Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

Kinetic studies of the photopolymerisation of acrylamide in aqueous solution:effects of bromoform as a Chain transfer agent

The effects of adding bromoform (CHBr3) as a potential chain transfer agent in the photopolymerisation of acrylamide (AM) in aqueous solution have been studied both in terms of influencing the rate of polymerisation and the molecular weight of the polyacrylamide (PAM) formed. Using 4,4′-azo-bis(4-cyanopentanoic acid) (ACPA) as photoinitiator, two different CHBr3 concentrations as chain transfer agent were compared: 0.5 and 2.0 mol % (relative to AM), the higher of which was determined by the limit of CHBr3 water solubility. The results showed that CHBr3 was an effective chain transfer agent that could regulate the molecular weight of the PAM formed without seriously affecting the polymerisation rate. It is concluded that chain transfer to CHBr3occurs by both Br and H atom transfer although Br transfer is the more favoured due to the weaker C-Br bond. Furthermore, Br transfer leads to Br-terminated chains in which the terminal C-Br bond can re-dissociate leading to re-initiation and re-propagation of the same chain, thereby maintaining the polymerisation rate. Continuing studies into how this mechanism can be exploited in order to synthesize water-soluble block copolymers of potential biomedical importance are currently in progress.

Enhanced spectral sensitivity of fibre long period gratings to refractive index of aqueous solutions utilising copper patterned coatings

A set of long period grating devices have been fabricated in photosensitive single mode fibre coated with a series of copper rings (period of 380μm, 50% duty cycle and length of 4cm). The long period gratings were inscribed with a uniform UV-laser exposure across the entire length of the copper ring patterned coating. The devices ranged in copper thickness from 0.5μm to 1.5μm. In addition, a control long period grating was fabricated in the same type of fibre with the same period for comparison. The refractive index and temperature spectral sensitivity of these devices were investigated and it was found that the index and temperature sensitivity is a function of the thickness of the copper rings, as supported by theoretical modelling. Furthermore, the index sensitivity of these devices in the 1.333 index region is greater than the control long period grating. The patterned 0.5μm coated long period grating gave a sensitivity of Δλ/Δn = -74 nm leading to a resolution of 1.4×10-3 compared to the control which had a sensitivity of Δλ/Δn = -32 nm with a resolution of 3.2×10-3 in the index region of 1.320 to 1.380 (aqueous solution regime). This demonstrates a two fold increase in the sensitivity. This novel fibre long period grating device shows potential for increasing the resolution of measurements of the index of aqueous solutions.