Molecular Biology Series: The Structure of DNA

By: Bijay Dhungel , MSc

Being a deoxyribose nucleic acid, a strand of DNA is made up of by the repetition of nucleotides each of which consists of a deoxyribose sugar, attached to one of the four nucleic acid bases (adenine, guanine, cytosine and uracil). Each sugar-base combination is joined with each other by a phosphodiester linkage between the sugar molecules thus forming a polynucleotide.

DNA is a double helical molecule; there are two strands running in anti-parallel direction i.e. opposite in polarity. These two strands are held together by weak hydrogen bonds between the bases.

This pairing between the bases is made possible by the specific structure and meticulous precision of the specificity of possible pairing between the 4 bases. Adenine can pair only with thymine but not with other bases and vice versa. Similarly, cytosine can pair with guanine and not any other bases and vice versa. This means that the number of adenine must be equal to the number of thymine and the number of cytosine must be equal to the number of guanine in a stretch of DNA. This is often called Chargaff’s rule named after its discoverer.

Since DNA is a polymer of deoxyribose nucleotide the sequence of the bases which appear in a certain stretch of DNA determines the information it codes for. Human genome consists of about 3 billion bases. Not all DNA in the chromosome encode for a protein, some DNA sequences encode a protein (called genes), others encode only RNAs but those never form proteins. These two are called structural DNA. Other DNA sequences either function as regulatory DNA to regulate the production of RNA and/or protein or are vestige of evolution. Surprisingly, structural DNA sequences make up less than 2% of the human genome. Most of it consists of what was previously considered to be “junk DNA” i.e. DNA stretches without function. Today it is known that “junk DNA” is not junk after all. Everyday scientists are discovering specific roles for these non-structural DNA elements especially related to regulation of production of RNA/proteins. Thus the “information” about an organism or its “blue print” is encoded in the DNA but for that information to manifest as a visible trait or phenotype either as physical appearance, behavior or mental state, that information needs to transfer into proteins. After an enormous complexity of regulation and interaction with the environment, protein is formed and it gets involved in its specific function. At an instant of time, enormous amounts of genes continuously produce proteins which continuously perform their functions to keep a cell alive. A group of working cells make tissues, group of tissues make organs and a proper combination of functional organs make up an organism.

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Schematic diagram showing the base pairing: Due to the structure of the bases adenine can only base pair with thymine and cytosine can base pair only with guanine. This hydrogen-bond is what holds the two strands of DNA together.

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Structure of a nucleotide: The sugar (deoxyribose) pairs with one of the bases to form a nucleotide.

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Structure of a polynucleotide: Adjacent nucleotides join to form a DNA strand. Nucleotides connect through a phosphodiester bond between phosphate group (P) of one nucleotide and the deoxyribose sugar (D) of another.

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Double helical structure of a DNA: Two strands of DNA (polynucleotides: colored red and blue) are helically coiled around each other and held together by weak hydrogen bonds between the bases of each nucleotide.

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