PubMed Health⌕ Search

Biomedical subjects

Roland Krämer

Publications and source records attributed to Roland Krämer.

At least 19 recordsLinked to original sources
PubMed2006

Probing single-stranded DNA and its biomolecular interactions through direct catalytic activation of factor XII, a protease of the blood coagulation cascade.

Triggered self-activation of factor XII, a blood coagulation protease, was utilized for the amplified visual detection of ss-DNA targets in a non-sequence specific way. Factor XII holds potential as a low-affinity and therefore non-interfering probe for DNA secondary structure and for the screening of protein binding to ss-DNA. The observation that ss-DNA also accelerates coagulation of human blood plasma is relevant to the emerging field of aptamer therapeutics.

Blood Coagulation↗
PubMed2006

Zn2+ dependent DNA binders based on terminally modified peptide nucleic acids.

Two ligand-intercalator-peptide nucleic acid conjugates (L-NADI-PNAs) have been synthesized. Affinity of these conjugates to their complementary DNAs was found to be affected by Zn(2+). The magnitude of this effect could be controlled by a variation of the ligand. Upon binding Zn(2+) the L-NADI-PNAs form positively charged ZnL complexes, which interact with the negatively charged DNA backbone. This electrostatic interaction stabilizes PNA/DNA duplexes. It has been found that Zn(2+) dependent stabilization takes place only if the ZnL complex has a higher total positive charge than the ligand. Linear correlation has been observed between Zn(2+) induced stabilization of PNA/DNA duplexes and difference of charges of the ZnL complex and the ligand.

DNA↗
PubMed2005

Catalytic transesterification of dialkyl phosphates by a bioinspired dicopper(II) macrocyclic complex.

For a number of phosphoryltransfer enzymes, including the exonuclease subunit of DNA polymerase I, a mechanism involving two-metal ions and double Lewis-acid activation of the substrate, combined with leaving group stabilization, has been proposed. Inspired by the active site structure of this enzyme, we have designed as a synthetic phosphoryl transfer catalyst the dicopper(II) macrocyclic complex LCu(2). Crystal structures of complexes [(L)Cu(2)(mu-NO(3))(NO(3))](NO(3))(2) (1), [(L)Cu(2)(mu-CO(3))(CH(3)OH)](BF(4))(2) (2), and [(L)Cu(2)(mu-O(2)P(OCH(3))(2))(NO(3))](NO(3))(2) (3) illustrate various possibilities for the interaction of oxoanions with the dicopper(II) site. 1 efficiently promotes the transesterification of dimethyl phosphate (DMP) in CD(3)OD, k(cat) = 2 x 10(-)(4) s(-)(1) at 55 degrees C. 1 is the only available catalyst for the smooth transesterification of highly inert simple dialkyl phosphates. From photometric titrations and the pH dependence of reactivity, we conclude that a complex [(L)Cu(2)(DMP)(OCH(3))](2+) is the reactive species. Steric bulk at the -OR substituents of phosphodiester substrates O(2)P(OR)(2)(-) drastically reduces the reactivity of 1. This is explained with -OR leaving group stabilization by Cu coordination, an interaction which is sensitive to steric crowding at the alpha-C-atom of substituent R. A proposed reaction mechanism related to that of the exonuclease unit of DNA polymerase I is supported by DFT calculations on reaction intermediates. The complex [(L)Cu(3)(mu(3)-OH)(mu-CH(3)O)(2)(CH(3)CN)(2)](ClO(4))(3) (4) incorporates a [Cu(OH)(OCH(3))(2)(CH(3)CN)(2)](-) complex anion, which might be considered as an analogue of the [PO(2)(OCH(3))(2)(OCD(3))](2)(-) transition state (or intermediate) of DMP transesterification catalyzed by LCu(2).

Journal Article↗
PubMed2005

A fluorogenic and chromogenic probe that detects the esterase activity of trace copper(II).

Bis(picolinoyl)fluorescein, a new fluorogenic and chromogenic probe for monitoring the esterase activity of metal ions, has been synthesized. The probe is highly selective for Cu2+ and is applicable both to quantification of the free ion and detection of esterolytic activity of Cu bound to organic ligands or biomolecules, with a detection limit of 100 nM by fluorimetry.

Chromogenic Compounds↗
PubMed2005

Templated metal catalysis for single nucleotide specific DNA sequence detection.

A catalytic DNA-templated reaction of hydrolysis of an ester group in an N-modified peptide nucleic acid, which is activated by a Cu2+ complex-PNA, has been discovered and optimized. Both the ester-containing PNA and the metal complex PNA bind neighboring sites on a template DNA. This brings the reacting groups (the ester and the Cu2+ complex) in proximity to each other and accelerates the hydrolysis of the ester approximately 500 times in comparison with its hydrolysis in the absence of the template. The hydrolysis reaction provides >10(2)-fold kinetic discrimination between DNAs that are different from each other at a single nucleotide position. Natural enzyme T4 DNA ligase is slightly less selective. On the basis of this reaction a fully homogeneous and sensitive assay for sequence-specific DNA detection has been developed (10 fmol DNA). Identification of one of four DNAs (variation at one position) can be done in a single experiment. Since the Cu2+ ion is tightly bound in an associate containing the ester PNA, the metal complex PNA, and the template DNA, application of this method in buffers containing other Cu2+-binding ligands, e.g., PCR buffer and physiological buffer, is possible.

