What is DNA Structure?

What do a human, a rose, and a bacterium have in common? Each of these things along with every other organism on Earth contains the molecular instructions for life, called deoxyribonucleic acid or DNA. Encoded within this DNA (Deoxyribonucleic Acid) are the directions for traits as diverse as the color of a person’s eyes, the scent of a rose, and the way in which bacteria infect a lung cell.

DNA is found in nearly all living cells. However, its exact location within a cell depends on whether that cell possesses a special membrane-bound organelle called a nucleus. Organisms composed of cells that contain nuclei are classified as eukaryotes, whereas organisms composed of cells that lack nuclei are classified as prokaryotes. In eukaryotes, DNA is housed within the nucleus, but in prokaryotes, DNA is located directly within the cellular cytoplasm, as there is no nucleus available.

But what, exactly, is DNA? In short, DNA is a complex molecule that consists of many components, a portion of which are passed from parent organisms to their offspring during the process of reproduction. Although each organism’s DNA is unique, all DNA is composed of the same nitrogen-based molecules. So how does DNA differ from organism to organism? It is simply the order in which these smaller molecules are arranged that differs among individuals. In turn, this pattern of arrangement ultimately determines each organism’s unique characteristics, thanks to another set of molecules that “read” the pattern and stimulate the chemical and physical processes it calls for.

DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group, and a nitrogen base. The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determines DNA’s instructions, or genetic code. Similar to the way the order of letters in the alphabet can be used to form a word, the order of nitrogen bases in a DNA sequence forms genes, which in the language of the cell, tells cells how to make proteins. Another type of nucleic acid, ribonucleic acid, or RNA, translates genetic information from DNA into proteins.

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The entire human genome contains about 3 billion bases and about 20,000 genes. Nucleotides are attached together to form two long strands that spiral to create a structure called a double helix. If you think of the double helix structure as a ladder, the phosphate and sugar molecules would be the sides, while the bases would be the rungs. The bases on one strand pair with the bases on another strand: adenine pairs with thymine, and guanine pairs with cytosine.

DNA molecules are long so long, in fact, that they can’t fit into cells without the right packaging. To fit inside cells, DNA is coiled tightly to form structures we call chromosomes. Each chromosome contains a single DNA molecule. Humans have 23 pairs of chromosomes, which are found inside the cell’s nucleus.

Why does a DNA molecule consist of two strands? The primary function of DNA is to store and transmit genetic information. To accomplish this function DNA must have two properties. It must be chemically stable so as to reduce the possibility of damage. DNA must also be capable of copying the information it contains. The two-stranded structure of DNA gives it both of these properties. The nucleotide sequence contains the information found in DNA. The nucleotides connect the two strands through hydrogen bonds. Because each nucleotide has a unique complementary nucleotide, each strand contains all the information required to synthesize a new DNA molecule. The double-stranded structure also makes the molecule more stable.

DNA is the information molecule. It stores instructions for making other large molecules, called proteins. These instructions are stored inside each of your cells, distributed among 46 long structures called chromosomes. These chromosomes are made up of thousands of shorter segments of DNA, called genes. Each gene stores the directions for making protein fragments, whole proteins, or multiple specific proteins.

DNA is well-suited to perform this biological function because of its molecular structure, and because of the development of a series of high-performance enzymes that are fine-tuned to interact with this molecular structure in specific ways. The match between DNA structure and the activities of these enzymes is so effective and well-refined that DNA has become, over evolutionary time, the universal information-storage molecule for all forms of life. Nature has yet to find a better solution than DNA for storing, expressing, and passing along instructions for making proteins.

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Alternative DNA structures

DNA Structure A-DNA B-DNA and Z-DNA
DNA Structure A-DNA B-DNA and Z-DNA

DNA (Deoxyribonucleic Acid) exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although, only B-DNA and Z-DNA have been directly observed in functional organisms. The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases, the type and concentration of metal ions, and the presence of polyamines in solution.

The first published reports of A-DNA X-ray diffraction patterns—and also B-DNA—used analyses based on Patterson transforms that provided only a limited amount of structural information for oriented fibers of DNA. An alternative analysis was then proposed by Wilkins et al., in 1953, for the in vivo B-DNA X-ray diffraction scattering patterns of highly hydrated DNA fibers in terms of squares of Bessel functions. In the same journal, James Watson and Francis Crick presented their molecular modeling analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double-helix.

Although the B-DNA form is most common under the conditions found in cells, it is not a well-defined conformation but a family of related DNA conformations that occur at the high hydration levels present in living cells. Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular para crystals with a significant degree of disorder.

Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in partly dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, and in enzyme-DNA complexes. Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form. These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.

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