A and b dna

A and b dna DEFAULT

Transitions of Double-Stranded DNA Between the A- and B-Forms

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A-DNA is one of the possible double helical structures which DNA can adopt. A-DNA is thought to be one of three biologically active double helical structures along with B-DNA and Z-DNA. It is a right-handed double helix fairly similar to the more common B-DNA form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in B-DNA. It was discovered by Rosalind Franklin, who also named the A and B forms. She showed that DNA is driven into the A form when under dehydrating conditions. Such conditions are commonly used to form crystals, and many DNA crystal structures are in the A form.[1] The same helical conformation occurs in double-stranded RNAs, and in DNA-RNA hybrid double helices.


A-DNA is fairly similar to B-DNA given that it is a right-handed double helix with major and minor grooves. However, as shown in the comparison table below, there is a slight increase in the number of base pairs (bp) per turn (resulting in a smaller twist angle), and smaller rise per base pair (making A-DNA % shorter than B-DNA). The major groove of A-DNA is deep and narrow, while the minor groove is wide and shallow. A-DNA is broader and apparently more compressed along its axis than B-DNA.[2]

Comparison geometries of the most common DNA forms[edit]

Side and top view of A-, B-, and Z-DNA conformations.
Yellow dots represent the location of the helical axis of A-, B-, and Z-DNA with respect to a Guanine-Cytosine base pair.
Geometry attribute: A-formB-formZ-form
Helix senseright-handedright-handedleft-handed
Repeating unit1 bp1 bp2 bp
Mean bp/turn111012
Inclination of bp to axis+19°−°−9°
Rise/bp along axis Å (&#;nm) Å (&#;nm) Å (&#;nm)
Rise/turn of helix Å (&#;nm) Å (&#;nm) Å (&#;nm)
Mean propeller twist+18°+16°
Glycosyl angleantiantipyrimidine: anti,
purine: syn
Nucleotide phosphate to phosphate distance Å ÅC: Å,
G: Å
Sugar puckerC3'-endoC2'-endoC: C2'-endo,
G: C3'-endo
Diameter23 Å (&#;nm)20 Å (&#;nm)18 Å (&#;nm)

Biological function[edit]

Dehydration of DNA drives it into the A form, and this apparently protects DNA under conditions such as the extreme desiccation of bacteria.[3] Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of several hyperthermophilic archaeal viruses, including rod-shaped rudiviruses SIRV2 [4] and SSRV1,[5] enveloped filamentous lipothrixviruses AFV1,[6] SFV1 [7] and SIFV,[5]tristromavirus PFV2 [8] as well as icosahedral portoglobovirus SPV1.[9] A-form DNA is believed to be one of the adaptations of hyperthermophilic archaeal viruses to harsh environmental conditions in which these viruses thrive.

It has been proposed that the motors that package double-stranded DNA in bacteriophages exploit the fact that A-DNA is shorter than B-DNA, and that conformational changes in the DNA itself are the source of the large forces generated by these motors.[10] Experimental evidence for A-DNA as an intermediate in viral biomotor packing comes from double dye Förster resonance energy transfer measurements showing that B-DNA is shortened by 24% in a stalled ("crunched") A-form intermediate.[11][12] In this model, ATP hydrolysis is used to drive protein conformational changes that alternatively dehydrate and rehydrate the DNA, and the DNA shortening/lengthening cycle is coupled to a protein-DNA grip/release cycle to generate the forward motion that moves DNA into the capsid.

See also[edit]


