An Introduction to DNA Structure
David Marcey
I. The DNA Polymer
II. The B-DNA Double Helix
III. DNA Conformers

Nota Bene:
Within each of the three sections, below, you may activate buttons in any order of your choosing. However, when switching between sections, it is important that you reset the molecule before activating buttons in the new section.

I. The DNA Polymer

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In the left frame is a short stretch of a single strand of DNA. DNA is a polymer of linked deoxyribonucleotides. Here the atoms are colored according to the standard CPK coloring scheme (C, N, O, P). For simplicity, hydrogen atoms are not shown.

In the tetrameric example shown, each of the four deoxyribonucleotide building blocks (dA, dT, dC, dG) is represented.

As shown here for dC, each deoxyribonucleotide in the chain comprises a nitrogenous base, a deoxyribose sugar, and a phosphate group (phosphorus plus oxygens). The carbons of the sugar are numbered 1'-5' as indicated.

The nitrogenous base is linked to the sugar by a glycosidic bond between a nitrogen and the 1' carbon of the deoxyribose sugar.

The 5' carbon of each sugar is linked to a phosphorus through an oxygen (ester bond). The phosphorus is in turn linked to the 3' oxygen of the next nucleotide in the chain.

The connection between nucleotides in a DNA strand is thus referred to as a phosphodiester linkage.

The molecule can be viewed as a series of nitrogenous bases (CPK coloration) connected through a sugar-phosphate backbone.

For study (using CPK coloration):

  • identify the four nitrogenous bases
  • identify the 5' and 3' carbons of the ribose sugars
  • identify the phosphodiester linkages connecting the nucleotides
  • moving top to bottom, how would you label the polarity of the sugar-phosphate backbone, 3' ---> 5' or 5' --->3' ? Why?

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II. The B-DNA Double Helix

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DNA in the cell functions as a double-stranded helix of B-form DNA, the structure of which was first determined by Watson and Crick. Here the two strands are differentially colored to illustrate the right handed B-form helix clearly.

The polar sugar-phosphate backbones of each strand form the helical scaffold, with the nitrogenous bases in the interior of the molecule, their planes nearly perpendicular to the helical axis. Each base forms hydrogen bonds (indicated by dashed lines) with a base from the opposite strand.

The polarity of the backbones is antiparallel, with one strand running 3' ---> 5' and the other 5' --->3'. This can readily be seen by observing the reversed orientations of the ribose sugars on opposite strands.

The diameter of the B-DNA is ~20 Angstroms, and the distance between base pairs is ~3.4 Angstroms.

The base pairing of opposite strands is stereochemically selective, Adenine always pairing with Thymine, and Guanine with Cytosine. Two and three hydrogen bonds are formed in A-T and G-C base pairs, respectively.

A-T and G-C base pairing results in strand complementarity, with one strand of the double helix forming a sequence of bases complementary in hydrogen bonding to that of the other strand. As noted by Watson and Crick in their 1953 paper describing the first model of the DNA double helix, base complementarity provides a means by which the genetic material can replicate with fidelity. Each strand of a parent double helix serves as a template upon which complementary strands are built, producing two daughter molecules identical to the parent, with one strand of each daughter helix conserved from the parent molecule.

This semi-conservative mode of replication is here illustrated schematically for 1 strand of DNA.

The attachment of bases to the backbone sugars through glycosidic bonds is asymmetrical. This results in the formation of two different grooves on opposite sides of the base pairs, the major and minor grooves. Although the grooves are of similar depth in B-DNA, the major groove is considerably wider than the minor groove.

The edges of the base pairs present a more complex sterochemical environment in the major groove than in the minor groove. As can be observed in the T-A base pair shown, the major groove edge contains a methyl group (CH3), a hydrogen bond acceptor (HA), a hydrogen bond donor (HD), and a second hydrogen bond acceptor (HA) - for simplicity, hydrogens are not shown. The minor groove edge, in contrast, presents only a HA, a hydrogen (H), and a second HA. Whereas a switch to an A-T base pair would present a reversed edge chemistry in the major groove (HA-HD-HA-CH3), the edge in the minor groove would remain the same as in a T-A pair (HA-H-HA). Similar considerations apply to C-G and G-C base pairs. Since many proteins that bind DNA recognize specific sequences of bases, it is not surprising that most bind to the floor of the major groove, as this provides more chemical information for recognition than the minor groove.

The distance between the sugar-phosphate backbones is greater in the major groove than in the minor groove.

The major and minor grooves lie 180o opposite each other in the double helix, spiraling along the axis of the molecule.

For study:

  • identify the base paired nitrogenous bases
  • identify the atoms involved in hydrogen bonding between base pairs
  • identify the hydrogen donor and acceptor atoms for each hydrogen bond
  • for both A-T and G-C base pairs, identify the edges of the bases that
    form the floors of the major and minor grooves
  • for both A-T and G-C base pairs, identify the groups on the floors of
    the grooves that could serve as recognition sites for interacting
  • for each base pair, explain why the major groove is richer in chemical information than the minor groove

For study:

  • identify the major and minor grooves in double helical DNA
  • compare the depth and width of the grooves, and note the distance
    between backbones in each groove
  • imagine that you are a protein that must recognize a particular sequence of base pairs in double helical DNA - list the reasons why you most likely will bind DNA in the major groove

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III. DNA Conformers

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To the left are shown the three known conformers of double stranded DNA, including A-, Z-, and B-DNA discussed above. Although B-DNA is the primary in vivo conformation, DNA-RNA hybrid molecules adopt the A conformation in cells, and Z-DNA may arise in GC rich stretches of chromosomal DNA. Whereas A- and B-DNA are right handed helices, Z-DNA is left handed. A-DNA forms under non-physiological conditions when B-DNA is dehydrated.

There are large differences in the depths of the grooves in the three conformers. Whereas B-DNA has major and minor grooves of similar depths, A-DNA has a cavernous major groove and a minor groove that is quite shallow. Z-DNA has the opposite arrangement, with a deep minor groove and a major groove into which the bases are extruded. In B-DNA, the bases are nearly perpendicular to the helical axis, which runs through the center of each base pair. In A-DNA, the helical axis runs through the major groove, the base pairs being pushed toward the surface of the minor groove. The A-DNA bases are tilted significantly (13o - 19o) with respect to the helical axis. The reader is invited to explore the DNA conformers using the following buttons. Also, mouse controls (e.g. click and drag) may be used to manipulate the molecules. A menu of Chime commands is available by right clicking in a particular frame.


For study:

  • compare and contrast the major structural features of A-, B-, and Z-DNA
  • speculate as to why the removal of water molecules from B-DNA might cause a switch to the A conformation


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