In molecular biology, the double helix is the shape formed by two strands of nucleic acid molecules, such as DNA. This structure results from the molecule's secondary structure and plays an important role in forming its tertiary structure.

The DNA double helix is made up of nucleotides that pair with specific matching nucleotides. In B-DNA, the most common form of DNA found in nature, the double helix twists to the right and has about 10 to 10.5 pairs of nucleotides for each full turn. The DNA double helix has two grooves: a major groove and a minor groove. In B-DNA, the major groove is wider than the minor groove. Because of this difference in width, many proteins that attach to DNA often bind through the wider major groove.

The double helix structure of DNA was first discovered by James Watson and Francis Crick. Their discovery was based on research conducted by scientists such as Rosalind Franklin, Raymond Gosling, and Maurice Wilkins. The term "double helix" became widely known after the 1968 book The Double Helix: A Personal Account of the Discovery of the Structure of DNA was published by James Watson.

History

In 1953, the double-helix model of DNA structure was first published in the journal Nature by James Watson and Francis Crick. This model was based on the work of Rosalind Franklin and her student Raymond Gosling, who took an important X-ray picture of DNA called "Photo 51," and Maurice Wilkins, Alexander Stokes, and Herbert Wilson. It also used information about how DNA bases pair together, discovered by Erwin Chargaff. Before this, in 1954, Linus Pauling and his collaborator Robert Corey incorrectly suggested that DNA would have a three-stranded structure.

Understanding that DNA has a double-helix structure helped scientists explain how genetic information is stored and copied in living things. This discovery is widely seen as one of the most important scientific achievements of the 20th century. In 1962, James Watson, Francis Crick, and Maurice Wilkins each received one-third of the Nobel Prize in Physiology or Medicine for their role in this discovery.

Nucleic acid hybridization

Hybridization is the process where matching base pairs join to create a double helix structure. Melting is when the connections between the two strands of the double helix are broken, causing the strands to separate. These connections are weak and can be easily broken by gentle heating, enzymes, or physical force. Melting happens more often in certain parts of the nucleic acid. Sections with more T and A bases are easier to separate than sections with more C and G bases. Some specific base pairs, such as T-A and T-G, are also more likely to separate during melting. These features are used in biology, for example, the sequence TATA near the start of many genes helps RNA polymerase separate the DNA strands for transcription.

Gentle heating can separate DNA strands, as used in the polymerase chain reaction (PCR), but this is only simple if the DNA has fewer than about 10,000 base pairs (10 kbp). The twisting of DNA strands makes long sections harder to separate. Cells solve this by using DNA-melting enzymes (helicases) along with topoisomerases. Topoisomerases can cut one DNA strand temporarily, allowing it to twist around the other strand. This action helps helicases separate the strands, making it easier for enzymes like DNA polymerase to read the DNA sequence.

Base-pair geometry

The shape of a base pair step in a nucleic acid molecule can be described using six measurements: shift, slide, rise, tilt, roll, and twist. These measurements show the exact position and direction of each base pair in the molecule compared to the one before it along the helix. Together, they explain the overall shape of the helix. When the normal structure of DNA or RNA changes, differences in these measurements can help describe the change.

For each base pair, when compared to the one before it, the following geometry terms apply:

• Shear
• Stretch
• Stagger
• Buckle
• Propeller: when one base in a pair rotates relative to the other
• Opening
• Shift: movement along an axis in the base-pair plane, from the minor groove to the major groove
• Slide: movement along an axis in the base-pair plane, from one strand to the other
• Rise: movement 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 distance between one full turn of the helix

Rise and twist determine the direction (left or right) and pitch of the helix. The other measurements can be zero. Slide and shift are usually small in B-DNA but larger in A- and Z-DNA. Roll and tilt make base pairs less parallel, and are usually small.

The term "tilt" has sometimes been used in scientific writing to describe how the axis between two bases in a pair deviates from being perpendicular to the helix axis. This movement is actually called "slide" when looking at a series of base pairs. In helix-based measurements, this is correctly called "inclination."

Helix geometries

At least three DNA shapes are found in nature: A-DNA, B-DNA, and Z-DNA. The B form, discovered by James Watson and Francis Crick, is most common in cells. It is 23.7 Å wide and extends 34 Å for every 10 base pairs. The double helix twists to the right, completing one full turn every 10.4–10.5 base pairs in solution. This twisting pattern, called the helical pitch, depends on how the bases in DNA stack together.

