Label-Free Detection of Single-Base Mismatches in DNA by Surface-Enhanced Raman Spectroscopy

Singles only: DNA sequences can be induced to spontaneously adsorb to the surfaces of Ag colloids through their nucleotide side chains (see picture). The SERS spectra of these nonspecifically bound strands are sufficiently reproducible that they can be used to identify single-base mismatches in short (25-mer and 23-mer) strands. Subtracting the spectra of different DNA sequences results in difference spectra that contain features corresponding to the exchanged nucleotides.

RESONANCE RAMAN-SPECTRA OF THE TRIPLET-STATE OF FREE-BASE TETRAPHENYLPORPHYRIN AND 6 OF ITS ISOTOPOMERS

The resonance Raman spectra of the ground state and the lowest excited tripler state of free-base tetraphenylporphyrin and six of its isotopomers have been obtained using two-color time-resolved techniques. Ground-state spectra were recorded using low-energy 447 nm probe laser pulses, and triplet-state spectra were probed, with similar pulses, 30 ns after high-energy excitation with 532 nm pump pulses. Polarization data on both the ground and triplet states are also reported. The resonance Raman spectrum of the triplet is very different from that of the ground state but the combination of extensive isotope substitution with polarization data allows bands in the ground state to be assigned and corresponding bands in the tripler state to be located. Isotope shifts of the same bands in the S-0 and T-1 states are similar, implying that the compositions of the vibrational modes do not change significantly on excitation. Two of the strongest bands in the T-1 spectra are associated with phenyl ring substituents; these are shifted less than 5 cm(-1) between the S-0 and T-1 states so that bonding in the phenyl substituents is barely affected by excitation to the T-1 state. The changes in position of the porphyrin ring bands are larger, but still only tens of cm(-1) or less, the main changes in the spectra being due to differences in relative band intensities in the two states. The relatively small shifts in the porphyrin ring band positions which are observed show that the excitation energy is not localized on a single small region of the molecule but is delocalized over the entire porphyrin skeleton. This picture of an excited species with high chemical reactivity, but with individual bonds only slightly perturbed from the ground state, is contrasted with molecules, such as benzophenone, where excitation causes a large perturbation in the bonding within a single functional group.

TIME-RESOLVED RESONANCE RAMAN-SPECTROSCOPY OF TRIPLET-STATE METALATED AND FREE-BASE TETRAARYLPORPHYRINS

Resonance Raman spectra of the T-1 excited states of Zn and free-base tetra-4-sulfonatophenylporphyrin (TPPS) have been recorded at room temperature in aqueous solution using two-colour time-resolved methods. The spectra of both sulfonated molecules are very similar to their tetraphenylporphyrin (TPP) analogues, which have been recorded in THF solution using the same pump-probe conditions, but they have higher signal-to-noise ratios because interference from strong solvent bands is reduced. Although two different T-1 spectra of Zn(TPP) have been reported these spectra differ slightly from each other and from the spectrum reported here, which has band positions very close (+/-6 cm(-1)) to those of Zn(TPPS). The high S/N ratios obtainable for the water-soluble porphyrins have allowed reliable polarization data to be recorded for their S-0 and T-1 states. This data set allows a realistic comparison of the changes in bonding associated with excitation of both free-base and Zn tetraarylporphyrins to the T-1 state.

TIME-RESOLVED RESONANCE RAMAN-SPECTROSCOPY OF EXCITED SINGLET AND TRIPLET-STATES OF FREE-BASE MESO-TETRAPHENYLPORPHYRIN

Two-color time-resolved resonance Raman spectroscopy has been used to probe the lowest excited singlet (S1) and triplet (T1) states of free-base meso-tetraphenylporphyrin and meso-tetrakis(4-sulphonatophenyl)porphyrin in solution at room temperature. The spectra were recorded using 532-nm excitation pulses and time-delayed probe pulses (DELTAT = 0-30 ns, 447 and 460 nm) near lambda(max) of the S1 and T1 states. Significant shifts in frequency of the porphyrin core vibrations were observed upon excitation to either the S1 or T1 state. Several of the strongest polarized bands in the spectra of both excited states, including nu1, nu2, nu4, nu6, and phi4, are assigned, and the information they give on the differences in electron distribution in the ground, S1, and T1 states is discussed.

Effect of column base strength on steel portal frames in fire

This paper presents the findings of a project part sponsored by an ICE Research and Development grant on portal frames in fire. The research reported here has also lead to a sucessful research grant from the IStructE. The paper describes a non-linear elasto plastic dynamic finite element model that captures the collapse of a portal frame in fire. It demonstrates that current guidance on the column base stiffness and strength, to prevent collapse, may in some cases be unconservative.

Novae in the SuperWASP data base

We present the results of trawling through the SuperWASP data base for classical and recurrent novae. We report light curves for a nova in eruption, and for classical novae and a recurrent nova in quiescence. For five objects in quiescence, we report periodicity, arising in most cases from orbital modulation of the light from the cool secondary star. The stability of the SuperWASP system means that these data have huge potential for the study not only of novae in eruption, but also of the long-term modulations of light during quiescence.

Cu-Based Nanoalloys in the Base-Free Ullmann Heterocyle-Aryl Ether Synthesis

We report the first liquid-liquid Ullmann etherification process mediated not only by oxidatively stable Cu but also by CuZn and CuSn nanoparticle catalysts in conjunction with microwave heating that also avoids the use of solid and expensive bases. Conditions have led to improved turnovers and excellent yields in heteroaromatic Ullmann-type coupling reactions. Further enhancement is achieved upon the addition of 18-crown-6 as a kinetic promoter.

A nine-base nucleotide sequence in the porcine circovirus type 2 (PCV2) nucleocapsid gene determines viral replication and virulence

Porcine circovirus type 2 (PCV2) was retrospectively identified by serology in swine populations as an asymptomatic infection at least 25 years prior to the first reported case of PCV2-associated postweaning multisystemit wasting syndrome (PMWS). To investigate the sudden emergence of PMWS, viral sequences were amplified from frozen archived (1970-1971) porcine tissues and the complete genome of archival PCV2 was determined. The ORF1 gene product (viral DNA replicase) was homologous to contemporary PCV2 ORF1. In ORF2 (viral nucleocapsid gene) archival PCV2, a consistent linear nine-base sequence difference at base positions 1331 through 1339 was observed.The deduced amino acid sequence from these base changes alters the nucleocapsid conformation within the second immunogenic epitope from a hydrophobic (contemporary PCV2) to a hydrophilic (archival PCV2) configuration.

An Evidence Base to Inform Rural Policy.:Department of Agriculture and Rural Development Northern Ireland.

Funded by ESRC Knowledge Research Fellowship Programme.

New anti-HIV aptamers based on tetra-end-linked DNA G-quadruplexes: effect of the base sequence on anti-HIV activity.

This communication reports on the synthesis and biophysical, biological and SAR studies of a small library of new anti-HIV aptamers based on the tetra-end-linked G-quadruplex structure. The new aptamers showed EC(50) values against HIV-1 in the range of 0.04-0.15 µM as well as affinities for the HIV-1 gp120 envelope in the same order of magnitude