DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally employed long (400–800 bp) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intra-species genetic variation. We report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterise four million SNPs and four hundred thousand structural variants, many of which are previously unknown. Our approach is effective for accurate, rapid and economical whole genome re-sequencing and many other biomedical applications.

Semiconductor nanocrystals or quantum dots (QDs) are highly photoluminescent materials with unique optical attributes that are being exploited in an ever-increasing array of applications. However, the complex surface chemistry of these finite-sized fluorophores gives rise to a number of photophysical phenomena that can complicate their use in imaging applications. Fluorescence intermittency (FI), photoluminescence enhancement (PLE) and spectral bluing are properties of QD emission that would appear, at first sight, detrimental to quantitative measurement. Fortunately, developments in rational QD synthesis and surface modification are promising to minimize the effects of these fluorescence instabilities, while applications that exploit them are now coming to the fore. We review recent experimental and theoretical studies of FI, PLE and bluing, highlighting the benefits, as well as complications, they bring to key applications.

We have used confocal fluorescence microscopy to study the diffusion of single molecules in solution, over a wide dynamic mass range. The results have been analyzed using both Poisson and autocorrelation methods and have been shown to be consistent with diffusion theory over extended time scales. We observe deviations from statistical behavior on short time scales due to a weak optically induced trapping effect. The power dependency of this effect has been measured and shown to be in good agreement with optical trapping theory. We find that for small molecules the optical biasing effect is only significant for molecules excitated at resonance.

We have re-examined critical experiments on collision induced rotational transfer (RT) and conclude that the probability of RT is controlled by the factors that control the probability of angular momentum (AM) change. The probability of energy change seems less important in this respect. In the light of this we suggest a model for RT in which the probability of AM change is calculated directly and present a formalism for this purpose. We demonstrate that such a calculation leads to an exponential-like fall of RT probabilities with transferred AM, a consequence of the radial dependence of the repulsive part of the intermolecular potential. Thus in this AM model, the exponential gap law has a simple physical origin. The AM model we describe may be used as the basis of an inversion routine through which it is possible to convert RT data into a probability density of the repulsive anisotropy. Through this model therefore it is possible to relate experimental RT data directly to the forces that are responsible for rotational transfer. The hard ellipse model is used in this work to relate calculated anisotropies to a form that includes an isotropic component. The result is a representation of the intermolecular potential through which new insights into the RT process are gained.