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

The two Chains the the dual Helix have actually 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 top top the two linked chains and gives DNA that self-encoding character. Because that example, if we have the succession 5"-ATCTC-3" ~ above one chain, opposing chain must have the complementary sequence 3"-TACAC-5

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

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An important feature of the double helix is that the 2 base bag have exactly the very 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 because the d¡stance in between the sugar attachment points are the same for both base pairs. Neither does T:A or C:G. In 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 base pairs.

The figure shows hydrogen bonding between (he bases.

there is an about twofold axis of symmetry the relates the two sugars and also all four base pairs have the right to be accommodated within the same arrangement without any kind of distortion that the all at once structure that the DNA. In addition, the base pairs can stack neatly on optimal of each other in between the two helical sugar-phosphate backbones.


fVi sugar

FIGURE 6-7 A:C incompatibility, the structure mirrors the i can not qualify of adenine to kind the suitable hydrogen bonds v cytosine the base parr is as such unstable.

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

Hydrogen Bonding Is crucial for the Specificity of basic Pairing

The hydrogen bonds in between complementary bases space a an essential feature that the dual helix, contributing come the thermodynamic security 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 stability of DMA because that the following reason. An essential molecule in aqueous equipment has every one of its hydrogen bonding nature satisfied by water molecules that come on and also off an extremely rapidly. Together a result, for every hydrogen bond the is made once a basic pair forms, a hydrogen bond through water is broken that to be there before the base pair formed. Thust the network energetic contribution of hydrogen bonds come the security of the twin helix would appear to it is in modest. However, when polynucleotide strands space separate, water molecules space lined up on the bases. When strands come together in the twin helix, the water molecules are displaced from the bases. This creates disorder and increases entropy, thereby stabilizing the double helix. Hydrogen bonds space not the only force that stabilizes the double helix. A second important contribution originates from stacking interactions between the bases. The bases space flat, relatively water-insoluble molecules, and also they have tendency to stack above each other roughly perpendicular to the direction that the helical axis. Electron cloud interactions (it— tr) between bases in the helical stacks contribute significantly to the stability of the twin helix.

Hydrogen bonding is also important for the specificity of basic pairing. Expect we tried come pair an adenine v a cytosine. Then us would have a hydrogen bond acceptor (Nl that adenine) lying opposite a hydrogen bond agree (N3 of cytosine) v no room to placed a water molecule in in between to accomplish the 2 acceptors (Figure 6-7), Likewise, 2 hydrogen bond donors, the NH; groups at C6 that adenine and also C4 that cytosine, would lie opposite every other. Thus, one A:C basic pair would certainly be unstable due to the fact that water would need to be stripped off the donor and also acceptor groups without restoring the hydrogen bond developed within the basic pair.

Bases can Flip the end from the double Helix

As we have seen, the energetics the the twin helix donate the pairing of every base top top one polynucleotide strand with the complementary basic on the various other strand. Sometimes, however, individual bases have the right to protrude from the twin helix in a impressive phenomenon known as basic flipping shown in figure 6-B. As we shall view in chapter 9, details enzymes the methylate bases or remove damaged bases carry out so with the base in one extra-helical construction in which it is flipped the end from the double helix, enabling the basic to sit in the catalytic cavity of the enzyme. Furthermore, enzymes involved in homologous recombination and DNA repair are thought to scan DNA because that homology or lesions by flipping the end one basic after another. This is no energetically expensive since only one basic is Hipped the end at a time. Clearly, DNA is an ext flexible than might be suspect at very first glance.

DNA Is typically a Right-Handed dual Helix

Applying the handedness dominion from physics, we deserve to see the each the the polynucleotide chain in the double helix is right-handed. In your mind"s eye, host your right hand approximately the DNA molecule in figure 6-9 v your ignorance pointing up and also along the long axis the the helix and 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. An alert that yuu go roughly the helix in the same direction together your fingers are pointing. This does not occupational if yuu usage your left hand. Try it!

A consequence of the helical nature the DNA is that periodicity. Each base pair is displaced (twisted) native the vault one by around 36c. Thus, in the X-ray crystal structure of DNA that takes a stack of around 10 basic pairs come go totally around the helix (360L) (see number 6-la). The is, the helical periodicity is generally 10 basic pairs per revolve of the helix. For more discussion, see Box 6-1, DIA has actually 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 structure of the two chains, the DNA molecule is a long expanded polymer with two grooves that space not equal in dimension to every other. Why space there a young groove and also a major groove? Tt is a simple consequence of the geometry of the basic pair. The angle at which the 2 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 large angle) (see figures 6-lb and 6-6). Together a result, as more and more base pairs stack on top of each other, the narrow angle between the sugars on one leaf of the base pairs generates a minor groove and the large angle on the various other edge generates a major groove. (If the sugars pointed away from each other in a right line, that is, at an angle of 180" climate the two grooves would be of equal dimensions and also there would be nu minor and major grooves.)

The significant Groove Is well-off in chemistry Information

The edge of each base pair space exposed in the significant and young grooves, producing a sample of hydrogen shortcut donors and acceptors and of van der Waals surfaces the identifies the basic pair (see figure 6-10). The leaf of an A:T base pair screens the following chemical groups in the complying with order in the major groove: a hydrogen bond agree (the N7 the adenine), a hydrogen shortcut donor (the exocyclic amino team on C6 of adenine), a hydrogen bond agree (the carbunyl team on C4 of

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