Protein Structure
Carboxypeptidase A
Alpha Chymotrypsin
Ribonuclease A
Receptor Sites
Double-Helix B-DNA


Download Title PDF

Double Helix B-DNA

Thus far, we have focused our attention on the role of hydration order in soluble enzymes and receptor proteins. Filamentous proteins, like collagen, actin and elastin, have hydration-ordering surfaces with hydroxyl groups in strategic locations to direct motions and associations with neighboring filaments. In contrast, double helix filaments of DNA have anionic surfaces with dielectric transient linear elements bridging between oxygens of surface phosphates and transferring charge to surrounding sodium ions. Although double helix DNA is never pictured surrounded with water, at least 13 water molecules per base pair are required to maintain it in its uniform repeating spatial B-form.28,76

In order to examine in more detail how transient linear elements of hydration may be involved in providing structural stability to the major (A) and minor (B) grooves of the B-form of double helix DNA, the helix is viewed below through three adjacent base pairs parallel to the axis.76

Double helix DNA with dielctric transient linear elements of hydration bridging between anionic oxygen atoms.

Overlaying the trimer on the standard 2.76A matrix, phosphate oxygens on opposite sides of the major groove are separated by six diagonally hydrogen-bonded water molecules (at 1), while those in the minor groove are separated by three (at 2). Although the minor groove has room for only a few water molecules to bridge between base pairs (at 3), those which bridge between A-T pairs are critical in holding the helix in its B form.77 The degree of hydration in the wide groove (at 4) is much greater and depends on the sequences of base pairs.78 Since oxygens of phosphates on adjacent base pairs on the surface can be bridged by two hydrogen-bonded water molecules (at 5), their anionic charges can be shared and dispersed out into surrounding water.

Double helix B-DNA with transient linear elements of hydration emanating out toward spherically-hydrated sodium Ions.

On the outer surfaces of the helix, water molecules are sufficiently free to continuously form transient dielectric elements of hydration, both perpendicular to the helix and diagonal to it. This permits maximum delocalization of charge and, at the same time, holds spherically hydrated sodium ions out away from the surface as they neutralize the surface charge.28

In the early 50’s, when many scientific groups were attempting to decipher the conformational structure of DNA, it was Rosalind Franklin at Kings College in London who sprayed a crystalline sample of DNA with water and obtained the interpretable diffraction pattern which was used by Watson and Crick to construct the now famous model which has become the symbol of modern molecular biology.27 Not long after that, it was found that the water which surrounds the double helix exhibits the spectral properties of the linear elements in ice and that sodium ions, which hydrate spherically, are held out away from the helix by multiple layers of “ice-like” water.28,76

The Transient Linear Hydration Model

Portraying the structure of DNA as anhydrous may be a misleading way to convey information regarding the molecular structure to the public, and yet, no natural molecules are presented as hydrated – even in text books and scientific journals. So little is known regarding the nature of surface hydration that it is rarely, if ever, portrayed. Often, X-ray crystallography, NMR and complex theoretical calculations are used to define thermodynamic positions of water molecules yet, water molecules on surfaces are not at rest – residence times are long enough to establish local stability but too short to establish thermodynamic stability with surrounding groups. Hydration order, if it exists at all, must be expressed by short-lived, kinetically-produced linear elements.

Although water on many surfaces, including DNA displays “ice like” properties,76 it does not mean that three-dimensional forms of ice are present. Based on the TLH hypothesis, it simply means that that the spin in water molecules in one short linear filament is close to those in other filaments. In fact, within and around ionic filaments, like DNA, dielectric covalent linear elements, most likely, do not conform to cubic patterning – they simply adopt whatever bridging orientation that provides a minimum in surface charge potential. The TLH model of B-DNA is illustrated with that view in mind,

The TLH Model of straight double-helix B-DNA.

In this Front View of the straight helix, six types of dielectric linear elements of hydration contribute to the uniform repeating structure. At 1, six water molecules bridge between phosphates in the wide groove. At 2, triplets bridge across the narrow groove.77 At 3, a single water molecule bridges between bases in the groove and, at 4, four water molecules bridge between surface phosphates and bases in the wide groove. At 5, two water molecules bridge between adjacent surface phosphates and, at 6, diagonal and horizontal linear elements delocalize negative charges in water molecules around the helix. At 7, spherically-hydrated sodium ions surround the helix to neutralize the charge.28 By not being bound to the helix and held out from it by multiple layers of linearizing water, hydrated sodium ions have the freedom to rotate relatively freely and retain entropy.37

Although the dynamic hydration-ordering principles described above employing quantized covalent hydrogen-bonded elements may seem contradictory to those based primarily on internal thermodynamics, it is hoped that this presentation will encourage others to explore in greater depths the role of surface water in the formation of proteins and the interactions of molecules and ions in living cells. Only then will we be able to interpret more accurately how they produce the incredible phenomenon we know as life.

Next Page