Design of Self-Assembling Materials by Ivan Coluzza

Author:Ivan Coluzza
Language: eng
Format: epub, pdf
Publisher: Springer International Publishing, Cham

3.2 Modelling DNA

3.2.1 The DNA Molecule

DNA (deoxyribonucleic acid) is a biological macromolecule composed of units called nucleotides. Each nucleotide is made of a phosphate, a sugar and a nucleobase, either A, C, G or T. Nucleotides are linked together by covalent bonds which join the sugar and the phosphate of consecutive nucleotides. The most common form of double-stranded DNA (dsDNA) is B-DNA, which is a right-handed double helix of diameter ≈2.0 nm and pitch ≈3.3 nm (roughly 10 base pairs). The helix is stabilised not only by hydrogen bonds between bases, but also by stacking interactions among the aromatic rings of consecutive nucleotides. These stacking interactions are largely responsible for the high stiffness of the double helix, which has a persistence length of ≈150 base pairs [29]. By contrast, single-stranded DNA (ssDNA) has a persistence length of a few bases. This large difference in stiffness between the two conformations is extremely important in applications, since it allows to produce hierarchical structures with tunable flexibility by employing rigid parts made of dsDNA joined together by flexible ssDNA linkers.

The structural and mechanical properties of DNA are highly dependent on external conditions. At high enough temperature T DNA is always in a single-stranded conformation. As T is lowered, base pairing becomes important and strands begin to hybridise, leading to the formation of secondary structure. The single- to double-stranded transition is identified by a melting temperature, defined as the temperature T m at which a system is half of the time in a conformation and half of the time in the other one, and by a transition width, which is a measure of the temperature range over which the transition occurs. Hybridisation of DNA duplexes is a cooperative transition, and as such its associated T m grows as the length of the strands increases. Temperature also affects, although to a lesser extent, the behaviour of single-stranded DNA having sequences that minimise secondary structure, such as poly(dA), which, at low T, exhibits stacked regions with mechanical properties intermediate between those of dsDNA and unstacked ssDNA.

Since DNA is a negatively charged macromolecule, its thermodynamic and dynamic behaviours, and to a lesser extent its structure, are affected by the ionic strength of the solution, usually measured in terms of the salt concentration c. Indeed, at high salt concentration (c ≥ 0.5 M [Na+]), at which most DNA nanotechnology experiments are carried out, electrostatic interactions are mostly screened out and the extent of the effective repulsion between DNA strands due to charges is greatly reduced with respect to physiological conditions (c ≈ 0.15 M [Na+]). Consequently, melting temperatures and association rates increase. In addition, the decrease of the DNA–DNA repulsion affects the conformation of junctions and of other motifs in regions of high local concentration. As a last point, we note that DNA conformation and mechanical properties, such as persistence length, are also sensitive to the valency of the salt in solution. For example, it has been shown that multivalent counterions can condensate dsDNA [30].

Different conditions of pH also affect DNA. In

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