Have the primary structures of biomacromolecules been selected in a Darwinian fashion to adapt to the surrounding environments of our planet?

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Paolo Ascenzi

Water is the most important environment of lives. In recent studies, the effects of aqueous environment on the supramolecular structure of DNA have been investigated by means of single molecule force spectroscopy. On one hand, the small energy cost of the water rearrangement upon the duplex formation ensures the stability of double-stranded DNA (dsDNA) in the aqueous environment. In contrast, by shaving off the water molecules binding to the duplex, dsDNA is destabilized and tends to be unwound. The aqueous environment is found to be crucial to the proper structure and function of DNA. In the other way around, we believe, it is more likely that the molecular structure of DNA was selected via the prebiotic chemical evolution from the ancestor molecules in a Darwinistic fashion, because the aqueous environment is an elementary condition of our planet.

It is assumed as a general strategy that to survive, all organisms have to adapt to the surrounding environments. This hypothesis is supported by plenty of living examples discovered at the macroscopic level. (1). Note that each organism is composed of numerous biomacromolecules, which substantially govern the macroscopic behavior of the life. Thus, are the biomacromolecules also environmental adaptable?

It is generally accepted that on our planet, the primitive life originates from the ocean or the seashore (2). Approximately 70% of the surface of our planet is covered by water. Moreover, more than half space of a living cell is filled with water. No living organism can survive without water. Therefore, it is reasonable to note that water is the most important environment of lives. In this way, the environmental adaptability of biomacromolecules should be embodied as the adaptability to aqueous environment. This environmental adaptability here can be expressed as follows: the molecular structures of the biomacromolecules are specially designed to fit the aqueous environment, where the biomacromolecules adopt proper structures and present proper functions.

Compared with proteins and RNA, the higher level structures of DNA are more uniform for all organisms. This feature entitles DNA the most appropriate object in a pilot study to demonstrate the hypothesis described in the above question. Recently, by utilizing single-molecule force spectroscopy, (3–5) Cui et al. carried out systematic investigation on the effects of the aqueous environment on the structures and functions of DNA, which present supportive evidences for the hypothesis (6–8).

THE EFFECTS OF ENVIRONMENT ON THE FORMATION OF THE DUPLEX

The self-assembly from single-stranded DNA (ssDNA) to double-stranded (dsDNA) is usually formularized below, where ssDNA′ denotes the complimentary chain of ssDNA:

• (1)

It has long been known that both ssDNA and dsDNA are hydrated in the aqueous solution (9,10). It is also clear that dsDNA has less binding sites with water than that of the sum of the two free ssDNA chains. Therefore, a partial dehydration process should occur prior to the self-assembly of ssDNA. Thus, eq. 1 should be revised into a more strict form as follows:

• (2)

Whether the supramolecular self-assembly described in eq. 2 can occur is hinged on the free energy change (ΔG₂) of the process, which was determined by differential scanning calorimetry to be −4.3 kJ/(mol·bp) (11). Like other complex reactions, eq. 2 can be separated into the following two simpler steps:

• (3)

• (4)

• (5)

All the water rearrangement is completed in eq. 3, whereas all the assembly between ssDNA chains occurs in eq. 4. It is reasonable to assume that the partial dehydration (eq. 3) is a non-spontaneous process (i.e., ΔG₃ > 0), whereas the self-assembly of the two ssDNA chain (eq. 4) is a spontaneous one (i.e., ΔG₄ < 0). Given that the total process in eq. 2 is a spontaneous one, the Gibbs free energy necessary to partially remove the hydration shell of the ssDNA (eq. 3) must be compensated (or overcompensated) by the Gibbs free energy of the basepairing (eq. 4). However, ΔG₃ (or ΔG₄) is neither a ready data in references, nor a value can be measured easily by traditional ensemble methods.

