Cover image for ChemBioChem

July 7, 2003

Volume 4, Issue 7

Pages 553–670

    1. Cover Picture: Chemical Restriction: Strand Cleavage by Ammonia Treatment at 8-Oxoguanine Yields Biologically Active DNA (ChemBioChem 7/2003) (page 553)

      Christoph Meyer, Dominik Meyer, Thomas A. Bickle and Bernd Giese

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200390084

    2. Graphical Abstract: ChemBioChem 7/2003 (pages 555–560)

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200390085

    3. Multidisciplinary Experimental Approaches to Characterizing Biomolecular Dynamics (pages 563–571)

      Floyd E. Romesberg

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300572

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      Proteins on the move: The techniques of organic synthesis and molecular biology have been used to develop biological systems amenable to dynamic characterization by spectroscopic techniques (see picture). This review focuses on three novel systems designed to study tautomerization dynamics in DNA, the role of protein dynamics in function and folding, and molecular recognition within the immune system. These studies illustrate our efforts to understand biomolecule dynamics and to test whether nature has evolved biomolecules with specific dynamic properties tailored to perform specific biological functions.

    4. Platinum(II)-Based Coordination Compounds as Nucleic Acid Labeling Reagents: Synthesis, Reactivity, and Applications in Hybridization Assays (pages 573–583)

      R. J. Heetebrij, E. G. Talman, M. A. v. Velzen, R. P. M. v. Gijlswijk, S. S. Snoeijers, M. Schalk, J. Wiegant, F. v.d. Rijke, R. M. Kerkhoven, A. K. Raap, H. J. Tanke, J. Reedijk and H.-J. Houthoff

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200200498

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      Nucleic acid labeling reagents: The synthesis of a series of platinum complexes (see scheme) modified with fluorescent and hapten tags is described. The reactivity profile and thus the mode of binding towards nucleic acids were studied. The tethered reporter group plays a significant role in reactivity towards mono- and polynucleotides. The application of these complexes in nucleic acid labeling and hybridization assays is illustrated in both a fluorescent in situ hybridization (FISH) and on a cDNA microarray.

    5. Modified DNA Bearing 5(Methoxycarbonylmethyl)-2′-deoxyuridine: Preparation by PCR with Thermophilic DNA Polymerase and Postsynthetic Derivatization (pages 584–588)

      Mohammad Mehedi Masud, Akiko Ozaki-Nakamura, Masayasu Kuwahara, Hiroaki Ozaki and Hiroaki Sawai

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200200539

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      Delivering DNA diversity: A thymidine analogue bearing a methyl ester at the C5 position was accepted as a substrate for the polymerase chain reaction (PCR) by the thermophilic family B DNA polymerases, but not by the thermophilic family A DNA polymerases. Modified DNA containing the analogue (1, R=OMe) was prepared on a large scale by PCR with KOD Dash DNA polymerase. The methyl ester of the modified DNA reacted with a variety of amines to form the corresponding derivatized DNAs. Hydrolysis of the methyl ester of the modified DNA gave a functionalized DNA bearing an anionic carboxy group (1, R=OH).

    6. Real-time Detection of Nucleotide Incorporation During Complementary DNA Strand Synthesis (pages 589–592)

      Alexander Krieg, Stephan Laib, Thomas Ruckstuhl and Stefan Seeger

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200200549

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      See polymerase live in action! We were able to detect the incorporation of Cy5-labeled dCTPs during complementary strand synthesis by use of a supercritical angle fluorescence instrument. For this purpose, we attached single-stranded DNA containing varying numbers of guanine bases to a poly-L-lysine surface and measured the increase in fluorescence during the polymerization in real time (see figure).

    7. Complex Formation of Divalent Metal Ions with Uridine 5′-O-Thiomonophosphate or Methyl Thiophosphate: Comparison of Complex Stabilities with Those of the Parent Phosphate Ligands (pages 593–602)

      Carla P. Da Costa, Andrzej Okruszek and Helmut Sigel

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200200551

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      The thiophosphate group has discriminating properties: By stability constant measurements it is shown that the affinity of the thiophosphate group (as in uridine 5′-O-thiomonophosphate; see scheme), if its reduced basicity is taken into account, corresponds to that of the parent phosphate group towards the alkaline earth ions, Mn2+, Co2+, or Ni2+. However, this affinity is considerably enhanced, despite the lower basicity, towards Zn2+, Cd2+, or Pb2+. The relevance of these observations, for example, for “rescue” experiments with ribozymes is evident.

