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the 2nd letter of the Roman alphabet (同)b
the blood group whose red cells carry the B antigen (同)type_B, group B
the 4th letter of the Roman alphabet (同)d

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deuteriumの化学記号
deoxyribonucleic acidディオキシリボ核酸

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2017/09/08 02:23:48」(JST)

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Two complementary regions of nucleic acid molecules will bind and form a double helical structure held together by base pairs.

In molecular biology, the term double helix^[1] refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure. The term entered popular culture with the publication in 1968 of The Double Helix: A Personal Account of the Discovery of the Structure of DNA, by James Watson.

The DNA double helix polymer of nucleic acid, held together by nucleotides which base pair together.^[2] In B-DNA, the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn.^[3] This translates into about 20-21 nucleotides per turn. The double helix structure of DNA contains a major groove and minor groove. In B-DNA the major groove is wider than the minor groove.^[2] Given the difference in widths of the major groove and minor groove, many proteins which bind to B-DNA do so through the wider major groove.^[4]

1 History
2 Nucleic acid hybridization
3 Base pair geometry
4 Helix geometries
- 4.1 Grooves
- 4.2 Non-double helical forms
5 Bending
- 5.1 Persistence length, axial stiffness
- 5.2 Models for DNA bending
- 5.3 Bending preference
- 5.4 Circularization
6 Stretching
7 Supercoiling and topology
- 7.1 The linking number paradox
8 See also
9 References

History

The double-helix model of DNA structure was first published in the journal Nature by James Watson and Francis Crick in 1953,^[5] (X,Y,Z coordinates in 1954^[6]) based upon the crucial X-ray diffraction image of DNA labeled as "Photo 51", from Rosalind Franklin in 1952,^[7] followed by her more clarified DNA image with Raymond Gosling,^[8]^[9] Maurice Wilkins, Alexander Stokes, and Herbert Wilson,^[10] and base-pairing chemical and biochemical information by Erwin Chargaff.^[11]^[12]^[13]^[14]^[15]^[16] The prior model was triple-stranded DNA.^[17]

The realization that the structure of DNA is that of a double-helix elucidated the mechanism of base pairing by which genetic information is stored and copied in living organisms and is widely considered one of the most important scientific discoveries of the 20th century. Crick, Wilkins, and Watson each received one third of the 1962 Nobel Prize in Physiology or Medicine for their contributions to the discovery.^[18] (Franklin, whose breakthrough X-ray diffraction data was used to formulate the DNA structure, died in 1958, and thus was ineligible to be nominated for a Nobel Prize.)

Nucleic acid hybridization

Hybridization is the process of complementary base pairs binding to form a double helix. Melting is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating, enzymes, or physical force. Melting occurs preferentially at certain points in the nucleic acid.^[19] T and A rich regions are more easily melted than C and G rich regions. Some base steps (pairs) are also susceptible to DNA melting, such as T A and T G.^[20] These mechanical features are reflected by the use of sequences such as TATA at the start of many genes to assist RNA polymerase in melting the DNA for transcription.

Strand separation by gentle heating, as used in polymerase chain reaction (PCR), is simple, providing the molecules have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. The cell avoids this problem by allowing its DNA-melting enzymes (helicases) to work concurrently with topoisomerases, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. Helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase.

Base pair geometry

Base pair geometries

The geometry of a base, or base pair step can be characterized by 6 coordinates: shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in a nucleic acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the helical structure of the molecule. In regions of DNA or RNA where the normal structure is disrupted, the change in these values can be used to describe such disruption.

For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider:^[21]^[22]^[23]

Shear
Stretch
Stagger
Buckle
Propeller: rotation of one base with respect to the other in the same base pair.
Opening
Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.
Slide: displacement along an axis in the plane of the base pair directed from one strand to the other.
Rise: displacement along the helix axis.
Tilt: rotation around the shift axis.
Roll: rotation around the slide axis.
Twist: rotation around the rise axis.
x-displacement
y-displacement
inclination
tip
pitch: the number of base pairs per complete turn of the helix.