  1. ^Rosalind, Franklin (). "The Structure of Sodium Thymonucleate Fibres. I. The Influence of Water Content"(PDF). Acta Crystallographica. 6 (8): – doi/sx
  2. ^Dickerson, Richard E. (). "DNA structure from a to Z". DNA Structures Part A: Synthesis and Physical Analysis of DNA. Methods in Enzymology. . pp.&#;67– doi/(92) ISBN&#;. PMID&#;
  3. ^Whelan DR, et&#;al. (). "Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation". J R Soc Interface. 11 (97): doi/rsif PMC&#; PMID&#;
  4. ^Di Maio F, Egelman EH, et&#;al. (). "A virus that infects a hyperthermophile encapsidates A-form DNA". Science. (): – BibcodeSciD. doi/science.aaa PMC&#; PMID&#;
  5. ^ abWang, F; Baquero, DP; Beltran, LC; Su, Z; Osinski, T; Zheng, W; Prangishvili, D; Krupovic, M; Egelman, EH (5 August ). "Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments". Proceedings of the National Academy of Sciences of the United States of America. (33): – doi/pnas PMC&#; PMID&#;
  6. ^Kasson, P; DiMaio, F; Yu, X; Lucas-Staat, S; Krupovic, M; Schouten, S; Prangishvili, D; Egelman, EH (). "Model for a novel membrane envelope in a filamentous hyperthermophilic virus". eLife. 6: e doi/eLife PMC&#; PMID&#;
  7. ^Liu, Y; Osinski, T; Wang, F; Krupovic, M; Schouten, S; Kasson, P; Prangishvili, D; Egelman, EH (). "Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile". Nature Communications. 9 (1): BibcodeNatCoL. doi/s PMC&#; PMID&#;
  8. ^Wang, F; Baquero, DP; Su, Z; Osinski, T; Prangishvili, D; Egelman, EH; Krupovic, M (). "Structure of a filamentous virus uncovers familial ties within the archaeal virosphere". Virus Evolution. 6 (1): veaa doi/ve/veaa PMC&#; PMID&#;
  9. ^Wang, F; Liu, Y; Su, Z; Osinski, T; de Oliveira, GAP; Conway, JF; Schouten, S; Krupovic, M; Prangishvili, D; Egelman, EH (). "A packing for A-form DNA in an icosahedral virus". Proceedings of the National Academy of Sciences of the United States of America. (45): – doi/pnas PMC&#; PMID&#;
  10. ^Harvey, SC (). "The scrunchworm hypothesis: Transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages". Journal of Structural Biology. (1): 1–8. doi/j.jsb PMC&#; PMID&#;
  11. ^Oram, M (). "Modulation of the packaging reaction of bacteriophage t4 terminase by DNA structure". J Mol Biol. (1): 61– doi/j.jmb PMC&#; PMID&#;
  12. ^Ray, K (). "DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA substrate". Virology. (2): – doi/j.virol PMC&#; PMID&#;

External links[edit]

Sours: https://en.wikipedia.org/wiki/A-DNA
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Sours: https://www.ncbi.nlm.nih.gov/books/NBK/

Nucleic acid double helix

Structure formed by double-stranded molecules

"Double helix" redirects here. For other uses, see Double helix (disambiguation).

Two complementaryregions 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 of The Double Helix: A Personal Account of the Discovery of the Structure of DNA by James Watson.

The DNA double helix biopolymer of nucleic acid is 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&#; base pairs per turn.[3] 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]


Further information: History of molecular biology

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

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 Nobel Prize in Physiology or Medicine for their contributions to the discovery.[17]

Nucleic acid hybridization[edit]

Main article: Nucleic acid thermodynamics

Hybridization is the process of complementarybase 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 mechanical force. Melting occurs preferentially at certain points in the nucleic acid.[18]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.[19] 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, 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[edit]

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:[20][21][22]

  • 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 height 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[edit]

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.[23] It is Å wide and extends 34 Å per 10 bp of sequence. The double helix makes one complete turn about its axis every – 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 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.

See also: Nucleic acid tertiary structure

Other conformations are possible; A-DNA, B-DNA, C-DNA, E-DNA,[24]L-DNA (the enantiomeric form of D-DNA),[25] P-DNA,[26] S-DNA, Z-DNA, etc. have been described so far.[27] 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.[28][29] 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 and the i-motif.

The structures of A-, B-, and Z-DNA.
The helix axis of A-, B-, and Z-DNA.
Geometry attribute A-DNA B-DNA Z-DNA
Helix senseright-handedright-handedleft-handed
Repeating unit1 bp1 bp2 bp
Inclination of bp to axis+19°−°−9°
Rise/bp along axis Å (&#;nm) Å (&#;nm) Å (&#;nm)
Pitch/turn of helix Å (&#;nm) Å (&#;nm) Å (&#;nm)
Mean propeller twist+18°+16°
Glycosyl angleantiantiC: anti,
G: syn
Sugar puckerC3'-endoC2'-endoC: C2'-endo,
G: C2'-exo
Diameter23 Å (&#;nm)20 Å (&#;nm)18 Å (&#;nm)


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

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.[33] 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[edit]

Alternative non-helical models were briefly considered in the late s 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.[34][35]


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[edit]

Main article: Persistence length

Sequence Persistence length
/ base pairs
Random ±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 to apply. 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.[citation needed]

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 – 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[edit]

Step Stacking ΔG
/kcal mol−1
T G or C A
A G or C T
A A or T T
G A or T C
C C or G G
A C or G T

At length-scales larger than the persistence length, the entropic flexibility of DNA is remarkably consistent with standard polymer physics models, such as the Kratky-Porodworm-like chain model.[37] 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. 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.[38]

Bending preference[edit]

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 trypanosomatidkinetoplast DNA. Typical sequences which cause this contain stretches of 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:


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.


