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5.2.1.2. Secondary structure of DNA

Secondary structure of DNA

The secondary structure of DNA is the arrangement in space of two nucleotide chains or strands in a double helix, with the nitrogenous bases facing each other and linked by hydrogen bonds. This structure was deduced from the following experimental data:

It was observed that the density and viscosity of the DNA in aqueous dispersion were higher than expected due to its chemical composition and molecular weight, so it was assumed that there must be hydrogen bonds  between the groups -NH 2, -CO-, and = NH.

Chargaff found that all DNAs had the same number of adenine (A) and thymine (T) molecules, and as many cytosine (C) as guanine (G).

n° adenine molecules / n° thymine molecules = 1
n° cytosine molecules / n° guanine molecules = 1

From this it was deduced that hydrogen bonds were formed between A and T and between C and G.

With X-rays it was discovered that DNA has a structure of 20 Å (0.2 nm) in diameter , in which certain units were repeated every 3.4 Å (0.34 nm), and that there was another greater repetition every 34 Å (3.4 nm).

1 nm (nanometer) = 10 Å (angstrom) = 1 × 10-9 meters = 1 × 10-6 millimeters

With all these data, J. Watson and F. Crick devised, in 1953, the model of the double helix of DNA, which says that DNA is made up of two antiparallel chains of polynucleotides, with the 5 '→3' bonds oriented in different sense, complementary and wound one on top of the other in a double helix or plectonemic form (for the two chains to separate, they must be unwound).

The fact that they are complementary chains implies that if there is adenine in a chain, in its complement, there will be the nitrogenous base thymine. And if there is guanine in one, cytosine in the other.

As in proteins, in the secondary structure of DNA, the hydrophobic groups -CH 3 and -CH= of the nitrogenous bases are oriented towards the interior of the molecule, establishing hydrophobic interactions between lipophilic groups, which collaborate with hydrogen bonds in give stability to the macromolecule. The pentoses and the phosphate groups are on the outside.

Estructura secundaria del ADN

By Deneapol [Public domain], via Wikimedia Commons

Complementarity between the bases

The two antiparallel chains that make up the DNA double helix are held together by hydrogen bonds between the complementary nitrogenous bases.

Adenine will always appear united with thymine , and cytosine with guanine, by means of hydrogen bonds between their polar groups. Thus, between adenine and thyminetwo hydrogen bonds are established , and between guanine and cytosinethree.

A=T y G≡C

  • Between A and T, two hydrogen bonds are established.

La unión entre bases nitrogenadas timina y adenina se prodecue mediante dos puentes de hidrógeno

By Yikrazuul (Own work) [Public domain], via Wikimedia Commons

  • Between C and G, three hydrogen bonds are established.

La unión entre las bases nitrogenadas guanina y citosina se produce mediante tres puentes de hidrógeno

By Yikrazuul (Own work) [Public domain], via Wikimedia Commons

They can never join two bases that are not complementary, since the structure and size of the puric and pyrimidine bases prevents the creation of hydrogen bonds.

In summary, the bonds that contribute to the formation of the double helix are:

  • Link phosphodiester, at the junction of two nucleotides.
  • Link N-glycosidic, at the junction of the deoxyribose and a nitrogenous base.
  • Link hydrogen bridge at the junction of nucleobases (A=T and G≡C).

    Alternative structures to the double helix (form B)

    Although the double helix described by Watson and Crick, the so-called B-shape, has been considered the only possible spatial conformation, other possible shapes are currently known.

    Form B is the one adopted by DNA in solution and in which it interacts with nuclear proteins.

    Video: The structure of DNA: Watson and Crick.

    DNA form A

    Form A of DNA is a right-handed double helix, like form B, but the base pairs do not form a plane perpendicular to the axis, but are inclined 20º with respect to the axis of the helix. It is wider and shorter than form B.

    Form A has only been observed in the laboratory, formed from Form B when the relative humidity drops to 75%.

    By Thorwald at en.wikipedia (Transferred from en.wikipedia) [Public domain], from Wikimedia Commons

    Z form of DNA

    The Z form of DNA is longer and narrower than the B form. It is left-handed, it rotates counterclockwise. Its shape is due to the presence of numerous alternating guanine and cytosine nucleotides (GCGCGCGC).

    Other secondary structures

    In addition to the B, A, and Z forms of DNA, there are a few other types:

    Fundamental ideas about the secondary structure of DNA

    Secondary structure of DNA

    • It is the arrangement in space of two nucleotide chains or strands in a double helix, with the nitrogenous bases facing each other and joined by hydrogen bonds.
    • Diameter: 20 Å = 0.2 nm
    • Nucleotides are linked by phosphodiester bonds  between the phosphate group at the 5 'carbon of one nucleotide and the hydroxyl group at the 3' carbon of the next.
    • Nitrogen bases are joined by hydrogen bonds (bridges) , two bonds between A and T, and three bonds between G and C.