Mechanical properties of DNA
Encyclopedia
In molecular biology
, the term double helix refers to the structure formed by double-stranded molecules of nucleic acid
s such as DNA
and RNA
. 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 is a spiral polymer
of nucleic acids, held together by nucleotides which base pair together. In B-DNA, the most common double helical structure, the double helix is right-handed with about 10–10.5 nucleotides per turn. The double helix structure of DNA contains a major groove and minor groove, the major groove being wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove.
structure was first published in the journal Nature
by James D. Watson
and Francis Crick
in 1953, (X,Y,Z coordinates in 1954) based upon the crucial X-ray diffraction image of DNA labeled as "Photo 51
", from Rosalind Franklin
in 1952, followed by her more clarified DNA image with Raymond Gosling
, Maurice Wilkins
, Alexander Stokes, and Herbert Wilson
, as well as base-pairing chemical and biochemical information by Erwin Chargaff
. The previous model was triple-stranded DNA
.
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 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. (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.)
base pair
s 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, enzyme
s, or physical force. Melting occurs preferentially at certain points in the nucleic acid. T and A rich sequences are more easily melted than C and G rich regions. Particular base steps are also susceptible to DNA melting, particularly T A and T G base steps. These mechanical features are reflected by the use of sequences such as TATAA
at the start of many genes to assist RNA polymerase in melting the DNA for transcription.
Strand separation by gentle heating, as used in 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 (helicase
s) to work concurrently with topoisomerase
s, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. Helicase
s unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase
.
For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider:
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. A diagram of these coordinates can be found in 3DNA website.
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".
, B-DNA, and Z-DNA
. The "B" form described by James D. Watson
and Francis Crick
is believed to predominate in cells. 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 (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain.
A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in crystallographic
experiments, and possibly in hybrid pairings of DNA and RNA
strands. 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, L-DNA (the enantiomer
ic form of D-DNA), P-DNA, S-DNA, Z-DNA, etc. have been described so far. In fact, only the letters F, Q, U, V, and Y are available to describe any new DNA structure that may appear in the future. However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems. There are also triple-stranded DNA
forms and quadruplex forms such as the G-quadruplex
.
. 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. 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 factor
s that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove. 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.
, but these were set aside in favor of the double-helical model due to X-ray crystallography
of DNA duplexes and later the nucleosome core particle, as well as the discovery of topoisomerases. The state of current understanding in the field was aptly outlined in an exchange of correspondence in Current Science in 2004..
Single-stranded nucleic acids do not adopt a helical formation, and are described by models such as the random coil
or worm-like chain
.
. It has three significant degrees of freedom; bending, twisting and compression, each of which cause particular limitations 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.
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:
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.
The entropic flexibility of DNA is remarkably consistent with standard polymer physics
models such as the Kratky-Porod worm-like chain
model. 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.
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 trypanosoma
tid 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:
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, 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.
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, a single 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.
The mechanical properties DNA under compression have not been characterized due to experimental difficulties in preventing the polymer from bending under the compressive force.
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 plasmid
s 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:
Analysis of DNA topology uses three values:
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 known as topoisomerase
s. 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.
displayed an over-twisted left-handed wrap of DNA around the histone
octamer, this "paradox" was considered to be solved by the scientific community.
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, the term double helix refers to the structure formed by double-stranded molecules of nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
s such as DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure
Nucleic acid secondary structure
The secondary structure of a nucleic acid molecule refers to the basepairing interactions within a single molecule or set of interacting molecules, and can be represented as a list of bases which are paired in a nucleic acid molecule....
, and is a fundamental component in determining its tertiary structure
Nucleic acid tertiary structure
300px|thumb|upright|alt = Colored dice with checkered background|Example of a large catalytic RNA. The self-splicing group II intron from Oceanobacillus iheyensis....
. 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
The Double Helix
The Double Helix: A Personal Account of the Discovery of the Structure of DNA is an autobiographical account of the discovery of the double helix structure of DNA written by James D. Watson and published in 1968. It was and remains a controversial account...
, by James Watson.
The DNA double helix is a spiral polymer
Polymer
A polymer is a large molecule composed of repeating structural units. These subunits are typically connected by covalent chemical bonds...
of nucleic acids, held together by nucleotides which base pair together. In B-DNA, the most common double helical structure, the double helix is right-handed with about 10–10.5 nucleotides per turn. The double helix structure of DNA contains a major groove and minor groove, the major groove being wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove.
