Clive Delmonte

The Paranaemic Structure for DNA
clivedelmonte@notahelix.com

 

Clive Delmonte is the creator of the Paranaemic Model of DNA structure. The word "paranaemic" implies a structure which is untwisted, or, to employ the language of this web site, a structure whose strands are "topologically non-linked (i.e., a "TN" structure).

The opposite, a twisted structure, is referred to as "plectonaemic". The Watson-Crick ("W-C") model is the best-known example of a plectonaemic structure.

A simple line drawing, shown to the right, will illustrate the concept. The structure is really quite similar to both the Watson-Crick structure and the Rodley Side-By-Side structure, but has several unique features. The sugar-phosphate backbones are antiparallel right-handed helices, but they don't cross one another, and the two strands are therefore topologically non-intertwined. This means that any circular chromosome having this structure can replicate without the need to break strands, unwind twists, or re-wind twists in the next generation.

The A-T and C-G base pairs in the Paranaemic Model are presumed to be the "standard" base pairs found in the W-C structure. There are 10 per helical turn, with an interbase distance/pitch close to the 3.4/34 angstrom dimensions of the "traditional" model.

The structure differs further from the W-C model in being asymmetric, compared with the traditional double helix, which is the same no matter what angle it is view from. In the words of Delmonte:

"There are two antiparallel right-handed sugar-phosphate helices, lying side by side with the phosphate charges around the outer edge of each helix, and in phase in the B form, with the Watson-Crick base pairs stacked on the same face of the duplex. Each individual helix has a diameter of 1.2 nm, giving the structure a minor axis of 1.2 nm, and a major axis of some 2.1 nm -- the dimensions reported by James & Mazia -- with a pitch of 3.4nm as in the double helix".

The investigators T.W. James and D. Mazia, whom they quote here (reference: Biochim Biophys Acta, 1953, 10:367-370), published a study of so-called "Langmuir troughs", in which a precisely-measured quantity of DNA is spread on the surface of a solution in such a way that the DNA forms a monolayer, i.e., a film exactly one molecule thick. By carefully measuring the dimensions of the film it was possible for James and Mazia to calculate the 1.2 nm dimension of [what Delmonte would call] the minor axis of DNA. The major axis dimension of 2.1 nm was calculated by Delmonte from other published data.

In the W-C model of DNA, the angular relationships between the bases and the sugar-phosphate backbone is everwhere the same. In the Paranaemic Model, each of the 10 bases in the repeat unit of the structure has a slightly different angular relationship with the sugar-phosphate backbone. This is difficult to depict in a longitudinal drawing. Axial drawings are available in Delmonte's books, of which there are three. The first, "Toward A New Structural Molecular Biology", is reproduced in its entirety on this web site (see below).

To the right is a framework molecular model of the Paranaemic Model, which will be helpful for those who can appreciate such models.

 

To see a full size picture of the framework molecular model shown to the right, click here.

 

To see a space-filling model, click here.

 

To read "Toward A New Structural Molecular Biology", click here.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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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    Reference

     

    Delmonte, C.S. and Mann, L.R.B. (2003). Variety in DNA secondary structure. Curr Sci 85(11), 1564-1570.

     

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