biology of the Cell (© Garland Science 2008)

8

4.2 DNAの複製：まとめ

親DNA2本鎖

新生リーディングDNA2本鎖

新生ラギングDNA2本鎖電子顕微鏡写真

Figure 5-44 Molecular Biology of the Cell (© Garland Science 2008)

9

化学的に恐ろしく安定なDNAの弱点：自然に起こる反応。

赤色矢印は酸化。青色は加水分解。緑はメチル化。→の大きさは起きやすさ。

教科書4.3

Figure 5-45 Molecular Biology of the Cell (© Garland Science 2008)

10

教科書4.3.2

水が変異原・・・まさか・・・？！

ごくまれに水はDNAに変異を誘発する。

脱プリン反応

脱アミノ反応

Figure 5-50a Molecular Biology of the Cell (© Garland Science 2008)

11

教科書4.3.2

でも大丈夫。全部修復してくれます。

天然DNA塩基 非天然DNA塩基

Figure 5-47 Molecular Biology of the Cell (© Garland Science 2008)

12

教科書4.3.2

DNAが変異すると、DNA複製の時に重大な問題がおこる。

セーフ

複製

脱アミノ化したC 脱プリンしたA

変異が遺伝（ヤバ） 欠損変異が遺伝（ヤバ）

セーフ

Figure 5-46 Molecular Biology of the Cell (© Garland Science 2008)

13

教科書4.3.3紫外線： DNAの[2+2]光環化反応を起こす

Figure 5-48a Molecular Biology of the Cell (© Garland Science 2008)

14

教科書4.3.4DNAの修復例：5種類の酵素が総がかりでこれに臨む。

老化すると酵素の働きが弱くなりor合成されづらくなり変異が蓄積されやすくなる。（老人は癌にかかりやすい）

脱アミノ化したC

ウラシル(U)はDNAに本来ないので酵素で除去される

2種類の酵素がDNA主鎖を除去する

DNA合成酵素と連結酵素がDNAの傷をふさぐ

Cに戻ってセーフ↓

Figure 5-48b Molecular Biology of the Cell (© Garland Science 2008)

15

教科書4.3.4

図 4.4

修復酵素の反応速度が追いつかなくなるような激しい日焼けは止めたほうが・・。

修復例２：紫外線の場合

チミンダイマーを認識して付近を丸ごと削る酵素

DNAをほぐす酵素

あとは同じ

Figure 5-62 Molecular Biology of the Cell (© Garland Science 2008)

16

教科書4.4.1受精時など、積極的なDNA組み換えが必要なとき：相同組換え

良く似た配列のDNA同士がホリデイ構造を作り組み換わる。

父DNA

母DNA

子DNA子DNA

ほぼ相補的ほぼ相補的

完全に相補的

完全に相補的

5.7 Holliday Junction

The Holliday junction, an important intermediate structure in homologous

DNA recombination, is formed when two homologous double-stranded DNA

molecules reciprocally exchange DNA strands.

This junction can be visualized directly in the electron microscope.

In the cell, this junction is formed and stabilized by a specific group of helicase

proteins, seen here in the background, which use ATP hydrolysis to move

the junction up and down the DNA, as shown in this animation.

17

教科書4.4.1

18

本日のまとめ

・DNAの性質：二本鎖・相補性・変性とハイブリダイゼーション

・DNAの複製：半保存的複製・DNA合成酵素による不連続合成・校正・テロメア

・DNAの変異と修復点変異（突然変異）・欠失変異・挿入変異・変異原・チミン２量体

・DNAの組換え相同組換え・ホリデイ構造