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Heinz-Bernhard Kraatz

Publications and source records attributed to Heinz-Bernhard Kraatz.

At least 19 recordsLinked to original sources
PubMed2006

Study of peptide dendrimers having a ferrocene core supported on mercaptoundecanoic acid.

Hydrogen-bonding interactions between the carboxylic acid groups of mercaptoundecanoic acid (MUA) coated gold substrates and the ester surface of peptide dendrimers allows the formation of glutamic acid dendrimers films. Dendrimer films were prepared for generations 1-6 (G1-G6) and analyzed by spectroscopic and electrochemical techniques. Electrochemical studies using cyclic voltammetry and differential pulse voltammetry show that all films except those of G6 were electrochemically active. Lack of activity of G6 films is rationalized by the total encapsulation of the ferrocene redox probe by the dendritic sheath and lack of ion pairing, which prevents its oxidation.

Dendrimers↗
PubMed2006

Electrochemical detection of single-nucleotide mismatches using an electrode microarray.

Gold electrode arrays with electrode diameters of 10 mum were used for the detection of eight single-nucleotide mismatches in unlabeled and prehybridized DNA by electrochemical impedance spectroscopy (EIS). Because of the differences in the electrical properties of films of duplex DNA (normal duplex DNA in B-form) in the presence and absence of Zn(2+) at pH > or = 8.6, Randles equivalent circuits were employed to evaluate the EIS results. The difference in the charge-transfer resistance (DeltaR(CT)) between B-DNA (absence of Zn2+ at pH > or = 8.6) and M-DNA (presence of Zn2+ at pH > or = 8.6) allows unequivocal detection of all eight single-nucleotide mismatches within a 20-mer DNA sequence. After dehybridization/rehybridization with target DNA, DeltaR(CT) allows the discrimination of single-nucleotide mismatches with concentrations of the target strand as low as 10 fM. Although the presence of protein impurities (bovine serum albumin, 10 microg/mL) interferes with the detection of the target strand (1 pM detection limit), the presence of nontarget DNA (calf thymus DNA, 10(-8) M) does not interfere, and the detection limit for recognition of the target strand remains at 10 fM.

Electrochemistry↗
PubMed2006

Ferrocene-modified pyrimidine nucleosides: synthesis, structure and electrochemistry.

This paper reports syntheses, crystal structures and electrochemical results for two ferrocene(Fc)-modified pyrimidine nucleosides that could potentially be used for investigating electron transfer in DNA. Fc was directly attached to the 5-position of deoxyuridine and deoxycytidine via the Stille coupling reaction. Fc-modified uridine was incorporated into DNA trinucleotides with standard solid-phase synthesis. The structures of corresponding detritylated compounds were determined by single-crystal X-ray analysis. Electrochemical investigations of all compounds by cyclic voltammetry revealed reversible redox processes.

Crystallography, X-Ray↗
PubMed2006

Transport of alpha-helical peptides through alpha-hemolysin and aerolysin pores.

A series of negatively charged alpha-helical peptides of the general formula fluorenylmethoxycarbonyl (Fmoc)-D(x)A(y)K(z) were synthesized, where x and z were 1, 2, or 3 and y was 10, 14, 18, or 22. The translocation of the peptides through single pores, which were self-assembled into lipid membranes, was analyzed by measuring the current blockade i(block) and the duration t(block). The pores were either alpha-hemolysin, which has a wide vestibule leading into the pore, or aerolysin, which has no vestibule but has a longer pore of a similar diameter. Many thousands of events were measured for each peptide with each pore, and they could be assigned to two types: bumping events (type I) have a small i(block) and long t(block), and translocation events (type II) have a larger i(block) and shorter t(block). For type-II events, both i(block) and t(block) increase with the length of the peptides on both pores tested. The dipole moment and the net charge of each peptide has a major effect on the transport characteristics. The ratio of type-II/type-I events increases as the dipole moment increases, and uncharged peptides gave mostly type-I events. The structural differences between the two nanopores were reflected in the characteristic values of i(block), and in particular, the vestibule of alpha-hemolysin helps to orient the peptides for translocation. Overall, the results demonstrate that the nanopore technology can provide useful structural information but peptide sequencing will require further improvements in the design of the pores.