    8. Acceptor Specificity and Inhibition of the Bacterial Cell-Wall Glycosyltransferase MurG (pages 603–609)

      Haitian Liu, Thomas K. Ritter, Reiko Sadamoto, Pamela S. Sears, Min Wu and Chi-Huey Wong

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300557

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      Analogues, assays, and antibiotics: The bacterial cell-wall biosynthesis pathway is an attractive target for antibiotics. In this pathway, the enzyme MurG catalyzes the transfer of N-acetylglucosamine to lipid I to form lipid II. The newly discovered lipid I analogue 1 is a substrate for MurG and was used in a fluorescence-based assay to develop new inhibitors of the enzyme.

    9. Chemical Restriction: Strand Cleavage by Ammonia Treatment at 8-Oxoguanine Yields Biologically Active DNA (pages 610–614)

      Christoph Meyer, Dominik Meyer, Thomas A. Bickle and Bernd Giese

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300587

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      Sharp chemicals: DNA oligonucleotides can be cleaved selectively at an 8-oxoguanine site X (shown in red) under conditions (NH3, O2, 60 °C) that yield DNA that can be successfully ligated. Cloning experiments demonstrate that this chemical restriction method is a practical alternative to enzymatic restriction. The advantage of chemical restriction is its lack of dependence on the DNA sequence.

    10. A Homology Model of Penicillin Acylase from Alcaligenes faecalis and In Silico Evaluation of its Selectivity (pages 615–622)

      Paolo Braiuca, Cynthia Ebert, Lutz Fischer, Lucia Gardossi and Paolo Linda

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200200545

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      GRID plan: Homology modeling, the GRID/principal component analysis (PCA) approach, and molecular docking were applied to study the previously unknown three-dimensional structure of penicillin acylase from Alcaligenes faecalis and its selectivity. A three-dimensional model of the enzyme was built and an in silico selectivity study was performed by means of GRID/PCA and molecular docking techniques. Structural differences between this penicillin acylase and that from Escherichia coli (shown in the figure) explain the different enantioselectivities of the enzymes and allow prediction of the selectivity of the Alcaligenes faecalis towards an acyl donor.

    11. Structures and Stabilities of Small DNA Dumbbells with Watson–Crick and Hoogsteen Base Pairs (pages 623–632)

      Nuria Escaja, Irene Gómez-Pinto, Manuel Rico, Enrique Pedroso and Carlos González

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300578

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      That ring's a bell! Small cyclic oligonucleotides can adopt stable dumbbell-like structures. Their structures and stabilities depend strongly on the oligonucleotide sequences. NMR data indicate that the solution structures (see figure) of dumbbells with G–C or A–T base pairs are different. In the case of dumbbells with G–C base pairs, the residues in the stem form a short segment of BDNA helix stabilized by two Watson–Crick base pairs. In contrast, dumbbells with A–T pairs in the stem have the glycosidic angles in the adenine bases that correspond to a syn conformation and these residues form Hoogsteen base pairs.

    12. Improvement of Hepatocyte-Specific Gene Expression by a Targeted Colchicine Prodrug (pages 633–639)

      Sabine M. W. van Rossenberg, Karen M. Sliedregt-Bol, Gerben Koning, Hans van den Elst, Theo J. C. van Berkel, Jacques H. van Boom, Gijs A. van der Marel and Erik A. L. Biessen

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300582

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      Courier conjugation: The tubulin inhibitor colchicine (1) can improve the delivery of therapeutic genes to cells, but application of the drug is limited by its systemic toxicity. A targeted prodrug of colchicine was synthesized by conjugation to a high-affinity ligand for the asialoglycoprotein receptor on parenchymal liver cells. It was shown that the glycoconjugated colchicine displays a high affinity for the receptor and strongly improved polyplex-based gene expression to parenchymal liver cells in a receptor-dependent fashion. This nontoxic conjugate may be a useful tool to improve the transfection efficiency of hepatic nonviral gene transfer vehicles.