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 base pairs (&#;nm)[citation needed], with an integral number of turns of the DNA helix, i.e., multiples of base pairs. Having a non integral number of turns presents a significant energy barrier for circularization, for example a x 30 = base pair molecule will circularize hundreds of times faster than x ≈ base pair molecule.[39]

The bending of short circularized DNA segments is non-uniform. Rather, for circularized DNA segments less than the persistence length, DNA bending is localised to kinks that form preferentially in AT-rich segments. If a nick is present, bending will be localised to the nick site.[38]


Elastic stretching regime[edit]

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-Porodworm-like chain model under physiologically accessible energy scales.

Phase transitions under stretching[edit]

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.[26]

Evidence from mechanical stretching of DNA in the absence of imposed torque points to a transition or transitions leading to further structures which are generally referred to as S-form DNA. These structures have not yet been definitively characterised due to the difficulty of carrying out atomic-resolution imaging in solution while under applied force although many computer simulation studies have been made (for example,[40][41]).

Proposed S-DNA structures include those which preserve base-pair stacking and hydrogen bonding (GC-rich), while releasing extension by tilting, as well as structures in which partial melting of the base-stack takes place, while base-base association is nonetheless overall preserved (AT-rich).

Periodic fracture of the base-pair stack with a break occurring once per three bp (therefore one out of every three bp-bp steps) has been proposed as a regular structure which preserves planarity of the base-stacking and releases the appropriate amount of extension,[42] with the term "Σ-DNA" introduced as a mnemonic, with the three right-facing points of the Sigma character serving as a reminder of the three grouped base pairs. The Σ form has been shown to have a sequence preference for GNC motifs which are believed under the GNC hypothesis to be of evolutionary importance.[43]

Supercoiling and topology[edit]

Main article: DNA supercoil

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 ° per 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 , 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.[44]

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/, 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[edit]

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".[45] However, when experimentally determined structures of the nucleosome displayed an over-twisted left-handed wrap of DNA around the histone octamer,[46][47] this paradox was considered to be solved by the scientific community.

See also[edit]


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And b dna a

B-Form, A-Form, and Z-Form of DNA

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Three major forms of DNA are double stranded and connected by interactions between complementary base pairs. These are terms A-form, B-form,and Z-form DNA.

B-form DNA

The information from the base composition of DNA, the knowledge of dinucleotide structure, and the insight that the X&#;ray crystallography suggested a helical periodicity were combined by Watson and Crick in in their proposed model for a double helical structure for DNA. They proposed two strands of DNA -- each in a right&#;hand helix -- wound around the same axis. The two strands are held together by H&#;bonding between the bases (in anti conformation) as shown in Figure \(\PageIndex{1}\).

Major groove Major groove


Minor groove Minor groove

Figure \(\PageIndex{1}\): (left) An A:T base pair and (right) a G:C base pair

Bases fit in the double helical model if pyrimidine on one strand is always paired with purine on the other. From Chargaff's rules, the two strands will pair A with T and G with C. This pairs a keto base with an amino base, a purine with a pyrimidine. Two H&#;bonds can form between A and T, and three can form between G and C. This third H-bond in the G:C base pair is between the additional exocyclic amino group on G and the C2 keto group on C. The pyrimidine C2 keto group is not involved in hydrogen bonding in the A:T base pair.

These are the complementary base pairs. The base&#;pairing scheme immediately suggests a way to replicate and copy the the genetic information.


The two strands are not in a simple side&#;by&#;side arrangement, which would be called a paranemic joint (Figure \(\PageIndex{3}\)). (This will be encountered during recombination in Chapter 8.) Rather the two strands are coiled around the same helical axis and are intertwined with themselves (which is referred to as a plectonemic coil). One consequence of this intertwining is that the two strands cannot be separated without the DNA rotating, one turn of the DNA for every "untwisting" of the two strands.