Aeromonas hydrophila↗
PubMed2006

Helically chiral ferrocene peptides containing 1'-aminoferrocene-1-carboxylic acid subunits as turn inducers.

We present a detailed structural study of peptide derivatives of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca), one of the simplest organometallic amino acids. Fca was incorporated into di- to pentapeptides with D- and L-alanine residues attached to either the carboxy or amino group, or to both. Crystallographic and spectroscopic studies (circular dicroism (CD), IR, and NMR) of about two dozen compounds were used to gain a detailed insight into their structures in the solid state as well as in solution. Four derivatives were characterized by single-crystal X-ray analysis, namely Boc-Fca-Ala-OMe (16), Boc-Fca-D-Ala-OMe (17), Boc-Fca-beta-Ala-OMe (18), and Boc-Ala-Fca-Ala-Ala-OMe (21) (Boc=tert-butyloxycarbamyl). CD spectroscopy is an extremely useful tool to elucidate the helical chirality of the metallocene core. Unlike in all other known ferrocene peptides, the helical chirality of the ferrocene is governed solely by the chirality of the amino acid attached to the N terminus of Fca. Depending on the degree of substitution of both cyclopentadiene (Cp) rings, different hydrogen-bonding patterns are realized. (1)H NMR and IR spectroscopy, together with the results from X-ray crystallography, give detailed information regarding not only the hydrogen-bonding patterns of the compounds, but also the equilibria between different conformers in solution. Differences in chemical shifts of NH protons in dimethyl sulfoxide ([D(6)]DMSO) and CDCl(3), that is, the variation ratio (vr), is used for the first time as a measure of the hydrogen-bonding strength of individual COHN bonds in ferrocenoyl peptides. In dipeptides with one intramolecular hydrogen bond between the pendant chains, for example, in dipeptide 16, an equilibrium between hydrogen-bonded and open forms is observed, as testified by a vr value of around 0.5. Higher peptides, such as tetrapeptide 21, are able to form two intramolecular hydrogen bonds stabilizing one single conformation in CDCl(3) solution (vr approximately 0). Due to the low barrier of Cp-ring rotation, new and unnatural hydrogen-bonding patterns are emerging. The systematic work described herein lays a solid foundation for the rational design of metallocene peptides with unusual structures and properties.

Carboxylic Acids↗
PubMed2006

Systematizing structural motifs and nomenclature in 1,n'-disubstituted ferrocene peptides.

Ferrocene peptide conjugates display an array of structural features including helical ferrocene based chirality and a number of different intramolecular hydrogen bonding patterns. In this tutorial review we present a rigorous nomenclature for these systems, followed by a section that summarises and categorises the structures known to date. The issues discussed herein are of general relevance for all metallocene-based chiral transition metal catalysts and peptide turn mimetics.

Ferrous Compounds↗
PubMed2006

Synthesis, characterization, and electrochemical studies on [1.1]ferrocenophanes containing aluminum, gallium, and indium.

The synthesis, characterization, structure, and electrochemistry of [1.1]ferrocenophanes, bridged by the heavier group 13 elements aluminum (1a), gallium (1b), and indium (1c), are described and discussed. Compounds 1a-c have been synthesized from dilithioferrocene and intramolecularly coordinated group 13 element dihalides Ar'EX(2) (Ar' = 2-(Me(2)NCH(2))C(6)H(4); EX(2) = AlCl(2), GaCl(2), InI(2)). Although the synthesis and characterization of 1a by single-crystal X-ray analysis has been described recently (Braunschweig, H.; Burschka, C.; Clentsmith, G. K. B.; Kupfer, T.; Radacki, K. Inorg. Chem. 2005, 44, 4906), compounds 1b and 1c are described for the first time. The galla (1b) and the inda (1c) [1.1]ferrocenophane have been characterized by single-crystal X-ray determination [1b: C(38)H(40)Fe(2)Ga(2)N(2), monoclinic, P2(1)/c, a = 10.3467(5) Angstroms, b = 11.6311(4) Angstroms, c = 14.0747(7) Angstroms, beta = 105.931(2) degrees, Z = 2; 1c: C(38)H(40)Fe(2)In(2)N(2), monoclinic, P2(1)/c, a = 10.5522(7) Angstroms, b = 11.8476(8) Angstroms, c = 13.9855(9) Angstroms, beta = 104.990(3) degrees, Z = 2]. All three compounds 1a-c are anti conformers with trans orientations of the two donating NMe(2) groups. For the [1.1]ferrocenophane 1a, an unprecedented fully reversible two-electron redox process was observed by cyclic voltammetry, whereas the corresponding Ga and In species exhibit a more conventional stepwise redox chemistry. According to the Robin-Day classification, 1a is a class I and 1b and 1c are class II species. In addition to the reversible processes, compound 1a shows an irreversible oxidation at higher voltages accompanied by adsorption processes. The irreversible adsorption process was investigated with an electrochemical quartz crystal microbalance (EQCM).