Rise and twist determine the handedness and pitch of the helix. The other coordinates, by contrast, can be zero. Slide and shift are typically small in B-DNA, but are substantial in A- and Z-DNA. Roll and tilt make successive base pairs less parallel, and are typically small.

Note that "tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand base-pair axis from perpendicularity to the helix axis. This corresponds to slide between a succession of base pairs, and in helix-based coordinates is properly termed "inclination".

Helix geometries

At least three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. The B form described by James Watson and Francis Crick is believed to predominate in cells.^[24] It is 23.7 Å wide and extends 34 Å per 10 bp of sequence. The double helix makes one complete turn about its axis every 10.4-10.5 base pairs in solution. This frequency of twist (termed the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain. The absolute configuration of the bases determines the direction of the helical curve for a given conformation.

A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. It was long thought that the A form only occurs in dehydrated samples of DNA in the laboratory, such as those used in crystallographic experiments, and in hybrid pairings of DNA and RNA strands, but DNA dehydration does occur in vivo, and A-DNA is now known to have biological functions. Segments of DNA that cells have been methylated for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis the opposite way to A-DNA and B-DNA. There is also evidence of protein-DNA complexes forming Z-DNA structures.

Other conformations are possible; A-DNA, B-DNA, C-DNA, E-DNA,^[25] L-DNA (the enantiomeric form of D-DNA),^[26] P-DNA,^[27] S-DNA, Z-DNA, etc. have been described so far.^[28] In fact, only the letters F, Q, U, V, and Y are now^[update] available to describe any new DNA structure that may appear in the future.^[29]^[30] However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems.^{[citation needed]} There are also triple-stranded DNA forms and quadruplex forms such as the G-quadruplex.

The structures of A-, B-, and Z-DNA.

The helix axis of A-, B-, and Z-DNA.

Structural features of the three major forms of DNA^[31]^[32]^[33]
Geometry attribute	A-DNA	B-DNA	Z-DNA
Helix sense	right-handed	right-handed	left-handed
Repeating unit	1 bp	1 bp	2 bp
Rotation/bp	32.7°	34.3°	60°/2
bp/turn	11	10.5	12
Inclination of bp to axis	+19°	−1.2°	−9°
Rise/bp along axis	2.3 Å (0.23 nm)	3.32 Å (0.332 nm)	3.8 Å (0.38 nm)
Pitch/turn of helix	28.2 Å (2.82 nm)	33.2 Å (3.32 nm)	45.6 Å (4.56 nm)
Mean propeller twist	+18°	+16°	0°
Glycosyl angle	anti	anti	C: anti, G: syn
Sugar pucker	C3'-endo	C2'-endo	C: C2'-endo, G: C2'-exo
Diameter	23 Å (2.3 nm)	20 Å (2.0 nm)	18 Å (1.8 nm)

Grooves

Major and minor grooves of DNA. Minor groove is a binding site for the dye Hoechst 33258.

Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.^[34] The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.^[4] This situation varies in unusual conformations of DNA within the cell (see below), but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.

Non-double helical forms

Alternative non-helical models were briefly considered in the late 1970s as a potential solution to problems in DNA replication in plasmids and chromatin. However, the models were set aside in favor of the double-helical model due to subsequent experimental advances such as X-ray crystallography of DNA duplexes and later the nucleosome core particle, and the discovery of topoisomerases. Also, the non-double-helical models are not currently accepted by the mainstream scientific community.^[35]^[36]

Single-stranded nucleic acids (ssDNA) do not adopt a helical formation, and are described by models such as the random coil or worm-like chain.^{[citation needed]}

Bending

DNA is a relatively rigid polymer, typically modelled as a worm-like chain. It has three significant degrees of freedom; bending, twisting, and compression, each of which cause certain limits on what is possible with DNA within a cell. Twisting-torsional stiffness is important for the circularisation of DNA and the orientation of DNA bound proteins relative to each other and bending-axial stiffness is important for DNA wrapping and circularisation and protein interactions. Compression-extension is relatively unimportant in the absence of high tension.

