FIGURE 6-5 Base tautomers. Amino ~ imino and also keto ^ enol tautomerisrr. (a)Cyto sine ts generally m the amino develop but hardly ever develops the imino configuration, (b) Guanine is usually in rhe keto create bin is hardly ever uncovered in the enot configuration

The Two Chains of the Double Helix Have Complementary Sequences

The pairing between adenine and also thymine, and also between guanine and also cytosine, results in a complementary relationship in between the sequence of bases on the 2 linked chains and provides DNA its self-encoding character. For example, if we have actually the sequence 5"-ATCTC-3" on one chain, the oppowebsite chain need to have the complementary sequence 3"-TACAC-5

The strictness of the rules for this "Watson-Crick" pairing derives from the complementarity both of shape and of hydrogen bonding properties between adenine and thymine and between guanine and cytosine (Figure fi-6). Adenine and also thymine match up so that a hydrogen bond deserve to develop in between the exocyclic amino team at C6 on adenine and also the carbonyl at C4 in thymine; and additionally, a hydrogen bond can develop in between Nl of adenine and also N3 of thymine. A corresponding plan have the right to be attracted in between a guanine and a cytosine, so that tbelow is both hydrogen bonding and also form complementarity in this base pair as well. A G:C base pair has actually three hydrogen bonds, because the exocyclic NH, at C2 on guanine lies opposite to, and also have the right to hydrogen bond with, a carbonyl at C2 on cytosine. Likewise, a hydrogen bond have the right to develop between N"t of guanine and N3 of cytosine and also in between the carbonyl at C6 of guanine and also the exocyclic NR, at C4 of cytosine. Watson-Crick base pairing requires that the bases are in their desired tautomeric, says.

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An essential attribute of the double helix is that the two base pairs have actually exactly the same geometry; having actually an A:T base pair or a G;C base pair in between the 2 sugars does not perturb the setup of the sugars bereason the d¡stance in between the sugar attachment points are the very 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 figure shows hydrogen bonding in between (he bases.

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

The figure shows hydrogen bonding between (he bases.

there is an around twofold axis of symmeattempt that relates the 2 sugars and all 4 base pairs have the right to be accommodated within the exact same plan without any type of distortion of the all at once framework of the DNA. In addition, the base pairs have the right to stack neatly on optimal of each other between the 2 helical sugar-phosphate backbones.


fVi sugar

FIGURE 6-7 A:C incompatibility, the framework shows the incapacity of adenine to form the proper hydrogen bonds via cytosine the base parr is therefore unstable.

FIGURE 6-fl Base flipping. Structure of isolated DMA, showing the flipped cytosine residue and the little distortions to the nearby base pairs. (Ktimasauskas S, Kumar 5., Roberts R.J., and Cheng X. 1994. Cell 76 357. Image prepared with BobScnpt, MolScripi, and Raster 3D )

Hydrogen Bonding Is Important for the Specificity of Base Pairing

The hydrogen bonds between complementary bases are a standard feature of the double helix, contributing to the thermodynamic stability of the helix and the specificity of base pairing. Hydrogen bonding might not, at initially glance, appear to add importantly to the stcapacity of DMA for the following factor. An organic molecule in aqueous solution has all of its hydrogen bonding properties satisfied by water molecules that come on and also off incredibly promptly. As an outcome, for eexceptionally hydrogen bond that is made as soon as a base pair creates, a hydrogen bond via water is broken that was there prior to the base pair formed. Thust the net energetic contribution of hydrogen bonds to the stability of the double helix would certainly show up to be modest. However, as soon as polynucleotide strands are sepaprice, water molecules are lined up on the bases. When strands come together in the double helix, the water molecules are disinserted from the bases. This creates disorder and also rises entropy, thereby stabilizing the double helix. Hydrogen bonds are not the only pressure that stabilizes the double helix. A second necessary contribution comes from stacking interactions in between the bases. The bases are flat, fairly water-insoluble molecules, and they tfinish to stack above each other about perpendicular to the direction of the helical axis. Electron cloud interactions (it— tr) between bases in the helical stacks add considerably to the stcapacity of the double helix.

