Minimalist protein design: a beta-hairpin peptide that binds ssDNA

A 28-residue beta-hairpin dimer (WKWK)2 with two Trp and two Lys residues on one face of each beta-sheet was shown to form a complex with single-stranded oligonucleotides at low micromolar concentrations. Each beta-hairpin of the dimer contains a cross-strand Trp-Trp pair in a diagonal orientation which has previously been shown to create a cleft for the intercalation of aromatic guests such as adenine (J. Am. Chem. Soc. 2003, 125, 9580). The beta-hairpin dimer binds 5-residue ssDNA sequences 5'-AAAAA-3', 5'-TTTTT-3', and 5'-CCCCC-3' in water with dissociation constants in the range of 12-30 muM. A weak energetic preference for binding to sequence 5'-AAAAA-3' was observed, which is believed to result from stronger stacking interactions between Trp and the adenine base. The interaction of 5'-AAAAA-3' with the Lys and Trp residues of the peptide was evident by NMR, and a 1:1 association was demonstrated. The recognition of an 11-residue ssDNA sequence occurred with a dissociation constant of 3 muM under near-physiological ionic strength and pH, demonstrating that the beta-hairpin dimer binds ssDNA as strongly as many naturally occurring proteins. The salt dependence of the interaction of the 11-residue oligonucleotide with the peptide dimer indicates that Trp-nucleobase stacking interactions contribute about -4 kcal/mol to recognition, which is much greater than the contribution of nonionic interactions in unstructured peptides containing Trp. Moreover, recognition of the ssDNA demonstrated reduced salt dependence relative to the corresponding duplex, resulting in selectivity for ssDNA under high salt conditions. Peptide (WKWK)2 is a relevant mimic of OB-fold (oligonucleotide/oligosaccharide-binding) proteins which bind ssDNA on the surface of a beta-sheet.     

Atmospheric chemistry of dimethyl phosphonate, dimethyl methylphosphonate, and dimethyl ethylphosphonate

Rate constants for the reactions of OH radicals and NO3 radicals with dimethyl phosphonate [DMHP, (CH3O)2P(O)H], dimethyl methylphosphonate [DMMP, (CH3O)2P(O)CH3], and dimethyl ethylphosphonate [DMEP, (CH3O)2P(O)C2H5] have been measured at 296 +/- 2 K and atmospheric pressure using relative rate methods. The rate constants obtained for the OH radical reactions (in units of 10(-12) cm3 molecule(-1) s(-1)) were as follows: DMHP, 4.83 +/- 0.25; DMMP, 10.4 +/- 0.6; and DMEP, 17.0 +/- 1.0, with a deuterium isotope effect of k(OH + DMMP)/k(OH + DMMP-d9) = 4.8 +/- 1.2. The rate constants obtained for the NO3 radical reactions (in units of 10(-16) cm3 molecule(-1) s(-1)) were as follows: DMHP, < 1.4; DMMP, 2.0 +/- 1.0; and DMEP, 3.4 +/- 1.4. Upper limits to the rate constants for the O3 reactions of < 8 x 10(-20) cm3 molecule(-1) s(-1) for DMHP and < 6 x 10(-20) cm3 molecule(-1) s(-1) for DMMP and DMEP were determined. Products of the reactions of OH radicals with DMHP, DMMP, and DMEP were investigated in situ using atmospheric pressure ionization mass spectrometry (API-MS) and, for the DMMP and DMEP reactions, Fourier transform infrared (FT-IR) spectroscopy. API-MS analyses showed the formation of products of molecular weight 96 and 126, attributed to CH3OP(O)(H)OH and (CH3O)2P(O)OH, respectively, from DMHP; of molecular weight 110, attributed to CH3OP(O)(CH3)OH, from DMMP; and of molecular weight 124 and 126, attributed to CH3OP(O)(C2H5)OH and (CH3O)2P(O)OH, respectively, from DMEP. FT-IR analyses showed formation (values given are % molar yields) of the following: from DMMP, CO, 54 +/- 6; CO2, 5 +/- 1 in dry air; HCHO, 3.9 +/- 0.7; HC(O)OH, < 1.4 in dry air; RONO2, approximately 4; and formate ester, approximately 8; and from DMEP, CO, 50 +/- 7; CO2, 11 +/- 4; CH3CHO, 18 +/- 8; HCHO, < 7; HC(O)OH, < 6; RONO2, < or = 5; and formate ester, 5.0 +/- 1.5. Possible reaction mechanisms are discussed.     

Photocatalytic Activity of Supported Metal Nanoparticles and Single Atoms

Photocatalysis has been known as one of the promising technologies due to its eco-friendly nature. However, the potential application of many photocatalysts is limited owing to their large bandgaps and inefficient use of the solar spectrum. One strategy to overcome this problem is to combine the advantages of heteroatom-containing supports with active metal centers to accurately adjust the structural parameters. Metal nanoparticles (MNPs) and single atom catalysts (SACs) are excellent candidates due to their distinctive coordination environment which enhances photocatalytic activity. Metal-organic frameworks (MOFs), covalent organic frameworks (COFs) and carbon nitride (g-C₃N₄) have shown great potential as catalyst support for SACs and MNPs. The numerous combinations of organic linkers with various heteroatoms and metal ions provide unique structural characteristics to achieve advanced materials. This review describes the recent advancement of the modified MOFs, COFs and g-C₃N₄ with SACs and NPs for enhanced photocatalytic applications with emphasis on environmental remediation.     

Toward Fluorescence‐Based High‐Throughput Screening for Enantiomeric Excess in Amines and Amino Acid Derivatives

A highly accurate and reliable screening method for enantiomeric excess of amine derivatives in the presence of water is reported. The fluorescence‐based screening system has been realized by self‐assembly of chiral diol‐type dyes (BINOL, VANOL and VAPOL), 2‐formylphenylboronic acid, and chiral amines forming iminoboronate esters. The structure and chirality of the amine analytes determine the stability of the diastereomeric iminoboronate esters, which in turn display differential fluorescence. The fluorescence signal reflects the enantiomeric purity of the chiral amines and was utilized in high‐throughput arrays. The arrays were able to recognize enantiomeric excess of amines, amino esters, and amino alcohols. In addition to qualitative analysis, quantitative experiments were successfully performed. Studies of the role of additives such as water or citrate were carried out to gain insight into the stability of the iminoboronate esters. It is shown that the above additives destabilize less stable esters while the stable esters remain unchanged. Thus, the presence of water and citrate leads to increased difference between the diastereomeric iminoboronates and contributes to the enantiodiscrimination of the chiral amines.     

Meeting Report: UK SR User Meeting

Diamond Light Source was delighted to welcome more than 250 delegates to the annual UK SR User Meeting on September 12–13, 2006. Trevor Rayment, of Birmingham University and chair of the UK SR Forum, welcomed delegates to the proceedings and invited Gerd Materlik, the CEO of Diamond, to give his progress report on Diamond.