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Having outlined the general principles of nucleic acid structures, we will now focus on how these principles influence the formation of specific structures found in DNA. The helical structure of DNA arises because of the specific interactions between bases and the non-specific hydrophobic effects described earlier.
Its structure is also determined through its active synthesis; that is, duplex DNA is synthesised by specialist polymerases upon a template strand.
We outlined earlier the general principle of base pairing. Now we will go into more detail about why these base pairs arise within a duplex DNA. The specificity of Watson-Crick base pairing results from both the hydrogen-bonding factors we described earlier and steric restrictions imposed by the two deoxyribose—phosphate backbones. Thus spatial considerations limit each base pair to being between a purine and a pyrimidine.
Note that mispairings, such as that between two purines, do occur during replication, but such mispairings distort the helix and are readily detected and corrected. Apart from the spatial considerations, specific requirements apply for the formation of hydrogen bonds between the bases in helical DNA, and the final positions of the hydrogen atoms within each base pair will be influenced by the positions of the bases after stacking interactions have occurred.
Consequently, each base pair has a well defined position. Look back at Figure 5a and try to visualise pairing between A and C bases. Describe the result. Similarly, there is only potential for formation of a single hydrogen bond between G and T bases. To satisfy steric restrictions of base pairing and to maximise the hydrophobic interactions between successive base pairs, the two polynucleotide chains in DNA are coiled around a common axis.
If you take a closer look at the sugar—phosphate backbone in B-DNA, you can see that it spirals around the core. These grooves result from the geometry of the sugar-base structure and base-pair interaction, as shown in Figure 9b.
Within the major groove, a large portion of the base is exposed and it will perhaps not surprise you to learn that this is where most protein—DNA interactions occur that depend upon the specific recognition of individual bases within the DNA.
Such interactions depend upon the formation of hydrogen bonds between amino acid side-chains in the protein and atoms in the bases that are not involved in base pairing; these atoms are identified in Figure 9c.
You will see later in this unit how the accessibility of bases within the major groove permits protein—DNA interactions without interfering with base pairing. If you have rotated it, then click here to reset it to its original orientation:. You can rotate the structure in the left-hand window at any time. You will not be surprised to see a simple stack of blocks!
However , the building blocks of macromolecules are in general chiral, asymmetric, molecules, not regular rectangular blocks. We can model this in a simple way by considering a wedge shaped block:.
Now we'll stack a block on top, as before. Adding more blocks causes the stack to curve around, in this case into a circle. But , there is no reason why the building blocks monomers will stack on top of each other in a regular face to face way. There is very likely to be some asymmetry in the way the blocks stack. Most DNA double helices are right-handed; that is, if you were to hold your right hand out, with your thumb pointed up and your fingers curled around your thumb, your thumb would represent the axis of the helix and your fingers would represent the sugar-phosphate backbone.
The DNA double helix is anti-parallel, which means that the 5' end of one strand is paired with the 3' end of its complementary strand and vice versa. As shown in Figure 4, nucleotides are linked to each other by their phosphate groups, which bind the 3' end of one sugar to the 5' end of the next sugar. Not only are the DNA base pairs connected via hydrogen bonding, but the outer edges of the nitrogen-containing bases are exposed and available for potential hydrogen bonding as well.
These hydrogen bonds provide easy access to the DNA for other molecules, including the proteins that play vital roles in the replication and expression of DNA Figure 4. Figure 4: Base pairing in DNA. Two hydrogen bonds connect T to A; three hydrogen bonds connect G to C. The bottom four base pairs are shown flattened instead of twisted, so this region can be easily seen in a cut-away showing a close-up view.
The cut-away shows the individual atoms and bonds in the DNA molecule. Phosphate groups are depicted within light brown spheres, and the bonds between the phosphate and oxygen atoms are shown. The sugars are represented by grey pentagons that show where oxygen atoms and hydrogen atoms are attached to the unmarked carbon atoms at the corners. An oxygen atom from each phosphate molecule is connected by a black line to a carbon atom from the sugar molecule. These black lines represent the covalent bonds between the sugars and phosphate groups.
The sugar molecules are each attached to a nitrogenous base. The nitrogenous bases from the two DNA strands meet in the center of the molecule, where they are connected with hydrogen bonds shown by dotted, red lines.
At the top left side, a guanine base with two fused rings G, shown in blue is bound to a cytosine base with a single ring C, shown in gold on the opposite strand. These two bases are held together by three hydrogen bonds. Below this base pair, a thymine base with a single ring T, shown in red is bound to an adenine base with two fused rings A, shown in green on the opposite strand. These two bases are held together by two hydrogen bonds. Below this pair, a single-ringed cytosine base is bound to a double-ringed guanine base by three hydrogen bonds.
In the final pair, an adenine base with two fused rings is bound to a single-ringed thymine by two hydrogen bonds. Figure 5: Three different conformations of the DNA double helix. A A-DNA is a short, wide, right-handed helix. Genetics: A Conceptual Approach , 2nd ed. All rights reserved. References and Recommended Reading Chargaff, E. Preface to a grammar of biology. Science , — Dahm, R. Human Genetics , — Levene, P. Journal of Biological Chemistry 40 , — Rich, A. Nature Reviews Genetics 4 , — link to article Watson, J.
Nature , — link to article Wolf, G. Article History Close. Share Cancel. Revoke Cancel. Keywords Keywords for this Article. Save Cancel. Flag Inappropriate The Content is: Objectionable. Flag Content Cancel. Email your Friend. Submit Cancel. This content is currently under construction. Explore This Subject. Applications in Biotechnology. DNA Replication. Jumping Genes. After her death, Crick said that her contribution had been critical. The double helix describes the appearance of double-stranded DNA, which is composed of two linear strands that run opposite to each other, or anti-parallel, and twist together.
Each DNA strand within the double helix is a long, linear molecule made of smaller units called nucleotides that form a chain. The chemical backbones of the double helix are made up of sugar and phosphate molecules that are connected by chemical bonds, known as sugar-phosphate backbones.
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