The thermodynamic energies of left and right handed DNA.

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In this earlier post, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2 and d(ATAT)2, an undertaking which has taken about two months of computer time! The geometries are finally optimised to the point where 2nd derivatives can be calculated, and which reveal up to 756 all-positive force constants and 6 translations and rotations which are close to zero! This now lets one compute the thermodynamic relative energies using ωB97XD/6-31G(d) (for 2nd derivatives) and 6-31G(d,p) (for dispersion terms). All geometries are optimized using a continuum solvent field (water), and are calculated, without a counterion, as hexa-anions.

Relative thermodynamic energies (kcal mol-1) of DNA duplexes.
system Total energy (duplex) Dispersion term ΔΔH298 Δ(-T.ΔS298) ΔΔG298 duplex ΔG298 single chain ΔΔG298 (Duplex)
Z-CGCG 0.0 0.0 0.0 0.0 0.0 0.0 -60.3
B-CGCG 6.2 -4.2 8.0 3.9 11.9 +3.1 -54.7
Z-ATAT 0.0 0.0 0.0 0. 0.0 0.0 -44.9
B-ATAT -7.6 -12.8 -7.0 2.7 -4.3 -1.8 -45.7

Note how the CGCG duplex is more stable as a Z-helix, whilst the ATAT duplex prefers the B-helix. I will discuss the precise reasons for this elsewhere.

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4 Responses to “
The thermodynamic energies of left and right handed DNA.

  1. […] will update this post (as a comment) when the relative free energies of the two forms are available (this calculation takes a while), but there is little doubt that the Z-form is indeed the more […]

  2. […] relatively rigid structure of proteins would inevitably win a Nobel prize (and of course this did happen for that other biologically important system, DNA some 17 years later). Compelling structures for […]

  3. […] earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the […]

  4. […] Firstly, it is important to note that Pauling was apparently not aware of the absolute handedness of amino acids (which are (S) in CIP terminology). This had in fact only been established a few months before Pauling’s publication by Bijvoet, and news of this might not have reached Pauling. So Pauling guessed (or perhaps, he had already built his models, and did not have time to reconstruct them) and his famous α-helix diagram turned out to be the enantiomer of the real McCoy. As with DNA itself, the helix bears a diastereomeric relationship to the chirality of the amino acids; both have to be inverted to get the proper enantiomer (which is what Pauling did). The secret that Pauling had discovered was hydrogen bonding, and particular, weak N-H…O=C interactions (Wrinch had thought it was strong covalent N-C-OH bonding instead). Of course, there are other effects at work, which include van der Waals or dispersion interactions, electrostatic effects resulting from the large dipoles in peptides (not least due to the zwitterionic character), the planarity of the peptide bond itself, the potential for other types of hydrogen bond (e.g. C-H…O) and entropic effects. I have split some of these down for left and right handed forms of DNA in another post. […]

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