Recently, Cui et al. have simulated the process of the partial dehydration (eq. 3) by manipulating an individual ssDNA chain in aqueous solutions and organic non-solvents, respectively (6,8). The interactions between the non-polar organic solvent molecules and the solute molecules are van der Waals interactions in general, which are the weakest intermolecular interactions. In this condition, it is to be expected that the solute molecules' behavior is close to that in the vacuum condition. Therefore, we were able to obtain the inherent elasticity of a single ssDNA chain by stretching it in organic non-solvents. The experimental inherent elasticity is consistent with the theoretical value that obtained from ab-initio calculations (6,8,12). Similarly, the elasticity of ssDNA was obtained in aqueous environments. A comparison between the mechanical behaviors of ssDNA in the two environments reveals a remarkable difference, see Fig. 1.

Figure 1. The comparison of normalized force-extension curves obtained in different environments, i.e., aqueous solutions (black curve) and organic non-solvents (red curve). The force curves are smoothed and zoomed in to show a clearer deviation between them. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

There are many functional groups containing H-bonding acceptors and donors in ssDNA chain. SsDNA is soluble in water, and can form H-bonds with water molecules in various combinations. It is possible that one water molecule can form two H-bonds with one ssDNA molecule and create a water “bridge” around ssDNA chain (13,14). To meet the length requirement of the water “bridge”, the ssDNA chain may be shortened in some extent. Upon stretching by external force, the ssDNA chain is lengthened and the length requirement no longer meets, which will break the water “bridges” consequently. The rearrangement of water molecules around the ssDNA chain will consume additional energy besides those contributions stored in the “pure” elastic behavior. In this way, the elongation of ssDNA in water will consume more energy (0.58 k_BT/base, or 1.4 kJ/mol·base) than that consumed in organic solvents, as reflected by the deviation between the force curves shown in Fig. 1.

The rearrangement of the water molecules around the ssDNA chain upon stretching can be considered as partial dehydration (eq. 6); ΔG₆ = 1.4 kJ/mol·base.

• (6)

It can be observed that eq. 6 and eq. 3 are very similar. Although the values of z and y/2 are not necessarily to be identical, the free energy changes of the two equations are expected to be very close, i.e., ΔG₃ ≈ ΔG₆.

Then, we can estimate that the ΔG₄ ≈ −5.7 kJ/mol·base by eq. 5. Note that the value of ΔG₄ is not far from zero, making the eq. 2 rather sensitive to ΔG₃. Comparing with other systems having water rearrangement upon stretching, it is found that ssDNA costs the lowest energy among them (6,13,14). The rather small value of ΔG₃ is crucial to life: If ΔG₃ is a much larger value like the poly(N-vinyl-2-pyrrolidone)/water system (13.0 kJ/mol·unit) (13) or the poly(ethylene-glycol)/water system (7.2 kJ/mol·unit) (14), ΔG₂ would be larger than zero, and the self-assembly from ssDNA to dsDNA will not be a favorable process. We may conclude that it is the weak disturbance of water molecules on ssDNA that makes the self-assembly possible.

THE EFFECTS OF ENVIRONMENT ON THE DISSOCIATION OF THE DUPLEX

To read the gene information encoded in dsDNA, the strands of the double helix need to be separated. There are several traditional methods to dissociate the duplex in vitro, including thermal induced melting and reagent denaturation. However, almost all organisms live in a temperature below that needed to melt dsDNA, nor can a cell contain a high concentration of denaturant like urea. It is clear that a different mechanism should be exploited to dissociate the duplex in vivo.

Previous extensive studies showed that in aqueous environment, the DNA duplex was maintained by several weak intermolecular interactions, including hydrogen bond, pi-pi stacking, van der Waals interactions and hydrophobic force. Differ from the covalent bond, these weak intermolecular interactions are known to be environment dependent (15), see Table 1. It is expected that if a different environment, e.g., a non-polar one, is provided for dsDNA, the total binding force within the duplex will be weakened. Previous ensemble measurements showed that non-polar organic solvents are poor solvents for dsDNA, where dsDNA condensated or even precipitated (16–18). Other detailed information of DNA in poor solvents is still unclear. The ensemble measurement methods encountered limitations here.