Persistence length, axial stiffness

Example sequences and their persistence lengths (B DNA)^{[citation needed]}
Sequence	Persistence length / base pairs
Random	154±10
(CA)_repeat	133±10
(CAG)_repeat	124±10
(TATA)_repeat	137±10

DNA in solution does not take a rigid structure but is continually changing conformation due to thermal vibration and collisions with water molecules, which makes classical measures of rigidity impossible. Hence, the bending stiffness of DNA is measured by the persistence length, defined as:

"The length of DNA over which the time-averaged orientation of the polymer becomes uncorrelated by a factor of e".

This value may be directly measured using an atomic force microscope to directly image DNA molecules of various lengths. In an aqueous solution, the average persistence length is 46-50 nm or 140-150 base pairs (the diameter of DNA is 2 nm), although can vary significantly. This makes DNA a moderately stiff molecule.

The persistence length of a section of DNA is somewhat dependent on its sequence, and this can cause significant variation. The variation is largely due to base stacking energies and the residues which extend into the minor and major grooves.

Models for DNA bending

Stacking stability of base steps (B DNA)^[37]
Step	Stacking ΔG /kcal mol⁻¹
T A	-0.19
T G or C A	-0.55
C G	-0.91
A G or C T	-1.06
A A or T T	-1.11
A T	-1.34
G A or T C	-1.43
C C or G G	-1.44
A C or G T	-1.81
G C	-2.17

The entropic flexibility of DNA is remarkably consistent with standard polymer physics models, such as the Kratky-Porod worm-like chain model.^{[citation needed]} Consistent with the worm-like chain model is the observation that bending DNA is also described by Hooke's law at very small (sub-piconewton) forces. However, for DNA segments less than the persistence length, the bending force is approximately constant and behaviour deviates from the worm-like chain predictions.

This effect results in unusual ease in circularising small DNA molecules and a higher probability of finding highly bent sections of DNA.^{[citation needed]}

Bending preference

DNA molecules often have a preferred direction to bend, i.e., anisotropic bending. This is, again, due to the properties of the bases which make up the DNA sequence - a random sequence will have no preferred bend direction, i.e., isotropic bending.

Preferred DNA bend direction is determined by the stability of stacking each base on top of the next. If unstable base stacking steps are always found on one side of the DNA helix then the DNA will preferentially bend away from that direction. As bend angle increases then steric hindrances and ability to roll the residues relative to each other also play a role, especially in the minor groove. A and T residues will be preferentially be found in the minor grooves on the inside of bends. This effect is particularly seen in DNA-protein binding where tight DNA bending is induced, such as in nucleosome particles. See base step distortions above.

DNA molecules with exceptional bending preference can become intrinsically bent. This was first observed in trypanosomatid kinetoplast DNA. Typical sequences which cause this contain stretches of 4-6 T and A residues separated by G and C rich sections which keep the A and T residues in phase with the minor groove on one side of the molecule. For example:

¦

G

A

T

C

A

T

G

T

C

A

T

A

G

C

A

T

G

C

A

T

C

A

C

The intrinsically bent structure is induced by the 'propeller twist' of base pairs relative to each other allowing unusual bifurcated Hydrogen-bonds between base steps. At higher temperatures this structure is denatured, and so the intrinsic bend, is lost.

All DNA which bends anisotropically has, on average, a longer persistence length and greater axial stiffness. This increased rigidity is required to prevent random bending which would make the molecule act isotropically.

Circularization

DNA circularization depends on both the axial (bending) stiffness and torsional (rotational) stiffness of the molecule. For a DNA molecule to successfully circularize it must be long enough to easily bend into the full circle and must have the correct number of bases so the ends are in the correct rotation to allow bonding to occur. The optimum length for circularization of DNA is around 400 base pairs (136 nm), with an integral number of turns of the DNA helix, i.e., multiples of 10.4 base pairs. Having a non integral number of turns presents a significant energy barrier for circularization, for example a 10.4 x 30 = 312 base pair molecule will circularize hundreds of times faster than 10.4 x 30.5 ≈ 317 base pair molecule.^[38]

Stretching

Longer stretches of DNA are entropically elastic under tension. When DNA is in solution, it undergoes continuous structural variations due to the energy available in the thermal bath of the solvent. This is due to the thermal vibration of the molecule combined with continual collisions with water molecules. For entropic reasons, more compact relaxed states are thermally accessible than stretched out states, and so DNA molecules are almost universally found in a tangled relaxed layouts. For this reason, one molecule of DNA will stretch under a force, straightening it out. Using optical tweezers, the entropic stretching behavior of DNA has been studied and analyzed from a polymer physics perspective, and it has been found that DNA behaves largely like the Kratky-Porod worm-like chain model under physiologically accessible energy scales.

