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Andreas Marx

Publications and source records attributed to Andreas Marx.

At least 19 recordsLinked to original sources
PubMed2007

New branched DNA constructs.

The Watson-Crick base pairing of DNA is an advantageous phenomenon that can be exploited when using DNA as a scaffold for directed self-organization of nanometer-sized objects. Several reports have appeared in the literature that describe the generation of branched DNA (bDNA) with variable numbers of arms that self-assembles into predesigned architectures. These bDNA units are generated by using cleverly designed rigid crossover DNA molecules. Alternatively, bDNA can be generated by using synthetic branch points derived from either nucleoside or non-nucleoside building blocks. Branched DNA has scarcely been explored for use in nanotechnology or from self-assembling perspectives. Herein, we wish to report our results for the synthesis, characterization, and assembling properties of asymmetrical bDNA molecules that are able to generate linear and circular bDNA constructs. Our strategy for the generation of bDNA is based on a branching point that makes use of a novel protecting-group strategy. The bDNA units were generated by means of automated DNA synthesis methods and were used to generate novel objects by employing chemical and biological techniques. The entities generated might be useful building blocks for DNA-based nanobiotechnology.

Automation↗
PubMed2006

Frequent homogeneous HER-2 amplification in primary and metastatic adenocarcinoma of the esophagus.

HER-2 is the target for antibody based treatment of breast cancer (Herceptin). In order to evaluate the potential role of such a treatment in esophageal cancers, HER-2 amplification and overexpression was investigated in primary and metastatic cancers of the esophagus. A tissue microarray was constructed from 255 primary esophageal cancers (110 adenocarcinomas and 145 squamous cell carcinomas), 89 nodal and 33 distant metastases. Slides were analyzed by immunohistochemistry (HercepTest; DAKO) and fluorescence in situ hybridization (FISH; PathVysion; Vysis-Abbott) for HER-2 amplification and overexpression. Amplification was seen in 16/110 (15%) adenocarcinomas and in 7/145 (5%) squamous cell carcinomas. There was a strong association between HER-2 amplification and overexpression, especially in adenocarcinomas (P<0.0001, log rank). There was a 100% concordance of the HER-2 results in primary tumor and corresponding metastases in 84 analyzed pairs. Amplification was typically high-level with more than 10-15 HER-2 copies per tumor cell. Amplification was unrelated to survival, grading, pT, pN, pM or UICC stage. We conclude that esophageal adenocarcinomas belong to those cancer types with relevant frequency high-level HER-2 gene amplification clinical trials or individual case studies investigating the response of metastatic HER-2-positive esophageal cancers to Herceptin((R)) should be undertaken. The strong concordance of the HER-2 status in primary and metastatic cancers argues for a possible response of metastases from patients with HER-2-positive primary tumors to Herceptin.

Adenocarcinoma↗
PubMed2006

Synthesis of DNA oligonucleotides containing 5-(mercaptomethyl)-2'-deoxyuridine moieties.

Recently thiolated oligonucleotides have attracted significant interest due to their ability to efficiently undergo stable bond formation with gold nanoparticles and surfaces to form DNA conjugates. In this respect we became interested in the synthesis of oligonucleotides that bear short thioalkyl functions located at the nucleobase. Here we present a strategy for the synthesis of DNA oligonucleotides that bear 5-(mercaptomethyl)-2'-deoxyuridine moieties. The building blocks were synthesized in a straightforward manner from thymidine. Only moderate changes of standard protocols for automated DNA synthesis are required for the generation of modified oligonucleotides containing the thiolated building blocks.

DNA↗
PubMed2006

A new photoactive building block for investigation of DNA backbone interactions: photoaffinity labeling of human DNA polymerase beta.

The cross-linking of target proteins or nucleic acids to light-activatable ligands is an important tool for elucidating molecular interactions. Through the use of photoaffinity-labeling reagents, several new insights into nucleic acid interactions have been obtained, for example in DNA replication and repair. In most known photoprobes, the applied light-sensitive functionalities are placed directly at the nucleobase or are attached via linkers to either the nucleobase or the phosphate backbone. Here we describe the first photoprobe that bears a light-sensitive aryl(trifluoromethyl)diazirine at the sugar moiety of a DNA oligonucleotide. We devised a route for the synthesis of the modified nucleoside and its incorporation into an oligonucleotide. The photoactive species was proven to be stable under the conditions employed in routine automated DNA synthesis. The modified oligonucleotide was shown by subsequent photolabeling studies of human DNA polymerase beta to form a covalent complex to the enzyme upon irradiation with near-UV light.

DNA↗
PubMed2005

Genotyping--from genomic DNA to genotype in a single tube.