Table 1. Intermolecular interactions involved in the dsDNA assembly (15)

	In aqueous solutions	In non-polar organic solvents
H-Bonding	√	√
pi-pi stacking	√	√
VdW	√	√
solvophobic effect	√	×

Recent single-molecular studies by Cui et al. showed that when DNA is dragged into a non-polar organic solvent, the mechanical behavior of a dsDNA molecule is undistinguishable to that of an ssDNA molecule, see Fig. 2 (7). Since it was already known that the mechanical behavior can be a fingerprint to identify the stranding status of DNA, (19–21) the above result implies that dsDNA is denatured in a non-polar organic solvent. Control experiments indicated that different non-polar organic solvents have the same effect on dsDNA. Possible influences from the substrate were also excluded, for that similar results could be obtained from different type of substrates. These results strongly suggest that the non-polar organic solvents have similar effects that denature dsDNA into ssDNA. This hypothesis was supported by molecular dynamics (MD) simulations, which showed that dsDNA underwent a strand separation at the interface of the two kinds of liquids (7).

Figure 2. Normalized force curves of denatured dsDNA (blue line) and ssDNA (black line) both obtained on amino-modified substrate in 1-propanol. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

The solvents can be classified into two types, according to the stranding status of DNA, see Table 2 (7,22). It can be seen that the double-stranded structure is only maintained in water and water-like solvents, which have multi-hydroxyl groups. Other solvents, despite the large difference in polarity, are denaturant for dsDNA actually. Note that for most time, DNA exists in its double-stranded status. When needed, dsDNA is unwound into ssDNA by enzymes. Another fact is that water is the usual environment for DNA, while the enzymes seem to provide an unusual environment. Those local environments, which are helpful to remove the water shell around DNA, are expected to destabilize the supramolecular structure and unwind the duplex at the binding position. If this mechanism is truly happening in vivo, the phenomenon of the diversity of helicases can also be explained, since various micro-environments, ranging broadly from very apolar to very polar (see Table 2), can lead to strand separation.

Table 2. The stranding status of DNA and the corresponding liquid environments (7,22)

Stranding status of DNA	Mono-solvent liquid environment
Double-stranded	Water, glycerol and ethylene glycol
Single-stranded	DEBenzene, octane, 1-propanol, DMSO, and formamide

CONCLUSION AND IMPLICATIONS

As discussed in the previous sections, the aqueous environment plays a crucial role in the regulation of supramolecular structure of DNA, see Scheme 1. On one hand, the small energy cost of the water rearrangement upon the duplex formation ensures the stability of dsDNA in the aqueous environment. On the other hand, by shaving off the water molecules binding to the duplex, dsDNA is destabilized and tends to be unwound. Water is known to be a special solvent: it usually interferes the hydrogen-bonding directed self-assembly; at the same time, liquid water provides hydrophobic forces that often drive the self-assembly of organic molecules (9,23). There are many kinds of water soluble macromolecules, but few can form stable double-stranded structure. This fact implies that DNA is somewhat special in the molecular structure. The weak intermolecular interactions involved in the duplex formation seem to be handled carefully by a delicate “design” of the primary structure of DNA, so that the self-assembly between the complementary ssDNA chains can be reversible under a facile regulation (see Scheme 1). In this way, the aqueous environment is crucial to the proper structure and function of DNA. In the other way around, we believe, it is more likely that the primary structure of DNA has been selected via the prebiotic chemical evolution from the ancestor molecules in a Darwinian fashion (24–29) to adapt to the aqueous environment of our planet. After all, the aqueous environment is an elementary condition of our planet and exists prior to DNA. The aqueous environment adaptability of other type biomacromolecules awaits further investigation in the future.

Scheme 1. The hydration/dehydration processes regulate the supramolecular structures of DNA. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

New Questions

• 1
  How can a chemically well established antioxidant work differently when in the body?
• 2
  I saw in the Internet an advertisement indicating that resveratrol can “extend your life”. How is this possible?

Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant Nos. 20774062 and 20874063). The author thanks Prof. Dr. Jean-Marie Lehn for the helpful discussion.