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

The 2 Chains that the double Helix have Complementary Sequences

The pairing in between adenine and also thymine, and between guanine and cytosine, results in a safety relationship in between the succession of bases on the two linked chains and gives DNA its self-encoding character. Because that example, if we have the sequence 5"-ATCTC-3" on one chain, the opposite chain must have actually the complementary succession 3"-TACAC-5

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

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An crucial feature of the double helix is that the 2 base bag have precisely the very same geometry; having actually an A:T basic pair or a G;C basic pair between the 2 sugars does not perturb the plan of the sugars due to the fact that the d¡stance between the street attachment points space the same for both basic pairs. No does T:A or C:G. In various other words,


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

The figure shows hydrogen bonding in between (he bases.

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

The figure shows hydrogen bonding in between (he bases.

there is an roughly twofold axis of symmetry the relates the 2 sugars and also all four base pairs can be accommodated in ~ the same plan without any type of distortion the the overall structure of the DNA. In addition, the basic pairs can stack neatly on peak of every other between the 2 helical sugar-phosphate backbones.


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FIGURE 6-7 A:C incompatibility, the structure mirrors the i can not qualify of adenine to type the ideal hydrogen bonds through cytosine the basic parr is as such unstable.

FIGURE 6-fl base flipping. Structure of diverted DMA, mirroring 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. Cell 76 357. Photo prepared v BobScnpt, MolScripi, and Raster 3D )

Hydrogen Bonding Is vital for the Specificity of basic Pairing

The hydrogen bonds between complementary bases space a fundamental feature the the dual helix, contributing to the thermodynamic stability of the helix and also the specificity of base pairing. Hydrogen bonding can not, at very first glance, show up to contribute importantly come the security of DMA because that the following reason. An essential molecule in aqueous solution has every one of its hydrogen bonding nature satisfied by water molecules that come on and off really rapidly. As a result, because that every hydrogen bond that is made once a basic pair forms, a hydrogen bond through water is broken that was there before the basic pair formed. Thust the network energetic donation of hydrogen bonds come the stability of the dual helix would show up to be modest. However, as soon as polynucleotide strands room separate, water molecules are lined up on the bases. Once strands come with each other in the double helix, the water molecules space displaced native the bases. This creates disorder and also increases entropy, thereby stabilizing the twin helix. Hydrogen bonds are not the only force that stabilizes the twin helix. A second important contribution comes from stacking interactions between the bases. The bases are flat, relatively water-insoluble molecules, and also they tend to stack over each other about perpendicular to the direction of the helical axis. Electron cloud interactions (it— tr) between bases in the helical stacks contribute considerably to the security of the dual helix.

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

Bases deserve to Flip the end from the dual Helix

As we have seen, the energetics the the dual helix favor the pairing of each base top top one polynucleotide strand with the complementary base on the various other strand. Sometimes, however, separation, personal, instance bases can protrude from the double helix in a impressive phenomenon known as base flipping presented in figure 6-B. As we shall view in chapter 9, certain enzymes the methylate bases or eliminate damaged bases perform so with the basic in an extra-helical construction in which the is flipped the end from the twin helix, enabling the basic to sit in the catalytic cavity that the enzyme. Furthermore, enzymes connected in homologous recombination and DNA repair are believed to scan DNA because that homology or lesions by flipping out one base after another. This is not energetically expensive because only one base is Hipped the end at a time. Clearly, DNA is much more flexible than can be suspect at first glance.

DNA Is commonly a Right-Handed dual Helix

Applying the handedness ascendancy from physics, we deserve to see that each of the polynucleotide chain in the dual helix is right-handed. In your mind"s eye, host your right hand up to the DNA molecule in figure 6-9 v your ignorance pointing up and also along the lengthy axis that the helix and also your fingers complying with the grooves in the helix. Map along one strand that the helix in the direction in i beg your pardon your ignorance is pointing. Notice that yuu go around the helix in the same direction as your fingers room pointing. This walk not job-related if yuu usage your left hand. Shot it!

A consequence of the helical nature that DNA is that periodicity. Every base pair is displaced (twisted) native the vault one by about 36c. Thus, in the X-ray crystal structure of DNA it takes a ridge of around 10 basic pairs come go completely around the helix (360L) (see number 6-la). That is, the helical periodicity is typically 10 base pairs per turn of the helix. For further discussion, view Box 6-1, DIA has 10,5 case Pairs per rotate 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 framework of the two chains, the DNA molecule is a long expanded polymer with two grooves that space not equal in size to each other. Why are there a young groove and a significant groove? Tt is a simple an effect of the geometry of the base pair. The edge at i m sorry the 2 sugars protrude horn the basic pairs (that is, the angle in between the glycosidic bonds) is around 120° (for the narrow angle or 240" for the vast angle) (see numbers 6-lb and 6-6). As a result, as much more and an ext base bag stack on peak of each other, the small angle between the street on one edge of the base pairs generates a boy groove and the huge angle ~ above the other edge generates a major groove. (If the sugars pointed away from each various other in a right line, that is, in ~ an edge of 180" then the two grooves would be of equal dimensions and there would be nu young and major grooves.)

The major Groove Is wealthy in chemical Information

The edge of every base pair are exposed in the major and young grooves, producing a pattern of hydrogen shortcut donors and acceptors and of valve der Waals surfaces the identifies the base pair (see number 6-10). The edge of one A:T base pair screens the complying with 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 right-handed helices. The 2 polynucleotide chains in the double helix wrap roughly one one more in a ngbt handed manner.