Nucleotide variations in the human genome, such as single-nucleotide polymorphisms, have been researched more intensively since it became apparent that these deviations are linked to various diseases and also several side effects of drugs. The investigation of genomic DNA in the laboratory requires routine methods that are time-, labour-, and cost-effective. These criteria are fulfilled by so-called closed-tube methods, which are applied directly to isolated genomic DNA without any preamplification.

Cytogenetic Analysis↗
PubMed2005

Tuning single nucleotide discrimination in polymerase chain reactions (PCRs): synthesis of primer probes bearing polar 4'-C-modifications and their application in allele-specific PCR.

There are many methods available for the detection of nucleotide variations in genetic material. Most of these methods are applied after amplification of the target genome sequence by the polymerase chain reaction (PCR). Many efforts are currently underway to develop techniques that can detect single nucleotide variations in genes either by means of, or without the need for, PCR. Allele-specific PCR (asPCR), which reports nucleotide variations based on either the presence or absence of a PCR-amplified DNA product, has the potential to combine target amplification and analysis in one single step. The principle of asPCR is based on the formation of matched or mismatched primer-target complexes by using allele-specific primer probes. PCR amplification by a DNA polymerase from matched 3'-primer termini proceeds, whereas a mismatch should obviate amplification. Given the recent advancements in real-time PCR, this technique should, in principle, allow single nucleotide variations to be detected online. However, this method is hampered by low selectivity, which necessitates tedious and costly manipulations. Recently, we reported that the selectivity of asPCR can be significantly increased through the employment of chemically modified primer probes. Here we report further significant advances in this area. We describe the synthesis of various primer probes that bear polar 4'-C-modified nucleotide residues at their 3' termini, and their evaluation in real-time asPCR. We found that primer probes bearing a 4'-C-methoxymethylene modification have superior properties in the discrimination of single nucleotide variations by PCR.

Alleles↗
PubMed2005

4'C-ethynyl-thymidine acts as a chain terminator during DNA-synthesis catalyzed by HIV-1 reverse transcriptase.

Recently, 4'C-ethynyl nucleoside analogues have been identified as highly potent agents against HIV-1, including several multidrug-resistant strains. In contrast to most known nucleoside inhibitors 4'C-ethynyl nucleoside analogues possess a 3'-hydroxyl function. Here we show that the 5'O-triphosphate of 4'C-ethynyl thymidine gets readily incorporated into a nascent DNA strand by HIV-1 reverse transcriptase and significantly inhibits further post-incorporation chain extension by the enzyme.

Catalysis↗
PubMed2005

Evaluation of the stereotactic 8G vacuum-assisted breast biopsy in the histologic evaluation of suspicious mammography findings (BI-RADS IV).

PURPOSE: The purpose of this study was to evaluate the potential of the new 8G stereotactic vacuum-assisted breast biopsy (ST-driver, Mammotome; Ethicon Endosurgery) in the histologic evaluation of BI-RADS IV microcalcifications. MATERIALS AND METHODS: Fifty-eight patients with 61 mammographic BI-RADS IV microcalcifications underwent stereotactic vacuum-assisted breast biopsy (SVAB). The new 8G system was mounted on the ST driver, which was formerly used only with the hand-held version under sonographic guidance. The evaluation criteria for each biopsy were minimally invasive and operative histologies, the time needed for biopsy, the amount of bleeding, number of rotations and specimen, the degree of resection, and the complications. RESULTS: Fifty-eight of 61 biopsies were technically successful because > or = 50% were resected (29 x 100%, 8 x 90%, 5 x 80%, 6 x 70%, 3 x 50%, 3 x 0%). In 7 cases with representative biopsies of segmental suspicious microcalcifications, the degree of resection could not be exactly measured. All but 2 biopsies were performed without clinically relevant complications and after gaining enough specimens (Ø 12.6 specimen, 1.85 rotations). Those 2 patients showed evidence of severe bleeding into the breast tissue and operative revision had to be performed (3.5%). The size of intramammary hematoma was measurable in 27 biopsies and showed a range from 0.5 to 5 cm (Ø 2.7 cm). The average external bleeding was still low with 16 mL (5-80 mL). In 3 of 61 lesions, it was not possible to gain representative tissue as a result of displacement of the lesion after introducing or shooting the needle. The average time needed for all biopsies was 28.2 minutes for all but 5 very complicated biopsies, which took 16.1 minutes. The histologic findings with further operative workup were: 10 ductal carcinomas in situ (DCIS), 4 atypical ductal hyperplasias, 1 atypical lobular hyperplasias (ALH), 3 lobular carcinomas in situ (LCIS), and 6 invasive ductal carcinomas. In 7 of 12 of the initial DCIS histologies, the operative histology was also DCIS, whereas in 4 of 12, no residual malignant tumor was found. In 1 of 12 patients with an initial DCIS histology, operative histology revealed invasive ductal cancer (8.3%). The cases with lobular lesions (ALH, LCIS) did not show any evidence for residual tissue in the operative workup. Most frequent benign histologies were mastopathy (13), ductal hyperplasia (9), fibroadenoma (8), and sclerosing adenosis (5). The control examinations (maximum 1 year) did not show any signs for a false-negative biopsy. CONCLUSION: The 11-G SVAB has proven to be a perfect adjunct to the existing breast biopsy methods. The new 8G SVAB speeds up the method when used for the same size of lesions and enables the user to representatively biopsy lesions up to 3 cm in diameter. The method is still minimally invasive; however, the amount of hematomas as well as clinically relevant complications is increased.

