Toward A New Structural Molecular Biology

By Clive Delmonte

 

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Delmonte's calculation of the major axis dimension of DNA

 

THE OVERALL WIDTH OF EACH HELIX IN B-DNA MOLECULES UNDER LATERAL COMPRESSION FROM THE WORK OF JAMES & MAZIA (Biochim. Biophys. Acta 10 (1953) 367 - 370)

The 2M sodium chloride solution, being of moderate ionic strength, will allow close approach between neighbouring duplexes, and it seems likely that there will be no significant pockets of salt solution or aerial voids within the surface film because of the compressive force being imposed (which will also push an elliptical section up so that it rests on the surface along its narrow edge). (See Figure 3a below.) It is possible to check that this is a secure way to approach the forthcoming calculation by first comparing James & Mazia's experimental results with the known density, determined by other workers using other methods.

Then 1 mg of DNA produced 0.28 m2 of a film of height 21.6Å. With zero aerial voids and zero inclusions of salt solution within the film, the density of the DNA = mass of DNA / volume of DNA =

0.001 g / (21.6*10-8*0.28*102*102) cm3 = 1.65 gcm-3

This value compares with that of 1.63 gcm-3 from Astbury & Bell (34) and Franklin & Gosling's estimate of 1.625 gcm-3 (50). It is therefore an over-estimate of less than 2%, and supports the postulated model of the surface.

Now, for the sodium salt of calf thymus DNA it is known that each base pair has an average mass of 660 daltons and Astbury & Bell (34) estimated the thickness of each base pair to be 3.34Å.

Each with a thickness of 3.34Å, the number of base pairs in 0.001 g is

0.001*6.023*1023 / 660 = 9.09*1017.

For an ellipse of height hÅ, width wÅ and thickness 3.34Å, the total volume of a column of these base pairs lying along the surface of the saline solution is

(?/4)*w*h*3.34*9.09*1017 = 0.28*1010*1010*h Å3

Therefore w = 11.7Å

This value can be compared with recent determinations of the height of a single duplex DNA fibre of some 12 - 13 Å using scanning tunneling microscopy (STM) with a probable vertical resolution of 1 Å (242), applied to DNA also held on a surface, though this time with no compressive force available to raise the duplex from lying on its 22Å, oblate face (First book page 516 (Fig. 1(b)),First book page 521 (Figs. 1(F) & 3(D), reproduced with permission on page 55 as Figure 5.3(C).) Using STM, it seems that no uncomplexed duplex DNA fibre heights in the alleged range of diameters for the double helix, 19Å to 22Å, have been reported.

 

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Delmonte's publications

 

Delmonte has 3 books in print, which describe the many problems in DNA science which are raised by the presumption of the Watson-Crick structure, and which are solved by the SBS model:

  1. Delmonte, C. S., 'Towards A New Structural Molecular Biology', Kettering, UK. 1991.
    ISBN 0-9512276-0-2.

  2. Delmonte, C., 'Advances in AFM & STM Applied to the Nucleic Acids', Kettering, UK, 1997,
    ISBN 0-9512276-2-9.

  3. Delmonte, C., 'DNA Structure Puzzles', Kettering, UK, 2000.
    ISBN 0-9512276-3-7.

     

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