History
The double-helix model of DNADNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
structure was first published in the journal Nature
Nature (journal)
Nature, first published on 4 November 1869, is ranked the world's most cited interdisciplinary scientific journal by the Science Edition of the 2010 Journal Citation Reports...
by James D. Watson
James D. Watson
James Dewey Watson is an American molecular biologist, geneticist, and zoologist, best known as one of the co-discoverers of the structure of DNA in 1953 with Francis Crick...
and Francis Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
in 1953, (X,Y,Z coordinates in 1954) based upon the crucial X-ray diffraction image of DNA labeled as "Photo 51
Photo 51
Photo 51 is the nickname given to an X-ray diffraction image of DNA taken by Rosalind Franklin in 1952 that was critical evidence in identifying the structure of DNA. The photo was taken by Franklin while working at King's College London in Sir John Randall's group.James D...
", from Rosalind Franklin
Rosalind Franklin
Rosalind Elsie Franklin was a British biophysicist and X-ray crystallographer who made critical contributions to the understanding of the fine molecular structures of DNA, RNA, viruses, coal and graphite...
in 1952, followed by her more clarified DNA image with Raymond Gosling
Raymond Gosling
Raymond Gosling is a distinguished scientist who worked with both Maurice Wilkins and Rosalind Franklin at King's College London in deducing the structure of DNA, under the direction of Sir John Randall. His other KCL colleagues included Alex Stokes and Herbert Wilson.-Early years:He was born in...
, Maurice Wilkins
Maurice Wilkins
Maurice Hugh Frederick Wilkins CBE FRS was a New Zealand-born English physicist and molecular biologist, and Nobel Laureate whose research contributed to the scientific understanding of phosphorescence, isotope separation, optical microscopy and X-ray diffraction, and to the development of radar...
, Alexander Stokes, and Herbert Wilson
Herbert Wilson
Professor Herbert R. Wilson, FRS was a physicist, who was one of the team who worked on the structure of DNA at King's College London, under the direction of Sir John Randall.-College education:...
, as well as base-pairing chemical and biochemical information by Erwin Chargaff
Erwin Chargaff
Erwin Chargaff was an American biochemist who emigrated to the United States during the Nazi era. Through careful experimentation, Chargaff discovered two rules that helped lead to the discovery of the double helix structure of DNA...
. The previous model was triple-stranded DNA
Triple-stranded DNA
A triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix. In this structure, one strand binds to a B-form DNA double helix through Hoogsteen or reversed Hoogsteen hydrogen bonds....
.
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 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
Nobel Prize in Physiology or Medicine
The Nobel Prize in Physiology or Medicine administered by the Nobel Foundation, is awarded once a year for outstanding discoveries in the field of life science and medicine. It is one of five Nobel Prizes established in 1895 by Swedish chemist Alfred Nobel, the inventor of dynamite, in his will...
for their contributions to the discovery. (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 complementaryComplementarity (molecular biology)
In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...
base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
s 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, enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s, or physical force. Melting occurs preferentially at certain points in the nucleic acid. T and A rich sequences are more easily melted than C and G rich regions. Particular base steps are also susceptible to DNA melting, particularly T A and T G base steps. These mechanical features are reflected by the use of sequences such as TATAA
TATA box
The TATA box is a DNA sequence found in the promoter region of genes in archaea and eukaryotes; approximately 24% of human genes contain a TATA box within the core promoter....
at the start of many genes to assist RNA polymerase in melting the DNA for transcription.
Strand separation by gentle heating, as used in 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 (helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
s) to work concurrently with topoisomerase
Topoisomerase
Topoisomerases are enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double helical structure. For example, during DNA replication, DNA becomes overwound ahead of a replication fork...
s, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. Helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
s unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
.
Base pair geometry
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:
- Shear
- Stretch
- Stagger
- Buckle
- Propeller twist: 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 this axis.
- vRoll: rotation around this axis.
- Twist: rotation around the helix axis.
- vx-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. A diagram of these coordinates can be found in 3DNA website.
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-DNAA-DNA
A-DNA is one of the many possible double helical structures of DNA. A-DNA is thought to be one of three biologically active double helical structures along with B- and Z-DNA. It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more...
, B-DNA, and Z-DNA
Z-DNA
Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the double helix winds to the left in a zig-zag pattern...
. The "B" form described by James D. Watson
James D. Watson
James Dewey Watson is an American molecular biologist, geneticist, and zoologist, best known as one of the co-discoverers of the structure of DNA in 1953 with Francis Crick...
and Francis Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
is believed to predominate in cells. It is 23.7 Å
Ångström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
wide and extends 34 Å per 10 bp
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
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 (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain.
A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in crystallographic
Crystallography
Crystallography is the experimental science of the arrangement of atoms in solids. The word "crystallography" derives from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and grapho = write.Before the development of...
experiments, and possibly in hybrid pairings of DNA and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
strands. Segments of DNA that cells have been methylated
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
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
C-DNA
C-DNA also known as C form DNA. It is one of the many possible double helical structures of DNA. This form of DNA can be observed at some conditions such as relatively low humidity and the presence of certain ions, such as Li+ or Mg2+....