Under sufficient tension and positive torque, DNA is thought to undergo a phase transition with the bases splaying outwards and the phosphates moving to the middle. This proposed structure for overstretched DNA has been called P-form DNA, in honor of Linus Pauling who originally presented it as a possible structure of DNA.^[27]

The mechanical properties of DNA under compression have not been characterized due to experimental difficulties in preventing the polymer from bending under the compressive force.^{[citation needed]}

Supercoiling and topology

Supercoiled structure of circular DNA molecules with low writhe. The helical aspect of the DNA duplex is omitted for clarity.

The B form of the DNA helix twists 360° per 10.4-10.5 bp in the absence of torsional strain. But many molecular biological processes can induce torsional strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively supercoiled. DNA in vivo is typically negatively supercoiled, which facilitates the unwinding (melting) of the double-helix required for RNA transcription.

Within the cell most DNA is topologically restricted. DNA is typically found in closed loops (such as plasmids in prokaryotes) which are topologically closed, or as very long molecules whose diffusion coefficients produce effectively topologically closed domains. Linear sections of DNA are also commonly bound to proteins or physical structures (such as membranes) to form closed topological loops.

Francis Crick was one of the first to propose the importance of linking numbers when considering DNA supercoils. In a paper published in 1976, Crick outlined the problem as follows:

In considering supercoils formed by closed double-stranded molecules of DNA certain mathematical concepts, such as the linking number and the twist, are needed. The meaning of these for a closed ribbon is explained and also that of the writhing number of a closed curve. Some simple examples are given, some of which may be relevant to the structure of chromatin.^[39]

Analysis of DNA topology uses three values:

L = linking number - the number of times one DNA strand wraps around the other. It is an integer for a closed loop and constant for a closed topological domain.

T = twist - total number of turns in the double stranded DNA helix. This will normally tend to approach the number of turns that a topologically open double stranded DNA helix makes free in solution: number of bases/10.5, assuming there are no intercalating agents (e.g., ethidium bromide) or other elements modifying the stiffness of the DNA.

W = writhe - number of turns of the double stranded DNA helix around the superhelical axis

L = T + W and ΔL = ΔT + ΔW

Any change of T in a closed topological domain must be balanced by a change in W, and vice versa. This results in higher order structure of DNA. A circular DNA molecule with a writhe of 0 will be circular. If the twist of this molecule is subsequently increased or decreased by supercoiling then the writhe will be appropriately altered, making the molecule undergo plectonemic or toroidal superhelical coiling.

When the ends of a piece of double stranded helical DNA are joined so that it forms a circle the strands are topologically knotted. This means the single strands cannot be separated any process that does not involve breaking a strand (such as heating). The task of un-knotting topologically linked strands of DNA falls to enzymes termed topoisomerases. These enzymes are dedicated to un-knotting circular DNA by cleaving one or both strands so that another double or single stranded segment can pass through. This un-knotting is required for the replication of circular DNA and various types of recombination in linear DNA which have similar topological constraints.

The linking number paradox

For many years, the origin of residual supercoiling in eukaryotic genomes remained unclear. This topological puzzle was referred to by some as the "linking number paradox".^[40] However, when experimentally determined structures of the nucleosome displayed an over-twisted left-handed wrap of DNA around the histone octamer,^[41]^[42] this paradox was considered to be solved by the scientific community.

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UpToDate Contents

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2. 2本鎖（ds）DNA、Sm、およびU1 RNPに対する抗体 antibodies to double stranded ds dna sm and u1 rnp
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PMID 27235627

Photochromic switching of the DNA helicity induced by azobenzene derivatives.

