FIGURE 6-5 base tautomers. Amino ~ imino and keto ^ enol tautomerisrr. (a)Cyto sine ts usually m the amino type but rarely forms the imino configuration, (b) Guanine is commonly in rhe keto type bin is rarely found in the enot configuration

The two Chains of the double Helix have actually Complementary Sequences

The pairing in between adenine and also thymine, and also between guanine and also cytosine, outcomes in a complementary relationship between the succession of bases ~ above the two linked chains and gives DNA the self-encoding character. For example, if we have actually the succession 5"-ATCTC-3" ~ above one chain, the opposite chain must have actually the complementary sequence 3"-TACAC-5\

The strictness of the rules because that this "Watson-Crick" pairing derives native the complementarity both of shape and also of hydrogen bonding properties between adenine and also thymine and also between guanine and cytosine (Figure fi-6). Adenine and thymine match up so that a hydrogen link can kind between the exocyclic amino group at C6 ~ above adenine and the carbonyl in ~ C4 in thymine; and also likewise, a hydrogen bond can kind between Nl of adenine and also N3 the thymine. A corresponding plan can it is in drawn between a guanine and also a cytosine, so the there is both hydrogen bonding and shape complementarity in this base pair together well. A G:C base pair has actually three hydrogen bonds, due to the fact that the exocyclic NH, at C2 top top guanine lies the opposite to, and also can hydrogen link with, a carbonyl at C2 ~ above cytosine. Likewise, a hydrogen shortcut can type between N"t that guanine and also N3 that cytosine and between the carbonyl in ~ C6 that guanine and the exocyclic NR, at C4 that cytosine. Watson-Crick base pairing requires that the bases room in their wanted tautomeric, states.

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An important feature the the dual helix is that the 2 base pairs have exactly the same geometry; having actually an A:T basic pair or a G;C base pair in between the 2 sugars does not perturb the setup of the sugars since the d¡stance in between the sugar attachment points room the same for both base pairs. Neither does T:A or C:G. In other words,


FIGURE 6-6 A:Tand C:C base pairs.

The number shows hydrogen bonding in between (he bases.

FIGURE 6-6 A:Tand C:C base pairs.

The figure shows hydrogen bonding in between (he bases.

there is an approximately twofold axis the symmetry that relates the 2 sugars and all four base pairs can be accommodated within the same arrangement without any type of distortion the the in its entirety structure the the DNA. In addition, the basic pairs can stack nicely on height of every other in between the two helical sugar-phosphate backbones.


fVi sugar

FIGURE 6-7 A:C incompatibility, the structure mirrors the inability of adenine to form the ideal hydrogen bonds through cytosine the basic parr is as such unstable.

FIGURE 6-fl basic flipping. Framework of isolated DMA, reflecting the flipped cytosine residue and also the little distortions come the surrounding base pairs. (Ktimasauskas S, Kumar 5., Roberts R.J., and also Cheng X. 1994. Cabinet 76 357. Picture prepared v BobScnpt, MolScripi, and Raster 3D )

Hydrogen Bonding Is important for the Specificity of basic Pairing

The hydrogen bonds in between complementary bases room a fundamental feature of the dual helix, contributing come the thermodynamic security of the helix and also the specificity of basic pairing. Hydrogen bonding might not, at first glance, appear to add importantly to the stability of DMA because that the following reason. An necessary molecule in aqueous equipment has every one of its hydrogen bonding properties satisfied through water molecules that come on and also off very rapidly. As a result, for every hydrogen bond that is made as soon as a base pair forms, a hydrogen bond with water is damaged that to be there before the basic pair formed. Thust the network energetic contribution of hydrogen bonds to the security of the twin helix would appear to it is in modest. However, once polynucleotide strands are separate, water molecules room lined increase on the bases. When strands come together in the dual helix, the water molecules room displaced native the bases. This create disorder and also increases entropy, in order to stabilizing the double helix. Hydrogen bonds room not the only force that stabilizes the double helix. A second important contribution comes from stacking interactions in between the bases. The bases space flat, fairly water-insoluble molecules, and also they tend to stack above each other about perpendicular come the direction of the helical axis. Electron cloud interaction (it— tr) between bases in the helical stacks contribute considerably to the security of the double helix.

