The nucleotides of DNA are joined in polynucleotide strands by phosphodiester bonds that connect the 3' carbon atom of one nucleotide to the 5' phosphate group of the next. Each polynucleotide strand has polarity, with a 5' end and a 3' end.
The secondary structure of DNA refers to its three-dimensional configuration — its fundamental helical structure. DNA's secondary structure can assume a variety of configurations, depending on its base sequence and the conditions in which it is placed.
The double helix A fundamental characteristic of DNA's secondary structure is that it consists of two polynucleotide strands wound around each other—it's a double helix. The sugar - phosphate linkages are on the outside of the helix, and the bases are stacked in the interior of the molecule (see Figure 10.13). The two polynucleotide strands run in opposite directions — they are antiparallel, which means that the 5' end of one strand is opposite the 3' end of the second.
The strands are held together by two types of molecular forces. Hydrogen bonds link the bases on opposite strands (see Figure 10.13). These bonds are relatively weak compared with the covalent phosphodiester bonds that connect the sugar and phosphate groups of adjoining nucleotides. As we will see, several important functions of DNA require the separation of its two nucleotide strands, and this separation can be readily accomplished because of the relative ease of breaking and reestablishing the hydrogen bonds.
The nature of the hydrogen bond imposes a limitation on the types of bases that can pair. Adenine normally pairs only with thymine through two hydrogen bonds, and cytosine normally pairs only with guanine through three hydrogen bonds (see Figure 10.13). Because three hydrogen bonds form between C and G and only two hydrogen bonds form between A and T, C - G pairing is stronger than A - T pairing. The specificity of the base pairing means that wherever there is an A on one strand, there must be a T in the corresponding position on the other strand, and wherever there is a G on one strand, a C must be on the other. The two polynucleotide strands of a DNA molecule are therefore not identical but are complementary.
The second force that holds the two DNA strands together is the interaction between the stacked base pairs. These stacking interactions contribute to the stability of the DNA molecule and do not require that any particular base follow another. Thus, the base sequence of the DNA molecule is free to vary, allowing DNA to carry genetic information.
DNA consists of two polynucleotide strands. The sugar - phosphate groups of each polynucleotide strand are on the outside of the molecule, and the bases are in the interior. Hydrogen bonding joins the bases of the two strands: guanine pairs with cytosine, and adenine pairs with thymine. The two polynucleotide strands of a DNA molecule are complementary and antiparallel.
Different secondary structures As we have seen, DNA normally consists of two polynucleotide strands that are antiparallel and complementary (exceptions are single-stranded DNA molecules in a few viruses). The precise three-dimensional shape of the molecule can vary, however, depending on the conditions in which the DNA is placed and, in some cases, on the base sequence itself.
The three-dimensional structure of DNA that Watson and Crick described is termed the B-DNA structure (< Figure 10.14). This structure exists when plenty of water surrounds the molecule and there is no unusual base sequence in the DNA — conditions that are likely to be present in cells. The B-DNA structure is the most stable configuration for a random sequence of nucleotides under physiological conditions, and most evidence suggests that it is the predominate structure in the cell.
B-DNA is an alpha helix, meaning that it has a right-handed, or clockwise, spiral. It possesses approximately 10 base pairs (bp) per 360-degree rotation of the helix; so
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