A-DNA and Z-DNA have different shapes and sizes compared to B-DNA but still form helical structures. A-DNA was once thought to appear only in laboratory samples with little water or in DNA-RNA hybrids, but it is now known to exist in living cells and has biological roles. Z-DNA forms when certain DNA segments are chemically marked (methylated) for regulation. In Z-DNA, the strands twist in the opposite direction compared to A-DNA and B-DNA. Some protein-DNA complexes also form Z-DNA structures.

Other DNA shapes, such as C-DNA, E-DNA, L-DNA, P-DNA, S-DNA, and others, have been identified in labs. Only the letters F, Q, U, V, and Y remain to describe new DNA forms that might be discovered. Most of these shapes are made in labs and not found in natural biological systems. DNA can also form triple-stranded or four-stranded structures, such as G-quadruplexes and i-motifs.

DNA’s structure consists of two twisted strands. A second double helix can be seen by looking at the spaces, or grooves, between the strands. These grooves are next to the base pairs and may serve as binding sites. Because the strands are not directly opposite each other, the grooves are different sizes. The larger groove, called the major groove, is 22 Å wide, while the smaller groove, the minor groove, is 12 Å wide. The minor groove is narrower, so the edges of the bases are more exposed in the major groove. Proteins like transcription factors often bind to DNA by attaching to the sides of bases in the major groove. This pattern may change in unusual DNA shapes, but the terms "major" and "minor" grooves always refer to the size differences seen when DNA is twisted into the normal B form.

In the late 1970s, scientists briefly studied non-helical models of DNA to explain challenges in DNA replication in plasmids and chromatin. However, these models were replaced by the double-helix model after experiments like X-ray crystallography of DNA and the discovery of topoisomerases. Today, the double-helix model is widely accepted, and non-helical models are not supported by mainstream science.

Bending

DNA is a stiff molecule that is often compared to a worm-like chain. It can bend, twist, and be compressed, but each of these movements has limits that affect how DNA behaves inside a cell. The stiffness of DNA when it twists is important for forming circular DNA shapes and for how proteins attach to DNA. The stiffness of DNA when it bends helps DNA wrap around proteins and form circles. Compression is not important unless there is a lot of force applied.

In water, DNA is not rigid. Instead, it constantly changes shape because of heat and collisions with water molecules. This makes it hard to measure DNA's rigidity using traditional methods. Scientists use a value called the persistence length to describe how stiff DNA is. This value can be measured using a tool called an atomic force microscope. In water, the average persistence length of DNA is about 50 nanometers (or 150 base pairs). This measurement can vary between 45 and 60 nanometers (132–176 base pairs) depending on temperature, water conditions, and DNA length. This shows that DNA is somewhat stiff.

The persistence length of a DNA segment depends on its sequence. This variation is mainly caused by how DNA bases stack together and by parts of the DNA that extend into the spaces between the strands. At larger scales than the persistence length, DNA behaves in ways that match standard models of polymer physics, such as the Kratky-Porod worm-like chain model. At very small forces, DNA bending follows Hooke's law, which is a rule in physics that describes how springs stretch. For DNA segments shorter than the persistence length, the force needed to bend DNA remains nearly the same, and its behavior differs from predictions made by the worm-like chain model.

This behavior makes it easier to form circular DNA from small DNA molecules and increases the chance of finding highly bent DNA sections. DNA often prefers to bend in a specific direction, called anisotropic bending. This preference is due to the arrangement of DNA bases. A random sequence of bases causes DNA to bend in all directions equally, called isotropic bending.

The direction DNA prefers to bend depends on how stable the stacking of bases is. If unstable stacking occurs on one side of the DNA helix, DNA will bend away from that side. As the bend becomes sharper, physical obstacles and the ability of DNA parts to move relative to each other, especially in the minor groove, also affect bending. Bases like adenine (A) and thymine (T) are often found in the minor groove on the inside of bends. This is especially noticeable when DNA is tightly bent, such as in structures like nucleosomes.

Some DNA molecules have a strong preference for bending in a specific direction, making them naturally curved. This was first observed in DNA from certain types of cells. These DNA sequences often include repeated sections of A and T bases separated by sections rich in guanine (G) and cytosine (C) bases. This arrangement keeps A and T bases aligned with the minor groove on one side of the molecule. The natural curvature is caused by the way base pairs twist relative to each other, forming special hydrogen bonds between bases. At higher temperatures, this structure breaks down, and the natural bend disappears.