Hydrogen bonding is likewise important for the specificity of base pairing. Intend we tried to pair one adenine with a cytosine. Then us would have actually a hydrogen bond agree (Nl of adenine) lie opposite a hydrogen bond agree (N3 the cytosine) v no room to put a water molecule in in between to fulfill the 2 acceptors (Figure 6-7), Likewise, 2 hydrogen shortcut donors, the NH; groups at C6 the adenine and C4 the cytosine, would lie opposite every other. Thus, one A:C base pair would certainly be unstable since water would have to be stripped off the donor and acceptor groups without restoring the hydrogen bond formed within the basic pair.

Bases have the right to Flip the end from the dual Helix

As we have seen, the energetics of the dual helix favor the pairing of each base on one polynucleotide strand through the complementary base on the other strand. Sometimes, however, individual bases can protrude native the double helix in a remarkable phenomenon well-known as basic flipping shown in figure 6-B. Together we shall check out in thing 9, details enzymes that methylate bases or eliminate damaged bases execute so through the base in an extra-helical configuration in which the is flipped the end from the dual helix, allowing the base to sit in the catalytic cavity of the enzyme. Furthermore, enzymes involved in homologous recombination and also DNA fix are thought to scan DNA because that homology or lesions through flipping the end one basic after another. This is no energetically expensive since only one base is Hipped out at a time. Clearly, DNA is more flexible than could be suspect at first glance.

DNA Is normally a Right-Handed twin Helix

Applying the handedness rule from physics, we deserve to see that each that the polynucleotide chains in the double helix is right-handed. In your mind"s eye, organize your right hand as much as the DNA molecule in figure 6-9 v your ignorance pointing up and also along the long axis of the helix and your fingers following the grooves in the helix. Trace along one strand that the helix in the direction in which your ignorance is pointing. Notice that yuu go roughly the helix in the exact same direction together your fingers room pointing. This does not occupational if yuu usage your left hand. Try it!

A repercussion of the helical nature that DNA is that periodicity. Every base pair is displaced (twisted) from the previous one by around 36c. Thus, in the X-ray crystal framework of DNA that takes a stack of about 10 base pairs come go totally around the helix (360L) (see figure 6-la). The is, the helical periodicity is usually 10 base pairs per rotate of the helix. For further discussion, view Box 6-1, DI\A has actually 10,5 case Pairs per turn of the Helix in Solution: The Mica Experiment.

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The dual Helix has Minor and significant Grooves

As a result of the double-helical structure of the 2 chains, the DNA molecule is a long prolonged polymer with two grooves that space not equal in size to every other. Why are there a boy groove and a major groove? Tt is a simple consequence of the geometry that the basic pair. The edge at which the 2 sugars protrude horn the basic pairs (that is, the angle in between the glycosidic bonds) is about 120° (for the narrow angle or 240" because that the large angle) (see figures 6-lb and 6-6). As a result, as more and much more base pairs stack on height of every other, the small angle in between the sugars on one sheet of the basic pairs generates a minor groove and the huge angle on the other edge generates a significant groove. (If the sugars pointed far from each various other in a straight line, the is, in ~ an edge of 180"\ climate the two grooves would certainly be of same dimensions and also there would certainly be nu minor and significant grooves.)

The significant Groove Is rich in chemistry Information

The edges of every base pair space exposed in the major and boy grooves, developing a sample of hydrogen bond donors and acceptors and of valve der Waals surfaces that identifies the base pair (see number 6-10). The sheet of an A:T basic pair screens the adhering to chemical groups in the adhering to order in the major groove: a hydrogen bond acceptor (the N7 that adenine), a hydrogen bond donor (the exocyclic amino team on C6 of adenine), a hydrogen bond acceptor (the carbunyl group on C4 of

FIC U ft E 6-9 Left- and also right-handed helices. The 2 polynucleotide chains in the double helix wrap roughly one another in a ngbt handed manner.