Nucleic crystal packing

Dispersion interactions play a role of the attractive interaction between rare gas atoms and are also one of the important intermolecular interactions that govern the molecular organic world [93, 107]. Dispersion interactions are mostly responsible for the heats of sublimation of hydrocarbon molecules, make significant contributions to the solvent properties of polar and apolar neutral compounds [108, 109] and are also important for crystal packing of organic molecules [110] as well as for the stacking of nucleic acids in DNA [93, 111]. The world of dispersion interaction is rich (see [112] and references therein), despite the fact that it is a weaker form of intermolecular attractions. Dispersion forces as one of the two types of van der Waals force are also known as London forces, named after Fritz London [105, 106]. 

Later on we succeeded in partially aligning microcrystals within the sample they were placed in X-ray capillaries and pulled down by gently sucking their mother liquor, whereupon the needle-shaped crystals oriented along the capillary axis. Such samples sometimes, but only under perfect measuring conditions, produced pseudo fiber patterns which consisted of oriented arcs with average length of 60° (Fig. lb). In many cases these arcs were comj sed of distinct spots that could be clearly resolved by eye. Since such patterns may arise from partial orientation of the nucleic acid component within fairly well packed particles, these patterns indicated reasonable internal order. 

In protein crystals, due to the large size of the molecule, the empty space can have cross sections of 10-15 A or greater. The empty space between the protein molecules is occupied by mother liquor. This property of protein crystals, shared by nucleic acids and viruses, is otherwise unique among the crystal structures. In fact, the values of the packing coefficient of protein crystals range from 0.7 to 0.2, but the solvent molecules occupy the empty space so that the total packing coefficient is close to 1 [37]. Nevertheless, a detailed theoretical study has been carried out to examine the models of DNA-DNA molecular interactions on the basis of hard-sphere contact criteria. The hard-sphere computations are insufficient for qualitative interpretation of the packing of DNA helices in the solid state, but... 

Langella and coworkers validate against NMR and X-ray data their parameterizations of Peptide Nucleic Acids (PNAs) by performing MD simulations of two model systems constituted by a PNA-PNA duplex and a PNA-DNA hetero-duplex. New conformational features, related to the dynamics of the system, are found, in good agreement with the NMR data and with some difference to the crystal structure, due to packing effects. 

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