The crystal structure of di-ortho-tolylmercury

The structure of di-ortho-tolylmercury has been determined by single crystal X-ray methods from counter data. The compound crystallizes in the monoclinic space group C2/c with unit cell dimensions a 10.970(2), b 10.448(3), c 11.409(3) Å; β 115.48(2)°, V 1180.5(5) ų, ?_calc 2.158 g/cm³ and Z = 4. The structure was solved with conventional heavy atom techniques. The crystal consists of individual molecular units with the mercury atom located on the crystallographic 2-fold axis of symmetry. The CHgC fragment is nearly linear with an angle of 178.0(4)°. The methyl groups lie on the same side of the molecule and the rings are twisted with respect to one another by 58.9°. The HgC bond distance is 2.09(1) Å.     

Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Peptide nucleic acid (PNA) is a novel class of DNA analogues in which the entire sugar-phosphate backbone is replaced by a pseudopeptide counterpart. Owing to its neutral character and the consequent lack of electrostatic repulsion, PNA exhibits very stable heteroduplex formation with complementary nucleic acid that is essentially ionic strength independent and enables hybridization under minimum salt conditions. This feature as well as its superior ion stability and easy ionization compared to DNA renders PNA very attractive for hybridization-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) applications. We have developed an approach to DNA characterization that takes advantage of multiplexed PNA hybridizations analyzed by MALDI-TOFMS. Our motivation was the further development of oligonucleotide fingerprinting, an efficient technique for cDNA and genomic DNA library characterization. Through positive 'charge-tagging' of PNA the efficiency of detection in MALDI-TOFMS was considerably enhanced permitting an unparalleled degree of multiplexing. Results from the simultaneous hybridization of 21 charge-tagged PNA hexamer oligonucleotides showed that genomic DNA and cDNA clones are successfully characterized on the basis of their hybridization profiles. The degree of multiplexing achieved may render a significant increase in throughput and hence efficiency of oligonucleotide fingerprinting possible.     

Stabilization of excess charge in isolated adenosine 5'-triphosphate and adenosine 5'-diphosphate multiply and singly charged anions

Multiply charged anions (MCAs) represent highly energetic species in the gas phase but can be stabilized through formation of molecular clusters with solvent molecules or counterions. We explore the intramolecular stabilization of excess negative charge in gas-phase MCAs by probing the intrinsic stability of the [adenosine 5'-triphosphate-2H](2-) ([ATP-2H](2-)), [adenosine 5'-diphosphate-2H](2-) ([ADP-2H](2-)), and H(3)P(3)O(10)(2-) dianions and their protonated monoanionic analogues. The relative activation barriers for decay of the dianions via electron detachment or ionic fragmentation are investigated using resonance excitation of ions isolated within a quadrupole trap. All of the dianions decayed via ionic fragmentation demonstrating that the repulsive Coulomb barriers (RCB) for ionic fragmentation lie below the RCBs for electron detachment. Both the electrospray ionization mass spectra (ESI-MS) and total fragmentation energies for [ATP-2H](2-), [ADP-2H](2-), and H(3)P(3)O(10)(2-) indicate that the multiply charged H(3)P(3)O(10)(2-) phosphate moiety is stabilized by the presence of the adenosine group and the stability of the dianions increases in the order H(3)P(3)O(10)(2-) < [ADP-2H](2-) < [ATP-2H](2-). Fully optimized, B3LYP/6-31+G* minimum energy structures illustrate that the excess charges in all of the phosphate anions are stabilized by intramolecular hydrogen bonding either within the phosphate chain or between the phosphate and the adenosine. We develop a model to illustrate that the relative magnitudes of the RCBs and hence the stability of these ions is dominated by the extent of intramolecular hydrogen bonding.     

Photocontrol of DNA binding specificity of a miniature engrailed homeodomain

Control of DNA binding of HDH-3, a 18-residue polypeptide based on the recognition helix of the Q50K engrailed homeodomain, has been achieved. HDH-3 was linked to an azobenzene cross-linker through two cysteine residues in an i, i + 11 spacing. For the thermodynamically stable trans configuration of the cross-linker, the dark-adapted peptide (dad-HDH-3) adopted a mainly alpha-helical structure as judged by circular dichroism (CD) spectroscopy. After irradiation with light of 360 nm, the helical content of the peptide (irrad-HDH-3) was reduced significantly and the CD spectrum of the irradiated peptide resembled that of the largely unstructured, unalkylated peptide. Despite lacking helices-1 and -2 and the N-terminal arm of Q50K engrailed, dad-HDH-3 bound to its natural DNA target sequence TAATCC (QRE) with high affinity (K(D) = 7.5 +/- 1.3 nM). The binding affinity for the mutant DNA sequence, TAATTA (ERE), was reduced significantly (K(D) = 140 +/- 11 nM). Unlike irrad-HDH-3, which like the unalkylated parent peptide displayed only marginal DNA binding specificity, dad-HDH-3 specified base pairs 5 and 6 of QRE with an accuracy rivaling that of the intact wild-type Q50K engrailed homeodomain, making dad-HDH-3 the most specific designed DNA binding miniature homeodomain reported to date. Moreover, DNA binding affinity and specificity of HDH-3 could be controlled externally by irradiation with light.     

