The Structure of Double Stranded DNA

As mentioned above, the two individual strands are held together by hydrogen bonds between individual T-A and C-G base pairs. In DNA, the

\ ribose sugar

aJor groove s

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aJor groove s

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ribose sugar

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•l0or groove side

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Figure 2. Hydrogen bonding between the bases. Note that the sets of distances between the base pairs are almost identical for the two base pairs, so that the distance across the double helix is unchanged. Hoogsteen hydrogen bonding can link a double helix to a third strand, to make a triple helix.

distance between the atoms involved is 2.8 to 2.95 angstroms (10~10 meters). While individually weak, the large number of hydrogen bonds along a DNA chain provides sufficient stability to hold the two strands together.

The stabilization of duplex (double-stranded) DNA is also dependent on base stacking. The planar, rigid bases stack on top of one another, much like a stack of coins. Since the two purine.pyrimidine pairs (A.T and CG) have the same width, the bases stack in a rather uniform fashion. Stacking near the center of the helix affords protection from chemical and environmental attack. Both hydrophobic interactions and van der Waal's forces hold bases together in stacking interactions. About half the stability of the DNA helix comes from hydrogen bonding, while base stacking provides much of the rest.

Double-stranded DNA in its canonical B-form is a right-handed helix formed by two individual DNA strands aligned in an antiparallel fashion (a right-handed helix, when viewed on end, twists clockwise going away from the viewer). Antiparallel DNA has the two strands organized in the opposite polarity, with one strand oriented in the 5'-3' direction and the other oriented in the 3'-5' direction.

In the right-handed B-DNA double helix, the stacked base pairs are separated by about 3.24 angstroms with 10.5 base pairs forming one helical turn (360°), which is 35.7 angstroms in length. Two successive base pairs, therefore, are rotated about 34.3° with respect to each other. The width of the helix is 20 angstroms. An idealized model of the double helix is shown in Figure 3. As can be seen, the organization of the bases creates a major groove and a minor groove.

Adenine and thymine are said to be complementary, as are cytosine and guanine. Complementary means "matching opposite." The shapes and charges of adeninne and thymine complement each other, so that they attract one another and link up (as do cytosine and guanine). Indeed, one entire strand of duplex DNA is complementary to the opposing strand. During replication, the two strands unwind, and each serves as a template hydrophobic interactions attraction between portions of a molecule based on mutual repulsion of water van der Waal's forces weak attractive forces between two different molecules il

10.5

base pairs per turn

10.5

base pairs per turn

Figure 3. Canonical B-DNA double helix.

protonated possessing excess H+ ions; acidic for formation of new complementary strand, so that replication ends with two exact double-stranded copies.

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