DNA Structure : Phosphodiester bonds

DNA is a polymer of deoxyribonucleoside monophosphates (dNMP) covalently linked by 3′→5′-phosphodiester bonds. With the exception of a few viruses that contain single-stranded DNA (ssDNA), DNA exists as a double-stranded molecule (dsDNA), in which the two strands wind around each other, forming a double helix. [Note: The sequence of the linked dNMP is primary structure, whereas the double helix is secondary structure.] In eukaryotic cells, DNA is found associated with various types of proteins (known collectively as nucleoprotein) present in the nucleus, whereas the protein–DNA complex is present in a non–membrane-bound region known as the nucleoid in prokaryotes.
 3′→5′-Phosphodiester bonds
Phosphodiester bonds join the 3′-hydroxyl group of the deoxypentose of one nucleotide to the 5′-hydroxyl group of the deoxypentose of an adjacent nucleotide through a phosphoryl group (Fig. 30.2). The resulting long, unbranched chain has polarity, with both a 5′-end (the end with the free phosphate) and a 3′-end (the end with the free hydroxyl) that are not attached to other nucleotides. By convention, the bases located along the resulting deoxyribose-phosphate backbone are always written in sequence from the 5′-end of the chain to the 3′-end. For example, the sequence of bases in the DNA shown in Figure 1D (5′-TACG-3′) is read “thymine, adenine, cytosine, guanine.” Phosphodiester linkages between nucleotides can be hydrolyzed enzymatically by a family of nucleases, deoxyribonucleases for DNA and ribonucleases for RNA, or cleaved hydrolytically by chemicals. [Note: Only RNA is cleaved by alkali.]

Figure 1: A. DNA with the nucleotide sequence shown written in the 5′→3′ direction. A 3′→5′-phosphodiester bond is shown highlighted in the blue box, and the deoxyribose-phosphate backbone is shaded in yellow. B.DNA written in a more stylized form, emphasizing the deoxyribose-phosphate (p) backbone. C.A simpler representation of the nucleotide sequence. D.The simplest (and most common) representation. [Note: The nucleotide base sequence is assumed to be written in the 5′→3′ direction unless otherwise indicated.]