Double-helical structure, hydrogen-bonde

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

The ability of DNA to replicate lies in its double-helical structure. There is a precise correspondence between the bases in the two strands. Adenine in one strand always forms two hydrogen bonds to thymine in the other, and guanine always forms three hydrogen bonds to cytosine so, across the helix, the base pairs are always AT and GC (Fig. 19.29). Any other combination would not be held together as well. During replication of the DNA, the hydrogen bonds, which are... 

De Mendoza reported the first example of anion-directed helix formation in 1996 [91]. The assembly of this helical structure relies, not only on electrostatic interactions between the anionic template and the positively charged strands, but also on hydrogen bonding. The tetraguanidinium strand 69 (see Scheme 34) self-assembles around a sulfate anion via hydrogen bonding to produce a double helical structure. The formation of this assembly and its anion-dependence was proposed on the basis of NMR and CD spectroscopic studies. 

The structural characterization of this assembly has revealed that chloride coordination (via hydrogen bonding to the protonated pyridyl groups of the strands) induce the strands to adopt a double-helical structure in the solid state. 

DNA is made up ot two intertwined strands. A sugar-phosphate chain makes up the backbone of each, and the two strands are joined by way of hydrogen bonds betwen pairs of nucleotide bases, adenine, thymine, guanine and cytosine. Adenine may only pair with thymine and guanine with cytosine. The molecule adopts a helical structure (actually, a double helical structure or double helix ). 

Bases from two different strands interact to form a double-helical structure. Guanine forms three hydrogen bonds with cytosine, whereas adenine forms two hydrogen bonds with thymidine. Stacking interactions between the planar bases also stabilize the DNA structure. Phosphates and sugars form the backbone of DNA. 

Answer The double-helical structure is stabilized by hydrogen bonding between complementary bases on opposite strands and by base stacking between adjacent bases on the same strand. Base stacking in nucleic acids causes a decrease in the absorption of UV light (relative to the non-stacked structure). On denaturation of DNA, the base stacking is lost and UV absorption increases. 

There is evidence for indirect, water mediated intraresidue hydrogen bonding with water in the double helical structure of the p-nitrophenyl maltohexaose... 

The discovery of these base pairs, which imply the double helical structure of DNA, stimulated a series of crystal structural studies not only of complexes of purines and pyrimidines, but of other complexes involving related molecules and their derivatives. Although we can formulate a large number of possible heterocombinations in matrix form, as shown below these complexes are reluctant to crystallize even when there is spectroscopic evidence of hetero-complex formation in solution. This is presumably because self-(homo)-association is energetically more favorable and only in rare cases were crystals of hetero complexes actually formed. Because of their three hydrogen bonds, G-C complexes form and crystallize more readily. There have been many attempts to crystallize the Watson-Crick A-U base pair, but none was successful and it only formed when the dinucleoside phosphate adenylyl-3,5,-uridine (ApU [536]) or higher oligomers were crystallized (see Part III, Chapter 20). 

Based on the geometry of the central A-tract, a double helix was constructed. Compared with normal B-DNA, it displays a very narrow, deep minor groove and a wide, shallow major groove and has a pitch of 34 A with 10.0 base pairs per turn. The three-center hydrogen bonding which links all the base pairs of the double helix in axial direction confers extra stabilization to this double helical structure, which explains several experimental findings not understood previously [702, 703]. 

Describe the role of hydrogen bonding in maintaining the double helical structure of DNA. 

The key to DNA s functioning is its double-helical structure with complementary bases on the two strands. The bases form hydrogen bonds to each other, as shown in Fig. 22.38. Note that the structures of cytosine and guanine make them perfect partners for hydrogen bonding, and they are always found as pairs on the two strands of DNA. Thymine and adenine form similar hydrogen-bonding pairs. 

The thermodynamic and spectroscopic properties of short segments of duplex DNA containing a single CPD indicate that cis-syn CPD can be accommodated in the double helical structure of B-DNA such that hydrogen bonding with the opposite A residues is possible (41). The crystal structure of... 

Since the proposal of the double helical structure of DNA, it has been recognized that the fidelity of replication of genetic information depends on the hydrogen bonding interaction between the purine and pyrimidine bases of DNA, i.e., the cytosine-guanine and thymine-adenine complementarity. The importance of hydrogen bonds for fidelity depends on two... 

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