Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches.

Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bonding and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combinations of canonical base pairs in the same location under the same conditions. For a substantial number of single mismatch configurations, 15%, the measured melting temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches. To highlight the applicability of our results, we discuss a number of practical situations such as enzyme binding affinities, thymine DNA glycosylase repair activity, and trinucleotide repeat expansions.

Exposing latent fingermarks on problematic metal surfaces using time of flight secondary ion mass spectroscopy.

Fingermarks are a key form of physical evidence for identifying persons of interest and linking them to the scene of a crime. Visualising latent (hidden) fingermarks can be difficult and the correct choice of techniques is essential to develop and preserve any fingermarks or other (e.g. DNA) evidence that might be present. Metal surfaces (stainless steel in particular) have proven to be challenging substrates from which to reliably obtain fingermarks. This is a great cause for concern among police forces around the globe as many of the firearms, knives and other metal weapons used in violent crime are potentially valuable sources of fingermark evidence. In this study, a highly sensitive and non-destructive surface science technique called time of flight secondary ion mass spectroscopy (ToF-SIMS) was used to image fingermarks on metal surfaces. This technique was compared to a conventional superglue based fuming technique that was accompanied by a series of contrast enhancing dyes (basic yellow 40 (BY40), crystal violet (CV) and sudan black (SB)) on three different metal surfaces. The conventional techniques showed little to no evidence of fingermarks being present on the metal surfaces after a few days. However, ToF-SIMS revealed fingermarks on the same and similar substrates with an exceptional level of detail. The ToF-SIMS images demonstrated clear ridge definition as well as detail about sweat pore position and shape. All structures were found to persist for over 26 days after deposition when the samples were stored under ambient conditions.