Structural Engineering of DNA (With Diagram)

1. Engineering principles in DNA structure:

In 1953 Pauling had observed that physical structure of DNA might be some sort of a-helix.

Watson and Crick’s model show that by engineering physics DNA is organised as a double helix of nucleotides in which two nucleotide helix were wound around each other.

Components were held at certain distances and/or angles to each other. Each full turn structure of the helix follows certain design engineering dimensional measurement and configurationally features. These measurements were in agreement with those obtained from X-ray diffraction pattern of DNA.

The DNA double helix can adopt several conformations depending on nucleotide sequence and environmental conditions. Conformational design found in right handed DNA double helix is generally classified into two different types, A and B. The two types differ greatly in their base stacking overlaps and sugar packing modes. Stacking interaction has, therefore, been assumed to play a dominant role in determining the sequence dependent design of double helical DNA.

This design analysis has been confirmed by ab initio molecular orbital method. Energies of molecular orbitals of DNA or RNA varied from lowest empty orbitals to highest occupied orbitals. In intra-strand and inter-strand stacking interactions these energies have great significance. X-ray studies on single crystals of oligo-nucleotides have shown the detailed geometric design of DNA double helix to change from base to base pair and to be highly dependent on base sequences.

2. Biochemical/chemical structural unit design:

The fundamental biochemical/chemical organizational element of DNA is the sequence of purine (adenine A and guanine G) and pyrimidine (cytosine C, thymine T and uracil U) bases. Structurally these bases are attached to the C-1 position of the sugar deoxyribose and the bases are linked together through joining of the sugar moieties at their 3′ and 5′ positions via a phospho-diester bond (Fig. 2.6).

In each turn of the DNA double helix 10 dimer nucleotides are equally spaced from each other. It shows that the four nitrogenous bases of DNA did not occur in equal proportions. The total amount of pyrimidines equaled the total amount of purines (A + G = T + C). In addition the amount of adenine equaled the amount of thymine (A = T) residues and likewise for guanine and cytosine (G = C).

In order to account for Pauling’s observation Watson and Crick proposed that in biochemical/chemical structure of DNA the sugar-phosphate chains should be on the outside and the purines and pyrimidines on the inside, held together by hydrogen bond between bases of opposite chains/strands. When the two chains of the helix were tried to put together it was found that the chains fitted best when they ran in opposite directions. Moreover, because X-ray diffraction studies specified the diameter of the helix to be 20 A the space could only accommodate one purine and one pyrimidine. The alternating deoxyribose and phosphate groups form the backbone of the double helix.

The 3′-5′ linkages of the DNA molecule define the orientation of a given strand of the DNA molecule. Base pairing is one of the most fundamental bio-concept of DNA structural engineering and function. Adenine (A) and thymine (T) always pair by hydrogen bonding as do guanine (G) and cytosine (C). These base pairs are said to be complimentary.

In structural design of DNA/RNA, therefore, certain design engineering dimensions and conformation nature/feature were followed. For a common DNA these dimensions and conformation nature and feature may be listed as given in Table 2.3.

3. Electronic structural features:

The electronic spin density distribution in anionic bases of DNA/RNA structures is given in Fig. 2.7. They represent unique character for their interactive role. The double helical structure of DNA has been considered as a polymer construct from ten dinner units of stacked base pairs.

In taking into account both hydrogen bonds and nearest neighbour stacking interaction these units are of the smallest compounds of DNA polymers. Methods are now available to investigate the electronic structures induced by the differences in nearest neighbour stacking interactions.

The electronic spin density distribution in anionic bases of DNA/RNA provides unique character of their interactive role. The double helical structure of DNA has been considered as a polymer constructed from ten dimer units of stacked base pairs. In taking into account both hydrogen bonds and nearest neighbour stacking interaction, these units are the smallest components of DNA polymers.

Methods are now available to investigate the electronic structures induced by the differences in nearest-neighbour stacking interactions. Thus electron donor-electron acceptor features of DNA are of great importance. These features relate to resonance stabilization of the base pairing, best possible orientation of the bases, and the evolution of the resonance stabilization in the course of the de novo synthesis and enhanced activity of phosphate clusters in electrophilic reaction.

Therefore, significance of electronic/ionic potential in DNA/RNA molecules bears information in relation to biotechnological implications in terms of mutations and/or genetic engineering or genetic recombination reactions giving trans-formants.

The electron donor – electron acceptor properties of DNA bases as has to be estimated in terms of energy coefficients of molecular orbital’s and given in Table 2.4 below is important. The importance of the energies and features relates to resonance stabilization and enhanced activity of phosphate clusters in electrophilic reaction.