    13. Synthetic Potential of Molluscan Sulfatases for the Library Synthesis of Regioselectively O-Sulfonated D-Galacto-Sugars (pages 640–647)

      Hirotaka Uzawa, Yoshihiro Nishida, Kenji Sasaki, Norihiko Minoura and Kazukiyo Kobayashi

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300616

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        The sweet success of promotion: The substrate selectivities and regioselectivities of three molluscan sulfatases have been examined with a series of mono-, di-, and tri-O-sulfonated galacto-sugars derived from p-nitrophenyl galactopyranosides and lactosides. A unique phenomenon was observed: the hydrolysis of O-sulfo groups at the secondary positions is promoted by the presence of a 6O-sulfo group in the same substrate. These results show that sulfatases possess great potential for application to the library synthesis of regioselectively O-sulfonated D-galacto-sugars. Thirteen sorts of critically stereocontrolled p-nitrophenyl sulfo-D-galacto-sugars were synthesized in total by the sequential use of chemical sulfonation reactions (a) and enzyme-assisted desulfonation (b; see scheme).

    14. Selective Incorporation of 19F-Labeled Trp Side Chains for NMR-Spectroscopy-Based Ligand–Protein Interaction Studies (pages 649–650)

      Marilisa Leone, Ricard A. Rodriguez-Mias and Maurizio Pellecchia

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300597

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      F marks the spot: We report a new technique for selectively labeling Trp side chains in proteins with 19F by using 3β-indoleacrilic acid as an inhibitor of tryptophan biosynthesis. Our method finds useful application in the study of protein–protein or protein–ligand interactions (see figure) by means of 19F NMR spectroscopy.

    15. The First Example of an RNA Urea Synthase: Selection through the Enzyme Active Site of Human Neutrophile Elastase (pages 651–654)

      Dan Nieuwlandt, Madeline West, Xiaoqin Cheng, Gary Kirshenheuter and Bruce E. Eaton

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300610

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      RNA catalysts: In vitro selection from a random library of RNA sequences gave RNA urea synthases able to utilize tripeptides as substrates (see scheme; HNE, human neutrophile elastase). The tripeptide substrates were mechanism-based protease suicide substrates. Stereoselection of serine protease tripeptide phosphonate inhibitors was achieved by RNA catalysis. The RNA urea synthases showed a high degree of diastereoselectivity for the most potent protease suicide inhibitor.

    16. Conserved Amino Acid Residues Correlating With Ketoreductase Stereospecificity in Modular Polyketide Synthases (pages 654–657)

      Patrick Caffrey

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300581

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      Getting down to specifics: Key amino acid residues were found to correlate with ketoreductase domain stereospecificity in modular polyketide synthases. These residues may allow alcohol stereochemistry (see scheme; ACP, acyl carrier protein) in polyketides to be predicted from ketoreductase sequences. The results also suggest that polyketide synthase dehydratase domains have a preference for 3hydroxyacyl substrates with the same alcohol stereochemistry as the (3R)-hydroxyacyl chains used by dehydratases in fatty acid synthases.

    17. Bromobalhimycin and Chlorobromobalhimycins—Illuminating the Potential of Halogenases in Glycopeptide Antibiotic Biosyntheses (pages 658–662)

      Bojan Bister, Daniel Bischoff, Graeme J. Nicholson, Sigrid Stockert, Joachim Wink, Cristina Brunati, Stefano Donadio, Stefan Pelzer, Wolfgang Wohlleben and Roderich D. Süssmuth

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200300619

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      Can bromine beat bacteria? By varying the amounts of chloride and bromide salts in fermentation culture media, we have generated novel sets of vancomycin-type glycopeptides with bromine substitution. This study extends the sequence of substituents at the aglycon moiety of balhimycin from H through F and Cl to Br (see scheme) and opens up possibilites for the investigation of substituent effects upon the activity of glycopeptide antibiotics.

    18. Book Review: BioNMR in Drug Research Edited by Oliver Zerbe (pages 664–665)

      Gerhard Hessler and Stefania Pfeiffer-Marek

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200390087

    19. Preview: ChemBioChem 7/2003 (page 670)

      Article first published online: 27 JUN 2003 | DOI: 10.1002/cbic.200390091