Hydrogen bonding is additionally vital for the specificity of base pairing. Suppose we tried to pair an adenine via a cytosine. Then we would have a hydrogen bond acceptor (Nl of adenine) lying oppowebsite a hydrogen bond acceptor (N3 of cytosine) through no room to put a water molecule in between to satisfy the 2 acceptors (Figure 6-7), Likewise, two hydrogen bond donors, the NH; groups at C6 of adenine and also C4 of cytosine, would lie opposite each various other. Hence, an A:C base pair would be unstable bereason water would need to be stripped off the donor and acceptor teams without restoring the hydrogen bond created within the base pair.

Bases Can Flip Out from the Double Helix

As we have watched, the energetics of the double helix favor the pairing of each base on one polynucleotide strand via the complementary base on the various other strand also. Sometimes, but, individual bases deserve to protrude from the double helix in a remarkable phenomenon known as base flipping shown in Figure 6-B. As we shall see in Chapter 9, specific enzymes that methylate bases or remove damaged bases perform so via the base in an extra-helical configuration in which it is flipped out from the double helix, allowing the base to sit in the catalytic cavity of the enzyme. Furthermore, enzymes connected in homologous recombicountry and DNA repair are believed to scan DNA for homology or lesions by flipping out one base after another. This is not energetically expensive because just one base is Hipped out at a time. Clbeforehand, DNA is more functional than could be assumed at initially glance.

DNA Is Usually a Right-Handed Double Helix

Applying the handedness dominance from physics, we have the right to watch that each of the polynucleotide chains in the double helix is right-handed. In your mind"s eye, hold your appropriate hand approximately the DNA molecule in Figure 6-9 through your thumb pointing up and along the lengthy axis of the helix and your fingers complying with the grooves in the helix. Trace along one strand also of the helix in the direction in which your thumb is pointing. Notice that yuu go about the helix in the very same direction as your fingers are pointing. This does not job-related if yuu use your left hand. Try it!

A consequence of the helical nature of DNA is its periodicity. Each base pair is disinserted (twisted) from the previous one by about 36c. Therefore, in the X-ray crystal structure of DNA it takes a stack of about 10 base pairs to go entirely roughly the helix (360L) (watch Figure 6-la). That is, the helical periodicity is generally 10 base pairs per turn of the helix. For further conversation, see Box 6-1, DIA Has 10,5 Case Pairs per Turn of the Helix in Solution: The Mica Experiment.

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The Double Helix Has Minor and Major Grooves

As an outcome of the double-helical structure of the 2 chains, the DNA molecule is a lengthy extfinished polymer through two grooves that are not equal in dimension to each various other. Why are there a minor groove and a major groove? Tt is a straightforward consequence of the geomeattempt of the base pair. The angle at which the two sugars protrude horn the base pairs (that is, the angle in between the glycosidic bonds) is around 120° (for the narrow angle or 240" for the wide angle) (check out Figures 6-lb and also 6-6). As a result, as more and even more base pairs stack on peak of each other, the narrow angle between the sugars on one edge of the base pairs geneprices a minor groove and the big angle on the various other edge geneprices a significant groove. (If the sugars pointed ameans from each other in a straight line, that is, at an angle of 180" then the 2 grooves would be of equal dimensions and there would be nu minor and also significant grooves.)

The Major Groove Is Rich in Chemical Information

The edges of each base pair are exposed in the major and also minor grooves, developing a pattern of hydrogen bond donors and also acceptors and of van der Waals surfaces that identifies the base pair (check out Figure 6-10). The edge of an A:T base pair screens the following chemical groups in the adhering to order in the significant groove: a hydrogen bond acceptor (the N7 of adenine), a hydrogen bond donor (the exocyclic amino team on C6 of adenine), a hydrogen bond acceptor (the carbunyl team on C4 of

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