Biopsy, Needle↗
PubMed2004

Increased single-nucleotide discrimination of PCR by primer probes bearing hydrophobic 4'C modifications.

We report on significantly increased selectivity of real-time PCR through employment of primer probes that bear hydrophobic 4'C modifications at the 3'-terminal nucleotide. The primer probes were designed to bind the target sequences in such a way that the 3'-terminal nucleotide defines whether a matched or a single mismatched basepair is present depending on the respective target sequence. Several commercially available thermostable DNA polymerases belonging to different DNA polymerase families were tested for their efficacy in discriminating between PCR amplification of matched substrates and duplexes that contain a single mismatch. It turned out that, depending on the 4'C modification and the employed DNA polymerase, significantly increased differentiation between single matches and mismatches could be observed with real-time PCR. The degrees of the observed effects varied with the employed 4'C modification and the sequence context studied. The system is robust enough to work faithfully under several buffer conditions. Our approach should be useful for the direct diagnosis of single nucleotide variations within genes, like single nucleotide polymorphisms or mutations, by PCR without the need for further time- and cost-intensive post-PCR analysis.

DNA Primers↗
PubMed2004

Efficacy and safety of imatinib in adult patients with c-kit-positive acute myeloid leukemia.

This phase 2 pilot study was conducted to determine the efficacy and safety of imatinib mesylate in patients with c-kit-positive acute myeloid leukemia (AML) refractory to or not eligible for chemotherapy. Twenty-one patients were enrolled and received imatinib 600 mg orally once daily. Five responses were seen primarily in patients, starting with relatively low blast counts in bone marrow (BM) and peripheral blood (PB): 2 patients who were considered refractory on chemotherapy on the basis of persistence of blasts in PB and BM met the criteria for complete hematologic remission, 1 patient had no evidence of leukemia, and 2 patients achieved a minor response. Treatment with imatinib demonstrated a good safety profile and was well tolerated. Western blot analysis and immunohistochemistry demonstrated c-Kit activation in primary AML cells. Further, imatinib treatment of primary AML cells inhibited c-Kit tyrosine-phosphorylation. Genomic DNA-sequencing of c-KIT showed no mutations in exons 2, 8, 10, 11, 12, and 17. Although some of the responses derived from relatively small reductions in leukemic blasts and may be attributable, in part, to prior chemotherapy, these cases suggest that imatinib has interesting clinical activity in a subset of patients with c-kit-positive AML. Further clinical trials are warranted to explore the clinical potential of imatinib in AML and to identify the underlying molecular mechanism.

Acute Disease↗
PubMed2002

Sustained complete hematologic remission after administration of the tyrosine kinase inhibitor imatinib mesylate in a patient with refractory, secondary AML.

Imatinib mesylate, a tyrosine kinase inhibitor targeting bcr-abl, platelet-derived growth factor receptor (PDGF-R), and c-Kit, effectively induces hematologic and cytogenetic remissions in bcr-abl(+) chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL) with only mild to moderate side effects. Here, we describe the successful treatment of a 64-year-old man with c-Kit(+) secondary acute myeloid leukemia (AML) refractory to standard chemotherapy. Upon 2 weeks of imatinib mesylate administration, the patient achieved a complete hematologic remission in peripheral blood. In addition, complete clearance of leukemic blasts in bone marrow and a significant cytogenetic response lasting for more than 5 months was observed. Sequence analysis of exons 2, 8, 10, 11, and 17 of the c-Kit receptor did not reveal structural alterations as previously described in a subset of AML cases. This is the first report of complete remission achieved upon administration of imatinib mesylate in a patient with highly refractory, secondary AML.

Anemia, Refractory↗