Controlling the DNA binding specificity of bHLH proteins through intramolecular interactions

Reversible control of the conformation of proteins was employed to probe the relationship between flexibility and specificity of the basic helix-loop-helix protein MyoD. A fusion protein (apaMyoD) was designed where the basic DNA binding helix of MyoD was stablized by an amino-terminal extension with a sequence derived from the bee venom peptide apamin. The disulfide-stabilized helix from apamin served as a nucleus for a helix that extended for a further ten residues, thereby holding apaMyoD's DNA recognition helix in a predominantly alpha-helical conformation. The thermal stability of the DNA complexes of apaMyoD was increased by 13 degrees C relative to MyoD-bHLH. Measurements of the fluorescence anisotropy change on DNA binding indicated that apaMyoD bound to E-box-containing DNA sequences with enhanced affinity relative to MyoD-bHLH. Consequently, the DNA binding specificity of apaMyoD was increased 10-fold.     

β‐Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way to β‐Peptidic Zinc Fingers?

The correlation between β²‐, β³‐, and β^2,3‐amino acid‐residue configuration and stability of helix and hairpin‐turn secondary structures of peptides consisting of homologated proteinogenic amino acids is analyzed (Figs. 1–3). To test the power of Zn²⁺ ions in fortifying and/or enforcing secondary structures of β‐peptides, a β‐decapeptide, 1 , four β‐octapeptides, 2 – 5 , and a β‐hexadecapeptide, 10 , have been devised and synthesized. The design was such that the peptides would a) fold to a 14‐helix ( 1 and 3 ) or a hairpin turn ( 2 and 4 ), or form neither of these two secondary structures (i.e., 5 ), and b) carry the side chains of cysteine and histidine in positions, which will allow Zn²⁺ ions to use their extraordinary affinity for RS^? and the imidazole N‐atoms for stabilizing or destabilizing the intrinsic secondary structures of the peptides. The β‐hexadecapeptide 10 was designed to a) fold to a turn, to which a 14‐helical structure is attached through a β‐dipeptide spacer, and b) contain two cysteine and two histidine side chains for Zn complexation, in order to possibly mimic a Zn‐finger motif. While CD spectra (Figs. 6–8 and 17) and ESI mass spectra (Figs. 9 and 18) are compatible with the expected effects of Zn²⁺ ions in all cases, it was shown by detailed NMR analyses of three of the peptides, i.e., 2, 3, 5 , in the absence and presence of ZnCl₂, that i) β‐peptide 2 forms a hairpin turn in H₂O, even without Zn complexation to the terminal β³hHis and β³hCys side chains (Fig. 11), ii) β‐peptide 3 , which is present as a 14‐helix in MeOH, is forced to a hairpin‐turn structure by Zn complexation in H₂O (Fig. 12), and iii) β‐peptide 5 is poorly ordered in CD₃OH (Fig. 13) and in H₂O (Fig. 14), with far‐remote β³hCys and β³hHis residues, and has a distorted turn structure in the presence of Zn²⁺ ions in H₂O, with proximate terminal Cys and His side chains (Fig. 15).     

Solid-phase synthesis of lipidated peptides

A new flexible and efficient methodology for the solid-phase synthesis of lipidated peptides has been developed. The approach is based on the use of previously synthesized building blocks and overcomes the limitations of previously reported methods, since long doubly lipidated peptides can be synthesized by using this route. Furthermore, it was thus possible to prepare a large number of N- and H-Ras peptides bearing a wide range of reporter and/or linking groups--efficient tools for the investigation of biological processes. In terms of efficiency and flexibility this solid-phase method is superior to the solution-phase synthesis. It gives pure peptides in multimilligram amounts within a much shorter time and with superior overall yield.     

The spherical limit forn-vector correlations

We investigate then limit of then-vector model single-spin and pairspin correlation functions. In this limit we show that the correlation functions become those of the corresponding spherical model.     

Modular and tunable chemosensor scaffold for divalent zinc

A modular peptide scaffold has been developed for fluorescent sensing of divalent zinc. The signaling component of the chemosensor is the chelation-sensitive fluorophore 8-hydroxy-5-(N,N-dimethylsulfonamido)-2-methylquinoline, which is prepared as the protected amino acid derivative Fmoc-Sox-OH and integrated into peptide sequences. Nineteen synthetic peptides incorporating the signaling element exhibit a range of affinities for Zn(2+) through variation of the type and number of Zn(2+) ligands, ligand arrangement and the beta-turn sequence that acts as a preorganization element between the ligands. The stoichiometry of the peptide-Zn(2+) complexes is evaluated by several criteria. The fluorescence response of these peptides to pH and various important metal ions is reported. Eleven of these sequences form only 1:1 complexes with Zn(2+) and their affinities range from 10 nM to nearly 1 microM. When used in concert, these sensors can provide Zn(2+) concentration information in a valuable range.     

Absolute configuration of C2-symmetric spiroselenurane: 3,3,3',3'-tetramethyl-1,1'-spirobi[3 H,2,1]benzoxaselenole

The enantiomers of 3,3,3',3'-tetramethyl-1,1'-spirobi[3 H,2,1]benzoxaselenole have been separated on a chiral preparative chromatographic column. The experimental vibrational circular dichroism (VCD) spectra have been obtained for both enantiomers in CH(2)Cl(2). The theoretical VCD spectra have been obtained by means of density functional theoretical calculations with the B3 LYP density functional. From a comparison of experimental and theoretical VCD spectra, the absolute configuration of an enantiomer with positive specific rotation in CH(2)Cl(2) at 589 nm is determined to be R. This conclusion has been verified by comparing results of experimental optical rotatory dispersion (ORD) and electronic circular dichroism (ECD) to predictions of the same properties using the B3 LYP functional for the title compound.