The term "DNA helix" has a complex history and nature. By it, as a rule, is meant the model introduced by James Watson. A double helix of DNA is held together with the nucleotides that form a pair. In B-DNA, the most common helical structure found in nature, the double helix is right, with 10-10.5 base pairs per turn. The double helical structure of DNA contains a large groove and a shallow groove. In B-DNA, a large groove is wider than a small one. Given the difference in width between the main and minor grooves, many proteins that bind to B-DNA do this through a wider main.
Discovery story
A structural model of the DNA double helix was first published in the journal Nature by James Watson and Francis Crick in 1953 (X, Y, Z coordinates in 1954) based on a critical X-ray diffraction image of DNA labeled “Photo 51” from Rosalind Franklin 1952 of the year, followed by a clearer image by Raymond Gosling, Maurice Wilkins, Alexander Stokes and Herbert Wilson. A preliminary model was three-stranded DNA.
The realization that an open structure is a double helix explains the mechanism by which two strands of DNA are joined into a helix, through which genetic information is stored and copied in living organisms. This discovery is considered one of the most important scientific insights of the twentieth century. Creek, Wilkins, and Watson each received one-third of the 1962 Nobel Prize in Physiology or Medicine for their contribution to the discovery. Franklin, whose breakthrough X-ray diffraction data were used to formulate the DNA helix, died in 1958 and, therefore, was not eligible to be nominated for a Nobel Prize.
Hybridization Value
Hybridization is the process of joining base pairs that bind to form a double helix. Melting is the process by which the interactions between the double helix chains are broken, separating the two lines of nucleic acids. These bonds are weak, easily separated by mild heating, enzymes, or mechanical strength. Melting occurs predominantly at specific nucleic acid points. The regions of the DNA helix marked as T and A are more easily melted than regions C and G. Some basic steps (pairs) are also susceptible to DNA melting, such as TA and TG. These mechanical features are reflected using sequences such as TATA at the beginning of many genes to help RNA polymerase melt DNA for transcription.
Heat
The process of strand separation by superficial heating, which is used in the polymerase chain reaction (PCR), is simple, provided that the molecules have about 10,000 base pairs (10 kilobase pairs or 10 kb). The interlacing of DNA strands makes it difficult to separate long segments. The cell avoids this problem by allowing its DNA melting enzymes (helicases) to work simultaneously with topoisomerases, which can chemically cleave the phosphate base of one of the strands so that it can rotate around the other. Helicases unwind strands to facilitate the promotion of sequence-reading enzymes, such as DNA polymerase. A double helix of DNA is formed due to the bonds of these strands.
Spiral geometry
The geometric component of the DNA structure can be characterized by 6 coordinates: shear, slip, rise, tilt, twist and turn. These values accurately determine the location and spatial orientation of each pair of DNA strands. In areas of DNA or RNA where the normal structure is destroyed, a change in these values can be used to describe such a violation.
Lifting and turning are determined by the shape of the spiral. Other coordinates, in contrast, can be zero.
Note that the “slope” is often used in the scientific literature in different ways, referring to the deviation of the first axis of the interchain base from the perpendicularity to the axis of the spiral. This corresponds to the slip between the sequence of the bases of the double helix of DNA, and in geometric coordinates it is correctly called “tilt”.
Geometric differences in spirals.
It is believed that at least three conformations of DNA are found in nature: A-DNA, B-DNA and Z-DNA. Form B, described by James Watson and Francis Crick, is thought to predominate in cells. It has a width of 23.7 Å and extends 34 Å by 10 bp. sequence. A double helix of DNA is formed due to the bonds of two lines of ribonucleic acid, which make one complete revolution around its axis every 10.4-10.5 base pairs in solution. This twisting frequency (called the spiral pitch) is largely dependent on the stacking forces that each base exerts on its neighbors in the chain. The absolute configuration of the bases determines the direction of the spiral curve for a given conformation.
Differences and Functions
A-DNA and Z-DNA are significantly different in geometry and size compared to B-DNA, although they still form helical structures. For a long time, it was believed that Form A is found only in dehydrated DNA samples in the laboratory, which are used in crystallographic experiments, and in hybrid pairings of DNA and RNA chains, but DNA dehydration does occur in vivo, and A-DNAs now have biological functions known to us. DNA segments whose cells have been methylated for regulatory purposes can adopt the Z geometry, in which the strands rotate around the helical axis in the opposite way to A-DNA and B-DNA. There is also evidence of protein-DNA complexes forming Z-DNA structures. The length of the DNA helix does not change in any way, depending on the type.