Table 2.4 Energy coefficient of molecular orbital’s of base compounds of DNA

The estimation of intrinsic energies (Ei) of the molecular orbitals was carried out using the following relation and considering the mobile or n electrons of the molecular system.

Ei = α + Kiβ (2.7)

In this relation α is known as Coulomb Constant, β is resonance integration constant of the method and Ki is a factor dependent on the type of molecular orbital. Positive values of Ki correspond to occupied or bonding type of orbitals. Negative values of Ki correspond to empty or anti-bonding type of orbital’s. As can be seen from the Table 2.4 that energies of molecular orbital are of DNA varied from lowest empty orbital’s to highest occupied orbitals.

These energies are concerned with the following importance:

a. Resonance stabilization of the base pairing

b. The specific pairing is based entirely on the best possible orientation of the bases in the DNA double helix

c. The evolution of the resonance stabilization in the course of the de novo designing of DNA/RNA

The presence of lone pair (n) and n electrons in DNA bases as given in Table 2.5 bears significance of their electronic or ionic potential as presented in Table 2.6 and implications in biotechnology as listed in Table 2.7.

In general, the double helical structure of DNA has been considered as a polymer constructed from ten dimer units of stacked base pairs. In taking into account both hydrogen bonds and nearest neighbour stacking interaction these units are the smallest components of DNA polymers.

Present available methods for investigations of electrons structures induced by the differences in nearest – neighbour stacking interactions results electron donor – electron acceptor features in DNA molecules. These features relate to resonance stabilization in the course of de novo enhanced activity of phosphate clusters in electrophilic reaction. Therefore, significance of electronic/ionic potential in DNA/RNA molecules bear information’s in relation to biotechnological implications in terms (Table 2.7) of mutations and/or bio-molecular redesign engineering giving trans-formants.

4. Other engineering concerns:

Besides above considerations, other engineering inputs like mechanical structural concerns are also very important because in DNA structure one may note the following (Fig. 2.8 A and B)

(i) Each DNA helix turn is made to slide over the adjacent turn.

(ii) The pitch is held constant.

(iii) The pitch length/turn of the helix may change by an amount equal to the slide per turn.

These are related to the tension in DNA helix.

i. Some bacterial pathogen e.g. Chlamydia trachomatis contains an enzyme called ribo-nucleotide reductase that’s essential for making and repairing DNA.

5. Other molecular engineering concerns:

From the above concerns the number of turns in the helix

n₀ = L/2πr₀

Where L is the arc length per turn of the helix, r₀ = helix redius. The axial length, h₀ of the helix is

h₀ = n₀p (2.9)

Expressing as a function of r

h = pL/2πr, p is the pitch of the helix

Since L is the arc length per turn a decrease in arc represent a decrease in r. If s is the amount of slide to each turn relative to the one below then

s = 2π (r₀ – r)

Or r = r₀ – s/2π

Combining

h = pL/2πr₀ – s

The mechanical structural engineering parameter allows one to examine the relationship between a single helix and a system of several coaxial helices (m) of the same sense all lying on the same cylindrical surface. Considering each helix has a radius r₀ equal to the radius of the single helix and the same axial length h₀ and if p be the constant axial spacing separating adjacent helices then every helix in the set will have a pitch mp. It can be seen now that each one has (n_o/m) turns and the length of each helix h₀ must be (L/m). So the relation between h and r for each helix in the multiple helix system may become

h = (mp) (L/m)/ 2πr = pL/2πr

Which being  suggests that the same relation governs the dependence of h upon r in either a single on a multiple helix system. The relation of r and h as function of s considers

2πr ₀ – 2πr = ms

Provided there are m helices and s is the slide of one turn over the adjacent turn below. This is valid if

r >> mp

Thus for multiple helix system

r = r₀ – ms/2π (2.16)

and h = pL/2πr₀-ms

Now by principle of virtual work or by a force triangle analysis

T = rF

Where T = tension in the helix, r = radius of the helix and F is the outward force (Fig. 2.8 B) from the solid per unit arc length along the helix. This needed assumption that

r » n

The tension in helix and other in vivo DNA design properties are important in multi-forked chromosomal replication and division and overcoming plasmid DNA species barriers. From the above discussion on structural design engineering of DNA and scope of its design modifications one may think of the concerned facets as shown in Fig. 2.9. It also indicates the importance of in vivo design modification of DNA where transcription meets repair.