Deiana M1, Pokladek Z2, Olesiak-Banska J1, Młynarz P2, Samoc M1, Matczyszyn K1.
Scientific reports.Sci Rep.2016 Jun 24;6:28605. doi: 10.1038/srep28605.
The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (
PMID 27339811

Japanese Journal

Clinical significance of serial quantitative measurement of hepatitis B surface antigen in patients with chronic hepatitis B who were treated with nucleoside analogs

Ishikawa Kazuyoshi,Nitatori Tohru,Nakakarumai Chihoko [他],Isobe Naoko
岩手県立大学看護学部紀要 16, 1-9, 2014-03
… Nucleoside analog(NA)投与を行ったB 型慢性肝炎18 例(男性13 例、女性5 例、観察期間中央値55 ヵ月)を対象にした。 … 治療前後の比較が可能であった8 例では、治療前のHBsAg 量とHBV-DNA 量およびHBcrAg 量には相関傾向がみとめられた。 … 治療開始時に高値を示したHBV-DNA 量は、全例検出感度以下に著減した。 …
NAID 110009782846

Aspergillus niger とその近縁種黒麹菌のマイコトキシン産生性及び系統解析

橋本ルイコ,浅野勝佳,渡嘉敷唯章,陰地義樹,廣瀬（安元）美奈,高良亮,豊里哲也,吉野敦,池端真美,劉瑩,久米田裕子,横山耕治,髙橋治男
マイコトキシン 63(2), 179-186, 2013
… niger とその近縁種である黒麹菌は形態的に類別することは困難であることから，ミトコンドリアチトクローム b DNA 遺伝子などを用いて分子遺伝学的に解析し，これらの菌を正確に分類するとともに，マイコトキシン産生性との関係を明らかにすることによって黒麹菌など実用株の安全性についての検証を行った． …
NAID 130003384018

Hepatitis B DNA Vaccine-Polycation Nano-Complexes Enhancing Immune Response by Percutaneous Administration with Microneedle

Yin Dongfeng,Liang Wenqing,Xing Shuxing [他],Gao Zhixiang,Zhang Wei,Guo Zhili,Gao Shen
Biological and Pharmaceutical Bulletin 36(8), 1283-1291, 2013
… Percutaneous immune method is becoming an attractive alternative for DNA vaccine as a lot of antigen presenting cells are existed in the viable epidermis. … However, due to the barrier function of stratum corneum, it would be hard for DNA vaccine to reach the viable epidermis of the skin. …
NAID 130003361505

Related Pictures

★リンクテーブル★

リンク元	「B-form DNA」「B型DNA」
関連記事	「B」「D」「DNA」

「B-form DNA」

　　[★]

B型DNA

関: B-DNA、deoxyribonucleic acid、DNA、double-stranded DNA

「B型DNA」

　　[★]

英: B-form DNA、B-DNA
関: デオキシリボ核酸、二本鎖DNA

「B」

　　[★]

気管分岐部下緑
補体のalternative pathwayに関わる蛋白質

Mg2+存在下でC3, B, Dが反応してC3bBbとなり、これがC3転換酵素(C3bBb)あるいはC5転換酵素(C3bBb3b)を形成する。これらはP(properdin)と結合して活性化し、それぞれC3、C5を活性化する

「D」

　　[★]

アスパラギン酸
ジヒドロウリジン
遠位の distal,
うつ病 depression
下行結腸 descending colon(大腸内視鏡検査の結果を記載するときに用いる)

「DNA」

　　[★]

英: deoxyribonucleic acid
同: デオキシリボ核酸
関: リボ核酸 RNA

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[8] ttp://www.nature.com/nature/dna50/franklingosling.pdf

[9] The Structure of the DNA Molecule

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[28] List of 55 fiber structures

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v t e Biomolecular structure
Protein structure	Primary Secondary Tertiary Quaternary Determination Prediction Design Thermodynamics
Nucleic acid structure	Primary Secondary Tertiary Quaternary Determination Prediction Design Thermodynamics
See also	Protein Protein domain Protein engineering Nucleic acid DNA RNA Nucleic acid double helix

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案内

B-DNA