Name problems
In fact, only the letters F, Q, U, V, and Y are now available for the names of different types of DNA that may be discovered in the future. However, most of these forms were created synthetically and were not observed in natural biological systems. There are also three-chain (3 DNA helices) and quadrupole forms, such as the G-quadruplex.
Thread connection
A double helix of DNA is formed by bonds of helical strands. Since the threads are not directly opposite each other, the grooves between them are uneven in size. One groove, the main, has a width of 22 Å, and the other, a small one, reaches a length of 12 Å. The narrowness of the secondary groove means that the edges of the bases are more accessible in the main groove. As a result, proteins, such as transcription factors that can bind to specific sequences in the DNA double helix, usually come in contact with the sides of the bases open in the main groove. This situation changes in unusual DNA conformations within the cell, but primary and secondary grooves are always named to reflect differences in size that could be seen if the DNA is twisted back into normal B.
Model creation
In the late 1970s, alternative non-helical models were briefly considered as potential solutions to the problems of DNA replication in plasmids and chromatin. However, they were rejected in favor of a double model depicting a coil of DNA helix, due to subsequent experimental advances, such as x-ray crystallography of DNA duplexes. In addition, non-dual spiral models are not currently accepted by the mainstream scientific community.
Single stranded nucleic acids (ssDNAs) do not take a helical shape and are described by models such as random coils or worm chains.
DNA is a relatively rigid polymer, typically modeled as a worm-like chain. Model rigidity is important for DNA circularization and the orientation of the proteins associated with it relative to each other, and hysteretic axial rigidity is important for DNA wrapping and protein circulation and interaction. Compression-elongation is relatively unimportant in the absence of high voltage.
Chemistry and Genetics
DNA in a solution does not accept a rigid structure, but constantly changes conformation due to thermal vibration and collisions with water molecules, which makes it impossible to apply classical measures of rigidity. Therefore, the bending stiffness of DNA is measured by the length of the persistence, defined as "the length of the DNA over which the time-averaged orientation of the polymer becomes uncorrelated by coefficient".
This value can be accurately measured using an atomic force microscope to directly image DNA molecules of various lengths. In an aqueous solution, the average constant length is 46-50 nm or 140-150 base pairs (DNA diameter 2 nm), although it can vary significantly. This makes DNA a moderately stiff molecule.
The length of the continuation of a DNA site is highly dependent on its sequence, and this can lead to significant changes. The latter are mostly caused by stacking energy and fragments that extend to minor and large grooves.
Physical properties and bends
The entropy flexibility of DNA is surprisingly consistent with standard polymer physics models, such as the Kratka-Breed chainworm model. According to a model similar to worms, it is observed that bending DNA is also described by Hooke's law with very small (subpiconeonton) forces. However, for DNA segments shorter in duration and persistence, the bending force is approximately constant, and the behavior deviates from forecasts, in contrast to the already mentioned worm-shaped models.
This effect leads to an unusual ease in the circulation of small DNA molecules and a higher likelihood of finding strongly curved sections of DNA.
DNA molecules often have a preferred direction for bending, i.e. anisotropic bending. This, again, is connected with the properties of the bases that make up the DNA sequences, and they are the ones that connect the two DNA chains into a helix. In some cases, the sequences do not have the notorious bends.
DNA double helix structure
The preferred direction of DNA bending is determined by the stability of laying each base on top of the next. If the unstable steps of stacking the base are always on one side of the DNA helix, then the DNA will preferably bend away from this direction. The connection of two DNA strands into a spiral is carried out by molecules that depend on this direction. As the angle of bending increases, they play the role of steric obstacles, showing the ability to roll the residues in relation to each other, especially in the small groove. Deposits A and T will preferably occur in small grooves within the bends. This effect is especially evident in the binding of a DNA protein when hard DNA bending is induced, for example, in nucleosome particles.
