Introduction

Designed by nature for information and valued by molecular biologists for manipulation, DNA is also a favorite of physical chemists and physicists (1). Its mechanical properties (2), its interactions with other molecules (3), and its modes of packing (4) present tractable but challenging problems whose answers have in vivo and in vitro consequences. In the context of DNA transfection and gene therapy (5), what has been learned about molecular mechanics, interaction, and packing might teach us how to package DNA for more effective gene transfer. Among these modes of in vitro packaging are association with proteins, treatment with natural or synthetic cationic ''condensing agents,'' and combination with synthetic positively charged lipids (6).

In vivo, DNA is tightly held, not at all like the dilute solution form often studied in vitro (Fig. 1). This tight assembly necessarily incurs huge energetic costs of confinement, costs that create a tension under which DNA is expected to ravel or unravel its message. Through direct measurement of forces between DNA molecules (7) and direct observation of its modes of packing (8), we might see not only how to use concomitant energies to design better DNA transfer systems, but also how to better understand the sequences of events by which DNA is read in cells.

What binds these structures? To first approximation, for large, flexible biological macromolecules, the relevant interactions resemble those found among colloidal particles (9), where the size of the molecule (e.g., DNA molecules, lipid membranes, actin bundles) distinguishes it from simpler, smaller species (e.g., small solutes or salt ions). On the colloidal scale of tens of nanometers [1 nm = 10~9m], only the interactions between macromolecules are evaluated explicitly, whereas the small molecular species only ''dress'' the large molecules and drive the interactions between them.

The electrical charge patterns of multivalent ions such as Mn+2, Co3 + , or spermine+4 cation binding to negative DNA create attractive electrostatic and/or solvation forces that move DNA double helices to finite separations, despite the steric knock of DNA thermal Brownian motion (10). Solvation patterns about the cation-dressed structures create solvation forces: DNA-DNA repulsion because of water clinging to the surface, and attraction from the release of solvent (11). Positively charged histones will spool DNA into carefully distributed skeins, themselves arrayed for systematic unraveling and reading (12). Viral capsids will encase DNA, stuffed against its own DNA-DNA electrostatic and solvation repulsion, to keep it under pressure for release upon infection (13). In artificial preparations, the glue of positively charged and

Figure 1 In vivo DNA is highly compacted. The figure shows E. coli DNA and T2 bacteriophage DNA after an osmotic shock in distilled water that has allowed them to expand from their much more compacted in vivo configurations. (E. coli picture courtesy of Ruth Kavenoff, Bluegenes, Inc., Los Angeles (1994); T2 picture from Kleinschmidt et al. BBA 61 (1962) 252.)

Figure 1 In vivo DNA is highly compacted. The figure shows E. coli DNA and T2 bacteriophage DNA after an osmotic shock in distilled water that has allowed them to expand from their much more compacted in vivo configurations. (E. coli picture courtesy of Ruth Kavenoff, Bluegenes, Inc., Los Angeles (1994); T2 picture from Kleinschmidt et al. BBA 61 (1962) 252.)

neutral lipids can lump negative DNA into ordered structures that can move through lipids and water solutions (14).

Changes in the suspending medium can modulate intermolecular forces. One example is the change in van der Waals charge fluctuation forces (see below) between lipid bilayers when small sugars modifying the dielectric dispersion properties of water are added to the solution (15). More dramatic, the addition of salt to water can substantially reduce electrostatic interactions between charged molecules such as DNA or other charged macromolecules bathed by an aqueous solution (16). These changes can modify the behavior of macromolecules quantitatively or induce qualitatively new features into their repertoire among these, most notably, precipitation of DNA by addition of organic polycations to the solution (10).

Similar observations can be made about the small molecules essential to practically every aspect of interaction between macromolecules. Through the dielectric constant or dielectric permittivity, it enters electrostatic interactions; through pH, it enters charging equilibria; and through its fundamental molecular geometry, it enters the hydrogen bond network topology around simple solutes. This is, of course, the water molecule (17). In what follows, we limit ourselves to only three basic properties of macromolecules—charge, polarity (solubility), and conformational flexibility—that appear to govern the plethora of forces encountered in biological milieu. It is no surprise that the highly ordered biological structures, such as the quasicrystalline spooling of DNA in viral heads or the multilamellar stacking of lipid membranes in visual receptor cells (Fig. 2), can be explained through the properties of a small number of fundamental forces acting between mac-romolecules. Detailed experimental as well as theoretical investigations have identified hydration, electrostatic, van der Waals or dispersion, and conformational fluctuation forces as the most fundamental interactions governing the fate of biological macromolecules.

Our intent here is to sketch the measurements of these operative forces and to dwell on concepts that rationalize them. It is from these concepts, with their insight into what controls organizing forces, that we expect people to learn to manipulate and package DNA in more rewarding ways.

0 0

Post a comment