Aluminum↗
PubMed2005

Peptide electron transfer: more questions than answers.

Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.

DNA↗
PubMed2005

Chip-based microelectrodes for detection of single-nucleotide mismatch.

Microelectrode arrays having eight 10-microm-diameter gold microelectrodes arranged on a gold-covered Si chip were designed and characterized. The chips prove useful for the detection of single-nucleotide mismatches in unlabeled and prehybridized DNA by electrochemical impedance spectroscopy.

Base Pair Mismatch↗
PubMed2005

Amino acid conjugates of 1,1'-diaminoferrocene. Synthesis and chiral organization.

1,1'-bis(tert-butoxycarbonylamino)ferrocene (6), a protected derivative of 1,1'-diaminoferrocene, has been synthesized by a very convenient method and serves as a synthon for 1,1'-diaminoferrocene. Its structure in solid state and in solution has been studied by NMR and X-ray crystallography. 1,1'-bis(tert-butoxycarbonylamino)ferrocene serves as starting material for the synthesis of amino acid conjugates of L- and D-alanine. The structures of these bioconjugates have been studied by NMR and CD spectroscopy and X-ray crystallography and reveal that the chiral organization of the podant amino acid chains is controlled by the chirality of the attached amino acid. The substituents engage in strong intramolecular H-bonding generating 14-membered H-bonded rings, a motif previously unrealized in ferrocene-amino acid and peptide conjugates.

Amino Acids↗
PubMed2005

Scanning electrochemical microscopy. 51. Studies of self-assembled monolayers of DNA in the absence and presence of metal ions.

Scanning electrochemical microscopy was used to examine electron transfer across a self-assembled monolayer of thiol-modified DNA duplexes on a gold electrode. The apparent rate constant for heterogeneous ET from a solution redox probe, Fe(CN)6(3-/4-), to the gold surface through ds-DNA was 4.6 (+/-0.2) x 10(-7) cm/s. With the addition of Zn2+, which resulted in the formation of a metalated DNA (M-DNA) monolayer, the rate constant increased to 5.0 (+/-0.3) x 10(-6) cm/s. Upon treating M-DNA with EDTA, the zinc ions were released from the monolayer and the original rate constant for the DNA duplexes was restored. The enhanced ET rate was also observed at a DNA monolayer treated with Ca2+ or Mg2+, which does not complex by the DNA bases to form M-DNA. The binding of these cations facilitated the monolayer penetration by the probe mediator Fe(CN)6(3-/4-) and accordingly caused an increased redox signal of the mediator at the ds-DNA-modified electrode. Cationic or neutral mediators were not blocked by the ds-DNA monolayer. These results suggest that although the increased electron transport through M-DNA could partially be ascribed to the intrinsic enhancement of electric conductivity of M-DNA, which has been confirmed by photochemical studies, the change in the surface charge of DNA monolayers on the electrode caused by the binding of metal ions to DNA molecules may play a more important role in the enhancement of current with M-DNA.

Base Sequence↗
PubMed2005

Electrodeposition of ferrocenoyl peptide disulfides.

Using electrodeposition of cyclic and acyclic Fc-peptide disulfides tightly-packed Fc-peptide monolayers were conveniently formed, which exhibit significant differences in their electron transfer kinetics.

Disulfides↗
PubMed2004

Photophysics of pyrene-labelled compounds of biophysical interest.