, E-DNA, L-DNA (the enantiomer
Enantiomer
In chemistry, an enantiomer is one of two stereoisomers that are mirror images of each other that are non-superposable , much as one's left and right hands are the same except for opposite orientation. It can be clearly understood if you try to place your hands one over the other without...
ic form of D-DNA), P-DNA, S-DNA, Z-DNA, etc. have been described so far. In fact, only the letters F, Q, U, V, and Y are available to describe any new DNA structure that may appear in the future. However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems. There are also triple-stranded DNA
Triple-stranded DNA
A triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix. In this structure, one strand binds to a B-form DNA double helix through Hoogsteen or reversed Hoogsteen hydrogen bonds....
forms and quadruplex forms such as the G-quadruplex
G-quadruplex
In molecular biology, G-quadruplexes are nucleic acid sequences that are rich in guanine and are capable of forming a four-stranded structure...
.
| 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° | 35.9° | 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 Ring pucker Ring pucker is a technical term used in chemistry. In sugar chemistry, five-membered rings such as the furanose form of ribose are more flexible and have a greater tendency to pucker than six-membered rings such as the pyranose form of glucose... |
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) |
| Sources: | |||
Grooves
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 siteBinding site
In biochemistry, a binding site is a region on a protein, DNA, or RNA to which specific other molecules and ions—in this context collectively called ligands—form a chemical bond...
. 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. 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 factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove. 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
Other non-double helical forms of DNA have been theorized, for example the side-by-side (SBS) geometry where the two strands do not wind around each other. Side-by-side models of DNA were proposed early in the history of molecular biologyHistory of molecular biology
The history of molecular biology begins in the 1930s with the convergence of various, previously distinct biological disciplines: biochemistry, genetics, microbiology, and virology...
, but these were set aside in favor of the double-helical model due to X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
of DNA duplexes and later the nucleosome core particle, as well as the discovery of topoisomerases. The state of current understanding in the field was aptly outlined in an exchange of correspondence in Current Science in 2004..
Single-stranded nucleic acids do not adopt a helical formation, and are described by models such as the random coil
Random coil
A random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules...
or worm-like chain
Worm-like chain
The worm-like chain model in polymer physics is used to describe the behavior of semi-flexible polymers; it is sometimes referred to as the Kratky-Porod model.- Theoretical Considerations :...
.
Bending
DNA is a relatively rigid polymer, typically modelled as a worm-like chainWorm-like chain
The worm-like chain model in polymer physics is used to describe the behavior of semi-flexible polymers; it is sometimes referred to as the Kratky-Porod model.- Theoretical Considerations :...
. It has three significant degrees of freedom; bending, twisting and compression, each of which cause particular limitations 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
| 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
Atomic force microscope
Atomic force microscopy or scanning force microscopy is a very high-resolution type of scanning probe microscopy, with demonstrated resolution on the order of fractions of a nanometer, more than 1000 times better than the optical diffraction limit...
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
| 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
Polymer physics
Polymer physics is the field of physics that studies polymers, their fluctuations, mechanical properties, as well as the kinetics of reactions involving degradation and polymerisation of polymers and monomers respectively....
models such as the Kratky-Porod worm-like chain
Worm-like chain
The worm-like chain model in polymer physics is used to describe the behavior of semi-flexible polymers; it is sometimes referred to as the Kratky-Porod model.- Theoretical Considerations :...
model. Consistent with the worm-like chain
Worm-like chain
The worm-like chain model in polymer physics is used to describe the behavior of semi-flexible polymers; it is sometimes referred to as the Kratky-Porod model.- Theoretical Considerations :...
model is the observation that bending DNA is also described by Hooke's law
Hooke's law
In mechanics, and physics, Hooke's law of elasticity is an approximation that states that the extension of a spring is in direct proportion with the load applied to it. Many materials obey this law as long as the load does not exceed the material's elastic limit. Materials for which 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.
Bending preference
DNA molecules often have a preferred direction to bend, ie. 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
Nucleosome
Nucleosomes are the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a histone protein core. This structure is often compared to thread wrapped around a spool....
particles. See base step distortions above.
DNA molecules with exceptional bending preference can become intrinsically bent. This was first observed in trypanosoma
Trypanosoma
Trypanosoma is a genus of kinetoplastids , a monophyletic group of unicellular parasitic flagellate protozoa. The name is derived from the Greek trypano and soma because of their corkscrew-like motion. All trypanosomes are heteroxenous and are transmitted via a vector...
tid kinetoplast
Kinetoplast
A kinetoplast is a disk-shaped mass of circular DNA inside a large mitochondrion that contains many copies of the mitochondrial genome. Kinetoplasts are only found in protozoa of the class Kinetoplastida...