DNA that bends in a preferred direction generally has a longer persistence length and greater stiffness. This increased rigidity helps prevent random bending, which would make DNA behave in all directions equally.

For DNA to form a circle, it must be long enough to bend completely and have the correct number of base pairs so that its ends can connect properly. The best length for forming circular DNA is about 400 base pairs (136 nanometers), with a number of base pairs that is a multiple of 10.4. If the number of base pairs is not a multiple of 10.4, it becomes much harder for DNA to form a circle. For example, a DNA molecule with 312 base pairs (a multiple of 10.4) forms circles much faster than one with 317 base pairs (not a multiple of 10.4).

Short circular DNA segments do not bend evenly. Instead, bending is concentrated in one or two specific areas, often in sections rich in A and T bases. If a break (nick) is present in the DNA, bending is focused at the site of the break.

Stretching

Longer sections of DNA become stretchy when pulled. In water, DNA constantly changes shape because of the heat from the surrounding liquid. This happens due to the molecule vibrating and bumping into water molecules. Because of this, DNA tends to stay in a coiled, relaxed shape rather than being stretched out. When pulled, DNA straightens. Scientists have studied this behavior using tools called optical tweezers. These studies show that DNA acts similarly to a model called the Kratky-Porod worm-like chain under normal biological conditions.

When DNA is pulled strongly and twisted, it may change structure. In this form, the DNA bases spread apart, and the phosphate parts move to the center. This structure is called P-form DNA, named after scientist Linus Pauling who first suggested it.

Studies that stretch DNA without twisting it show that DNA can change into other structures called S-form DNA. These structures are not yet fully understood because it is hard to observe them clearly in water while applying force. Many computer models have been used to study them, but their exact shapes remain unclear.

Some S-DNA forms keep the DNA bases stacked together and bonded (common in sections with many GC pairs), while others allow the DNA to extend by tilting. Other forms may partially separate the bases but still keep them connected overall (common in sections with many AT pairs).

A structure called Σ-DNA has been proposed, where the DNA breaks apart regularly every three base pairs. This keeps the DNA flat and allows it to extend properly. The name Σ-DNA comes from the Greek letter Sigma, which has three points resembling the three base pairs in each group. This form is more likely to occur in sections with specific sequences, such as GNC patterns, which are thought to be important in evolution.

Supercoiling and topology

The B form of the DNA helix completes one full twist (360°) every 10.4 to 10.5 base pairs when there is no twisting force. However, many biological processes can create twisting force. A DNA segment that has more twisting than normal is called positively supercoiled, and one with less twisting is called negatively supercoiled. In living cells, DNA is usually negatively supercoiled, which helps the DNA strands separate (unwind) during RNA production.

Most DNA inside cells is topologically restricted. DNA is often found in closed loops, like plasmids in bacteria, which cannot be untangled. It can also be part of very long molecules that act like closed loops because they cannot move freely. Even linear DNA segments are often bound to proteins or structures, such as cell membranes, forming closed loops.

Francis Crick was one of the first scientists to explain the importance of linking numbers when studying DNA supercoiling. In a 1976 paper, he described the relationship between three key values:

• L (linking number): The number of times one DNA strand wraps around the other. For a closed loop, this number is always a whole number and does not change.
• T (twist): The total number of turns in the DNA double helix. Normally, this number approaches the number of turns a free DNA strand would make in solution, which is roughly the number of bases divided by 10.5, unless chemicals like ethidium bromide alter the DNA’s structure.
• W (writhe): The number of times the DNA helix coils around a superhelical axis.

The linking number is the sum of twist and writhe (L = T + W). Any change in twist within a closed loop must be balanced by an equal change in writhe, and vice versa. This balance creates complex DNA structures. A circular DNA molecule with zero writhe remains circular. If its twist increases or decreases through supercoiling, the writhe changes, causing the DNA to form plectonemic or toroidal coils.

When the ends of a DNA strand are connected to form a circle, the strands become topologically linked. This means the strands cannot be separated without breaking them, such as through heating. Enzymes called topoisomerases help untangle these knots by cutting one or both strands so another segment can pass through. This process is essential for copying circular DNA and for recombination in linear DNA with similar topological challenges.

For many years, scientists were unsure why eukaryotic DNA had leftover supercoiling, a problem called the "linking number paradox." However, when the structure of the nucleosome showed DNA wrapped tightly around a protein complex in a specific left-handed direction, the paradox was resolved.