The effects of the chemical constitution and structure of the substituent on the excited state dynamics of several model fluorescent pyrene-labelled molecules of biophysical interest have been examined. Nine new 1-substituted pyrenyl compounds, Py-NH-CO-C2H5, Py-NH-CO-Leu-Boc, Py-CH2-NH-CO-C2H5, Py-CH2-NH-CO-Leu-Boc, Py-CO-NH-C3H7, Py-CO-NH-Leu-OMe, Py-CH2-CO-NH-C3H7, Py-CH2-CO-NH-Leu-OMe and Py-C3H6-CO-NH-Leu-OMe, have been synthesized and their electronic spectra, fluorescence quantum yields and excited state lifetimes measured. These data have been used to calculate the radiative, kr, and non-radiative decay constants of their S1 states and the values of these constants correlated with the structures of the tethers. Non-radiative S1 decay rates (mainly intersystem crossing to T1) vary in parallel with the radiative rates so that the excited state lifetimes and radiative rate constants change considerably with the structure of the substituent whereas the quantum yields of fluorescence do not. An excellent correlation between [epsilon]max of the S1-S0 transition and either kr or the excited state lifetime is observed as long as no additional intermolecular or intramolecular excited state decay process of significant rate competes with the 'normal' radiative and non-radiative (ISC) decay processes of the pyrenyl chromophore. This correlation may have predictive value. Rates of bimolecular quenching of the S1 states of these molecules by molecular oxygen have been measured. The quenching process is diffusion-controlled with a spin statistical factor of 1, indicating that the S1-T1 electronic energy spacings of all the derivatives exceed the O2(1Deltag-3Sigmag-) electronic excitation energy of ca. 1 eV.

Journal Article↗
PubMed2004

Electrochemical detection of single-nucleotide mismatches: application of M-DNA.

The detection of a single-nucleotide mismatch in unlabeled duplex DNA by electrochemical methods is presented. Impedance spectroscopy is used to characterize a perfect duplex monolayer and three DNA monolayers differing in the position of the mismatch. The monolayers were studied as B-DNA (normal duplex DNA) and after conversion to M-DNA (a metalated duplex). Modeling of the impedance data to an equivalent circuit provides parameters that are useful in discriminating the four monolayer configurations. The resistance to charge transfer, R(CT), was lower for all duplexes after conversion to M-DNA. Contrary to expectations, R(CT) was also found to decrease for duplexes containing a mismatch. However, R(CT) was found to be diagnostic for mismatch detection. In particular, the difference in R(CT) between B- and M-DNA (deltaR(CT)) decreased from 190(22) omega.cm(2) for a perfectly matched duplex to 95(20), 30(20), and 85(20) omega.cm(2) for a mismatch at the top (distal), middle, and bottom (proximal) positions of the monolayer with respect to the gold surface. Further, a method to form loosely packed single-stranded (ss)-DNA monolayers by duplex dehybridization that is able to rehybridize to target strands is presented. Rehybridization efficiencies were in the range of 40-70%. Under incomplete hybridization conditions, the R(CT) was the same for matched and mismatched duplexes under B-DNA conditions. However, deltaR(CT) between B- and M-DNA, under incomplete hybridization, still provided a distinction. The deltaR(CT) for a perfect duplex was 76(12) omega.cm(2), whereas a mismatch in the middle of the sequence yielded a deltaR(CT) value of 30(15) omega.cm(2). The detection limit was measured and the impedance methodology reliably detected single DNA base pair mismatches at concentrations as low as 100 pM.

Base Pair Mismatch↗
PubMed2004

Synthesis, structure and electrochemistry of ferrocene-peptide macrocycles.

Redox active cyclopeptides Fc[CSA]2 (5), Fc[Gly-CSA]2 (6), Fc[Ala-CSA]2 (7), Fc[Val-CSA](2) and Fc[Leu-CSA]2 (9) (CSA = cysteamine) which are formed by the reaction of ferrocenedicarboxylic acid with peptide cystamines at high dilutions. These systems exhibit H-bonding involving the amide NH in solution as shown by their temperature dependent NMR spectra. With the exception of 5, the ferrocene macrocycles display intramolecular N...O cross-ring H-bonding in the solid state involving the amino acids proximal to the ferrocene.

Amides↗