What forces hold the two strands of DNA together

Most people have seen the famous double helix of DNA—two strands of DNA intertwined like a spiral staircase. All living things have DNA. Simple creatures like bacteria have just one long, circular piece of DNA made up of two intertwined DNA strands. The human genome, the set of DNA in people, has many more strands of DNA.

Most of humans’ DNA is typically packaged into 46 chromosomes located in the cell’s nucleus, which is a specialized compartment for storing DNA. Each of the chromosomes in the nucleus is made up of two linear DNA strands wrapped around each other.

A DNA strand is a long, thin molecule—averaging only about two nanometers (or two billionths of a meter) in width. That is so thin, that a human hair is about 40,000 times as wide. The incredible thinness of DNA strands allows them to be very tightly packed, as otherwise most DNA molecules would not fit inside of cells.

For perspective, if you stretched out every strand of DNA contained in just a single human cell end-to-end, it would measure almost two meters, or around 6.6 feet in length. If the nucleus of a cell were the size of a baseball, this would be the equivalent of 8.3 miles of DNA being stuffed inside.

Parts of a DNA Strand

Regardless of its length and location in the cell, all DNA strands share a common structure. They are all composed of building blocks called nucleotides that are linked together in a row. Nucleotides themselves are comprised of three joined parts: a sugar molecule, a phosphate group, and a nitrogenous base.

The sugars of one nucleotide link to the phosphates of the adjacent nucleotide to form the exterior of the DNA strand, known as the sugar-phosphate backbone. The interior of the DNA strand is made up of the nitrogenous bases. These bases bind together in pairs, forming weak bonds that nonetheless hold the two strands of DNA in a double helix together. Their sequence encodes an organism’s genetic information.

How Are the Two Strands of DNA Held Together?

The two strands of DNA in a double helix are held together by pairing between the nitrogenous bases in the nucleotides of each strand. The nitrogenous base of a DNA nucleotide can be one of four different molecules: adenine (A), guanine (G), thymine (T), and cytosine (C). Pairs of nitrogenous bases on opposing strands are held together by attractions called hydrogen bonds that occur in a specific pattern.

Every adenine on one DNA strand forms two hydrogen bonds with a thymine molecule on the complementary strand and vice versa. And every guanine molecule on one strand forms three hydrogen bonds with a cytosine molecule on the other and vice versa. In this way, the two DNA strands are stuck together by hydrogen bonds all along their length, forming the “steps” of the spiral staircase that is the double helix.

Why Do DNA Strands Have to Be Antiparallel?

The two complementary DNA strands that compose a double-stranded piece of DNA are described as being antiparallel to each other. The term antiparallel means that while the two strands are physically parallel to one another, they run in opposite directions— much like the right and left lanes of a street.

In other words, where the backbone of one DNA strand starts with a sugar molecule and ends in a phosphate group, the backbone of its complementary strand starts with a phosphate group and ends in a sugar molecule. The antiparallel orientation of the two DNA strands makes DNA more structurally stable and enables the complementary base pairing that holds the DNA strands together.

The direction of each DNA strand is significant to the process of copying the DNA (DNA replication) and reading the information contained in the genes of DNA (transcription), as cells can only read DNA in one direction. Just as we only read text from left to right, cells only read DNA by starting with the sugar end of the backbone and ending with the phosphate end.

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DNA consists of two strands, that wind around each other. Each strand has repeating units of a nitrogenous base, deoxyribose sugar, and a phosphate group. There are several interactions present within a strand and between two strands that stabilize the DNA.

Covalent Bonds (intrastrand bonds)

Each strand consists of the following:

• Base (Adenine, Thymine, Guanine, Cytosine)
• Deoxyribose sugar
• Phosphate group

There are four bases: Adenine and Guanine (purines); Cytosine and Thymine (Pyrimidines). Purines have two carbon-nitrogen rings while pyrimidines have a single carbon-nitrogen ring. Thus, there are four different nucleotides that can be incorporated into DNA.

Based on which base is attached, the nucleotides are called 2’-deoxyadenosine triphosphate, 2’-deoxycytidine triphosphate, 2’-deoxyguanosine triphosphate, or 2’-deoxythymidine triphosphate. Each of these bases is connected to 1’-carbon of the deoxyribose sugar.

In an unattached and free nucleotide, there is a triphosphate group on the 5’-carbon of the deoxyribose sugar. However, when a nucleotide is incorporated into a DNA strand, it loses two of the phosphate groups and only one phosphate group is added to the DNA strand.

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This addition involves formation of a covalent bond called the ‘phosphodiester bond’. This is formed between the 5’-phosphate group of one nucleotide and the 3’-OH group of another nucleotide forming a sugar-phosphate backbone of DNA.

Hydrogen bonds

The hydrogen bonds between the base pairs form the double helical structure of DNA. There is no exchange or sharing of electrons in hydrogen bonds as seen in covalent or ionic bonds. Hydrogen bonds occur over short distances and can be easily formed and broken. Although individually each hydrogen bond is much weaker than the covalent bond, they can stabilize the double helix because of their large numbers.

This pairing is very specific: adenine pairs with thymine and cytosine pairs with guanine. This selective pairing is called ‘complementary base pairing’. A-T pair forms two hydrogen bonds, while C-G pair forms three. The sugar-phosphate chains form the backbone of the ladder-like DNA structure and these base pairs form the rungs. The width of each of these ‘rungs’ are the same as it involves one purine (A or G) and one pyrimidine (C or T) base.

Stacking interactions

a) Hydrophobic effects

DNA has an interesting arrangement wherein the non-polar, uncharged bases are present in the interior of the structure, while the negatively charged phosphates are present on the outside. As the cellular environment is aqueous and polar, the hydrophobic bases in the interior of the helix are kept away from the surrounding water and the hydrophilic heads are exposed and interact with the exterior water. This property increases the solubility of DNA in water.

b) Van der Waals forces

The nitrogenous bases stacked upon one another are spaced based on their van der Waals distance. Van der Waals distance is the distance at which two molecules are attracted to each other. If this distance reduces, the electrons of the two molecules may overlap causing repulsion. These forces are very distance dependent and are inversely proportional to the sixth power of distance (r6 ). Although a single van der Waals interaction has a very small effect on the overall structure of DNA, the net effect of several interactions lead to substantial stability.

c) Ionic interactions

The electrostatic (ion-ion) repulsion of the negatively charged phosphates on the outside can make DNA potentially very unstable. However, magnesium ions (Mg2+) and cationic proteins along with arginine and lysine residues interact with the negatively charged groups in the DNA and stabilize it.

The strength and stability of DNA stacking interactions has been scientifically proved by demonstrating that the use of compounds (urea, formamide) that interfere with hydrogen bonds do not separate the strands completely, suggesting the presence of additional forces at work.

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Last updated Feb 26, 2019