Mark E Curtis

The geometry of DNA: a structural revision

Professor Karst Hoogsteen’s work and papers on the nucleoside published in Acta. Crystallagraphica between 1959 and 1963 are formidable pieces of work that have been ‘long buried’ precisely because they contradicted Crick and Watson’s base pairing solution. Interestingly his work directly supports the geometric pentagonal pairings that I propose - in every instance and diagram of his paper he illustrates the pentagonal part of the purine hydrogen-bonding with the pyrimidine and he states categorically that, given free will, the molecules refused to pair in the fashion proposed by Crick and Watson.

Karst Hoogsteen (1963) Acta. Cryst. vol 16, 907-916

In fact the large and beautifully illustrated diagram on page 913 of his 1963 paper (above) actually shows a collapsed version of an A/T keto base pair illustrated in my publication. The same diagram is shown with geometric over-drawing (below).

Geometric overdrawing of the Karst Hoogsteen base pair

Most interestingly he states that he did not have as much success with G/C pairings as with A/T and this I believe likely to be as a result of the blocks that he placed on the respective N1 pyrimidine and N9 purine positions in accordance with Crick and Watson’s structural proposal. I mention in my publication that the geometric proposal would require N9 of guanine to be available to form hydrogen bonds, as was indeed the case prior to 1953 and Crick & Watson fixing the sugar position to suit their own agenda and proposal. It would be very interesting to repeat Hoogsteen’s research, especially with respect to Guanine and Cytosine without blocking any of the potential hydrogen atoms but especially N9.

As a point of note: I do appreciate that bond lengths and angles will not adhere precisely to that of the mathematical structure. The molecular pentamer is unlikely to fall within the exact measurements of a compass derived equilateral pentagon. It is the overall principals of helical generation that I am concerned with and I would therefore expect a relative degree of variation - perhaps by as much as 9.5 to 10.5 bases per helical turn.

It is perhaps also worth mentioning that patterns and structures formed utilising the pentagon happen to destroy geometric congruence, a necessary means by which energy is able to dissipate. The hexagon and other even sided structures being congruent have a tendency to dissipate energy. Congruence allows energy to flow seamlessly whilst incongruence tends to focus energy. The pentagon, being incongruent, is deemed unsociable by reason of the fact that it ‘focuses' rather than ‘dissipates' energy (Johannes Kepler - Harmony of the World, Book II, prop IX). The upshot of this being that it is possible those hydrogen bonds formed utilising the pentamer are stronger and more resilient.