Dimensions of B-form (the most common) of DNA

  • nm between bp, nm per turn, about 10 bp per turn
  • nm (about nm or 20 Angstroms) in diameter

Major and minor groove

The major groove is wider than the minor groove in DNA (Figure \(\PageIndex{2d}\)), and many sequence specific proteins interact in the major groove. The N7 and C6 groups of purines and the C4 and C5 groups of pyrimidines face into the major groove, thus they can make specific contacts with amino acids in DNA-binding proteins. Thus specific amino acids serve as H&#;bond donors and acceptors to form H-bonds with specific nucleotides in the DNA. H&#;bond donors and acceptors are also in the minor groove, and indeed some proteins bind specifically in the minor groove. Base pairs stack, with some rotation between them.

A&#;form nucleic acids and Z&#;DNA

Three different forms of duplex nucleic acid have been described. The most common form, present in most DNA at neutral pH and physiological salt concentrations, is B-form. That is the classic, right-handed double helical structure we have been discussing. A thicker right-handed duplex with a shorter distance between the base pairs has been described for RNA-DNA duplexes and RNA-RNA duplexes. This is called A-form nucleic acid.

A third form of duplex DNA has a strikingly different, left-handed helical structure. This Z DNA is formed by stretches of alternating purines and pyrimidines, e.g. GCGCGC, especially in negatively supercoiled DNA. A small amount of the DNA in a cell exists in the Z form. It has been tantalizing to propose that this different structure is involved in some way in regulation of some cellular function, such as transcription or regulation, but conclusive evidence for or against this proposal is not available yet.

Differences between A-form and B-form nucleic acid

The major difference between A-form and B-form nucleic acid is in the conformation of the deoxyribose sugar ring. It is in the C2' endoconformation for B-form, whereas it is in the C3' endoconformation in A-form. As shown in Figure \(\PageIndex{4}\), if you consider the plane defined by the C4'-O-C1' atoms of the deoxyribose, in the C2' endoconformation, the C2' atom is above the plane, whereas the C3' atom is above the plane in the C3' endoconformation. The latter conformation brings the 5' and 3' hydroxyls (both esterified to the phosphates linking to the next nucleotides) closer together than is seen in the C2' endoconfromation (Figure ). Thus the distance between adjacent nucleotides is reduced by about 1 Angstrom in A-form relative to B-form nucleic acid (Figure \(\PageIndex{4}\)).


A second major difference between A-form and B-form nucleic acid is the placement of base-pairs within the duplex. In B-form, the base-pairs are almost centered over the helical axis (Figure \(\PageIndex{4}\)), but in A-form, they are displaced away from the central axis and closer to the major groove. The result is a ribbon-like helix with a more open cylindrical core in A-form.

Z-form DNA

Z-DNA is a radically different duplex structure, with the two strands coiling in left-handed helices and a pronounced zig-zag (hence the name) pattern in the phosphodiester backbone. As previously mentioned, Z-DNA can form when the DNA is in an alternating purine-pyrimidine sequence such as GCGCGC, and indeed the G and C nucleotides are in different conformations, leading to the zig-zag pattern. The big difference is at the G nucleotide. It has the sugar in the C3' endoconformation (like A-form nucleic acid, and in contrast to B-form DNA) and the guanine base is in the synconformation. This places the guanine back over the sugar ring, in contrast to the usual anticonformation seen in A- and B-form nucleic acid. Note that having the base in the anticonformation places it in the position where it can readily form H-bonds with the complementary base on the opposite strand. The duplex in Z-DNA has to accomodate the distortion of this G nucleotide in the synconformation. The cytosine in the adjacent nucleotide of Z-DNA is in the "normal" C2' endo, anticonformation.


Even classic B-DNA is not completely uniform in its structure. X-ray diffraction analysis of crystals of duplex oligonucleotides shows that a given sequence will adopt a distinctive structure. These variations in B-DNA may differ in the propeller twist (between bases within a pair) to optimize base stacking, or in the 3 ways that 2 successive base pairs can move relative to each other: twist, roll, or slide.

helix senseRight HandedRight HandedLeft Handed
base pairs per turn101112
vertical rise per bp Å Å19 Å
rotation per bp+36°+33°°
helical diameter 19 Å19 Å19 Å
Sours: https://bio.libretexts.org/Bookshelves/Genetics/Book%3A_Working_with_Molecular_Genetics_(Hardison)/Unit_I%3A_Genes_Nucleic_Acids_Genomes_and_Chromosomes/2%3A_Structures_of_Nucleic_Acids/%3A_B-Form_A-Form_and_Z-Form_of_DNA
Structural Forms Of DNA

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