Exceptionally bent DNA molecules can become bent. This was first discovered in the kinetoplast trypanosomatide DNA. Typical sequences that cause this include segments 4-6 T and A, separated by the principle of G and C, which contain residues A and T in phase with a small groove on one side of the molecule.
The internal curved structure is induced by the “scrolling of the screw” of the base pairs relative to each other, which allows the creation of unusual bifurcated hydrogen bonds between the base steps. At higher temperatures, this structure is denatured, and therefore the intrinsic bending is lost.
All DNA that bends anisotropically has, on average, a longer stop and greater axial rigidity. This increased stiffness is necessary to prevent accidental bending, which will cause the molecule to act isotropically.
DNA ringing depends on both the axial (bending) stiffness and the torsional (rotational) stiffness of the molecule. For a DNA molecule to circulate successfully, it must be long enough to easily bend into a full circle and have the right amount of base, so that the ends are in the correct rotation, in order to allow gluing of the helices. The optimal length for DNA circulation is about 400 base pairs (136 nm). The presence of an odd number of rotations represents a significant energy barrier for circuits, for example, a 10.4 x 30 = 312 pair molecule will circulate hundreds of times faster than a 10.4 x 30.5 ≈ 317 molecule.
Elasticity
Longer sections of DNA are entropically elastic when stretched. When DNA is in solution, it undergoes continuous structural changes due to the energy available in the thermal bath of the solvent. This is due to thermal vibrations of the DNA molecule in combination with constant collisions with water molecules. For entropic reasons, more compact relaxed states are thermally more accessible than stretched states, and therefore DNA molecules are almost universally found in intricate “relaxed” molecular models. For this reason, one DNA molecule will stretch under the influence of force, straightening it. Using optical tweezers, the entropic tensile behavior of DNA was studied and analyzed from the point of view of polymer physics, and it was found that DNA behaves mainly as a worm-like chain model of Short-Breed at physiologically accessible energy scales.
With sufficient tension and positive torque, DNA is believed to undergo a phase transition, with the bases diverging outward and the phosphates moving in the middle. This proposed structure for strained DNA was named P-shape DNA in honor of Linus Pauling, who originally presented it as a possible DNA structure.
Evidence of DNA mechanical stretching in the absence of superimposed torque indicates a transition or transitions leading to further structures, which are commonly called S-shapes. These structures have not yet been fully characterized due to the difficulty of imaging with the resolution of the atomic resonator in solution with the use of force, although many computer simulation studies have been done. Proposed S-DNA structures include those that retain the folding of the base pair and the hydrogen bond (enriched in GC).
Sigmoid model
A periodic fracture of the stack of the base pair with a break was proposed as a regular structure that preserves the regularity of the base stack and frees up the corresponding amount of expansion, and the term Σ-DNA is introduced as a mnemonic in which the three right points of the Sigma symbol serve as a reminder of three grouped pairs grounds. It was shown that the form Σ has a preference for sequences for GNC motifs, which, according to the GNC_h hypothesis, have evolutionary significance.
Melting, heating and unwinding a spiral
Form B of the DNA helix is twisted 360 ° by 10.4-10.5 bp. in the absence of twisting deformation. But many molecular biological processes can cause torsional stress. A DNA segment with excessive or insufficient helical twisting is mentioned, respectively, both in a positive and in a negative context. In vivo DNA is usually negatively twisted (i.e., it has curls twisted in the opposite direction), which facilitates the unwinding (melting) of the double helix, which is urgently needed for RNA transcription.
Inside the cell, most DNA is topologically limited. DNA is usually found in closed loops (such as plasmids in prokaryotes), which are topologically closed or very long molecules whose diffusion coefficients efficiently produce topologically closed regions. Linear sections of DNA are also usually associated with proteins or physical structures (such as membranes) to form closed topological loops.
Any change in the parameter T in a closed topological region must be balanced by a change in the parameter W, and vice versa. This leads to a higher order structure of the helix of DNA molecules. An ordinary DNA molecule with a root of 0 will be circular in its classification. If the torsion of this molecule is subsequently increased or decreased due to super-matching, then the roots will be correspondingly changed, which will result in the molecule being subjected to plectonemic or toroidal superhelical winding.
When the ends of the DNA double helix are connected so that it forms a circle, the strands are topologically tied. , , (, ). , .