Base Sequence↗
PubMed2005

N,N:N',N'-Bis(2,2'-dihydroxybiphenyl-3,3'-dimethylidene)benzene-1,2-diamine dimethyl sulfoxide tetrasolvate.

The title compound, 8,15,28,35-tetraazaheptacyclo[35.3.1.1(2,6).1(17,21).1(22,26).0(9,14).0(29,34)]tetraconta-1(41),2,4,6(42),7,9,11,13,15,17,19,21(43),22,24,26(44),27,29,31,33,35,37,39-docosaene-41,42,43,44-tetrol dimethyl sulfoxide tetrasolvate, C40H28N4O4.4C2H6OS, adopts a chair-shaped C(2h) symmetric conformation with crystallographically imposed inversion symmetry. Four intramolecular hydrogen bonds are observed between phenol O and imine N atoms.

Journal Article↗
PubMed2005

Hybridization dependent cleavage of internally modified disulfide-peptide nucleic acids.

Selectivity of the cleavage of single stranded over hybridized forms of internally modified disulfide-peptide nucleic acids (PNA) has been optimized using a series of phosphines and thiols, which have different sizes and charges. For the most selective cleaver found (tris-(carboxyethyl)-phosphine), reactivity of single stranded PNA is 33 times higher than that of the PNA-DNA duplex. Selectivity of single stranded disulfide-PNA cleavage has been explained in terms of electrostatic interaction between the substrate and the cleaver.

DNA↗
PubMed2004

Synthesis of a novel dinucleating aminocarboxylate macrocycle and structures of its dinuclear complexes with di- and trivalent transition and lanthanide metal ions.

The synthesis of the new ligand L1(H4L1= 3,8,16,21-tetrakis(carboxylmethyl)-3,8,16,21,27,28-hexaazatricyclo[21.3.1.1(10,14)]octacosa-1(27),10,12,14(28),23,25-hexaen-5,18-diine) is reported. The solid-state structures of the four homodinuclear chelate complexes, [Zn2(L1)(H2O)2] x 6H2O, [Fe2(L1)(mu-O)] x 4H2O, [La2(L1)(NO3)2(H2O)2] x 6H2O and Na[Eu2(L1)(mu-AcO)3] x 3H2O, were determined by single-crystal X-ray structural analysis.

Crystallography, X-Ray↗
PubMed2004

On, off and intermediate coordination of a bridgehead triarylamine donor in tripodal complexes: towards the tuning of coordinative bond distance.

A series of first row transition metal complexes of the tripodal ligand 2,2',2"-nitrilotribenzoic acid H3L has been prepared and characterised by X-ray crystallography: Mononuclear [M(L)]- species [Cu(H2O)4]3[Cu(L)(H2O)]6.25H2O (2), [Co(H2O)6][Co(L)(H2O)].8H2O (4), [Zn(H2O)6][Zn(L)(H2O)].8H2O (5) and a neutral [M(L)] complex [Fe(III)2(L)(H2O)3].5H2O (8) are formed as well as dimeric [M(L)]2 2- species (HNEt3)2[Cu(L)]2.2CH3CN (1), (HNEt3)3[Ni(L)]2(ClO4).H2O (3), (HNEt3)2[Fe(II)(L)]2.2CH3CN (6) and (HNEt3)2[Fe(III)2(L)2(mu-O)](7). The complexes display a unique variation in the M-N distance (2.09 A for Cu(II) to 3.29 A for Fe(III)) to the bridgehead triphenylamine donor and are classified into compounds with "On","Off" and "Intermediate" N-coordination. The trigonal-bipyramidal coordination polyhedron changes towards tetrahedral in the intermediate and octahedral in the Off-state. The M-N distance of individual complexes is reversibly tuned by external chemical input such as changes of metal ion oxidation state (Fe(II)/Fe(III)) or variation of the axial coligand as a consequence of solvent or pH variation. Possible reasons for the exceptional tolerance of the M-N bond to distance variations are discussed under consideration of gas phase DFT calculations of [Zn(L)]-.

Journal Article↗
PubMed2004

Synthesis and DNA binding properties of dioxime-peptide nucleic acids.

Peptide nucleic acids (PNAs) C- or N-modified with dioxime ligands were prepared by solid-phase synthesis using iron(II)-clathrochelates as protected dioxime building blocks. These PNA bind complementary DNA sequence specifically, though with much reduced affinity in comparison with nonmodified PNA. The dioxime-PNA conjugates bind Cu2+ and Ni2+ at microM concentration.

Base Sequence↗