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 T C C C A A A A A T G T C A A A A A A T A G G C A A A A A A T G C C A A A A A A T C C C A A 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, 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.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 bathThermal bath (thermodynamics)
In thermodynamics and statistical mechanics, a thermal bath is a reservoir of particles at finite temperature undergoing Brownian motion, and that in thermal contact with an object of interest. Because of its nonzero temperature, this system contains thermal energy. This yields an environment where...
of the solvent. This is due to the thermal vibration of the molecule combined with continual collisions with water molecules. For entropic
Entropy
Entropy is a thermodynamic property that can be used to determine the energy available for useful work in a thermodynamic process, such as in energy conversion devices, engines, or machines. Such devices can only be driven by convertible energy, and have a theoretical maximum efficiency when...
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, a single molecule of DNA will stretch under a force, straightening it out. Using optical tweezers
Optical tweezers
Optical tweezers are scientific instruments that use a highly focused laser beam to provide an attractive or repulsive force , depending on the refractive index mismatch to physically hold and move microscopic dielectric objects...
, the entropic stretching behavior of DNA has been studied and analyzed from a polymer physics
Polymer physics
Polymer physics is the field of physics that studies polymers, their fluctuations, mechanical properties, as well as the kinetics of reactions involving degradation and polymerisation of polymers and monomers respectively....
perspective, and it has been found that DNA behaves largely like the Kratky-Porod worm-like chain
Worm-like chain
The worm-like chain model in polymer physics is used to describe the behavior of semi-flexible polymers; it is sometimes referred to as the Kratky-Porod model.- Theoretical Considerations :...
model under physiologically accessible energy scales.
Under sufficient tension and positive torque, DNA is thought to undergo a phase transition
Phase transition
A phase transition is the transformation of a thermodynamic system from one phase or state of matter to another.A phase of a thermodynamic system and the states of matter have uniform physical properties....
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
Linus Pauling
Linus Carl Pauling was an American chemist, biochemist, peace activist, author, and educator. He was one of the most influential chemists in history and ranks among the most important scientists of the 20th century...
who originally presented it as a possible structure of DNA.
The mechanical properties DNA under compression have not been characterized due to experimental difficulties in preventing the polymer from bending under the compressive force.
Supercoiling and topology
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
.
Within the cell most DNA is topologically restricted. DNA is typically found in closed loops (such as plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...
s 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
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
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.
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., chloroquineChloroquineChloroquine is a 4-aminoquinoline drug used in the treatment or prevention of malaria.-History:Chloroquine , N'--N,N-diethyl-pentane-1,4-diamine, was discovered in 1934 by Hans Andersag and co-workers at the Bayer laboratories who named it "Resochin". It was ignored for a decade because it was...
) 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
Knot theory
In topology, knot theory is the study of mathematical knots. While inspired by knots which appear in daily life in shoelaces and rope, a mathematician's knot differs in that the ends are joined together so that it cannot be undone. In precise mathematical language, a knot is an embedding of a...
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 known as topoisomerase
Topoisomerase
Topoisomerases are enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double helical structure. For example, during DNA replication, DNA becomes overwound ahead of a replication fork...
s. 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
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...
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". However, when experimentally determined structures of the nucleosomeNucleosome
Nucleosomes are the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a histone protein core. This structure is often compared to thread wrapped around a spool....
displayed an over-twisted left-handed wrap of DNA around the histone
Histone
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation...
octamer, this "paradox" was considered to be solved by the scientific community.
See also
- Triple-stranded DNATriple-stranded DNAA triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix. In this structure, one strand binds to a B-form DNA double helix through Hoogsteen or reversed Hoogsteen hydrogen bonds....
- G-quadruplexG-quadruplexIn molecular biology, G-quadruplexes are nucleic acid sequences that are rich in guanine and are capable of forming a four-stranded structure...
- DNA nanotechnologyDNA nanotechnologyDNA nanotechnology is a branch of nanotechnology which uses the molecular recognition properties of DNA and other nucleic acids to create designed, artificial structures out of DNA for technological purposes. In this field, DNA is used as a structural material rather than as a carrier of genetic...
- Molecular models of DNAMolecular models of DNAMolecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in...
- Molecular structure of Nucleic AcidsMolecular structure of Nucleic AcidsThe "Molecular structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" was an article published by James D. Watson and Francis Crick in the scientific journal Nature in its 171st volume on pages 737–738 . It was the first publication which described the discovery of the double helix...
(publication) - Nucleic acid modeling