Research Interests and Projects

Research Foci

  • Organic Synthesis
  • Biomedical Evaluation
  • Medicinal Chemistry
  • C-Nucleosides
  • Prebiotic Chemistry
  • NMR-based Structure Elucidation
  • DNA-based Nanostructuring
  • Encapsulating Organic Crystals
  • One focus of our research is to synthesize molecules with the ability to selectively interact with biomolecular targets. This includes studies on the reactivity of functional biomolecules. It also includes studies on compounds whose properties are improved over those of unmodified biomolecules and to employ this capability to develop new functional entities. The molecular recognition phenomena of interest also include the recognition of transition states, i.e. the generation of new biomimetic catalysts. The following is a brief list of selected projects from recent years.

    Selected Projects

    Completed Projects

    Other Projects

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    Peptido RNA

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  • P. Tremmel, H. Griesser, U. E. Steiner, C. Richert, How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water. Angew. Chem. 2019, 131, 13221-13226; Angew. Chem. Int. Ed. 2019, 58, 13087-13092. [ Open Access ].
  • highlighted on: [Hot Topic: Organocatalysis]
  • H. Griesser, M. Bechthold, P. Tremmel, E. Kervio, C. Richert, Amino acid-specific, ribonucleotide-promoted peptide formation in the absence of enzymes. Angew. Chem. Int. Ed. 2017, 56, 1224-1228.
  • H. Griesser, P. Tremmel, E. Kervio, C. Pfeffer, U.E. Steiner, C. Richert, Ribonucleotides and RNA promote peptide chain growth. Angew. Chem. Int. Ed. 2017, 56, 1219-1223.
  • M. Jauker, H. Griesser, C. Richert, Spontaneous formation of RNA strands, peptidyl RNA and cofactors. Angew. Chem. Int. Ed. 2015, 54, 14564-14569.
  • highlighted on: [ (Deutsch), (Englisch)]

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    Capped and Enforced Oligonucleotides

    Many key techniques of modern molecular biology and medicine, including genomics, rely on sequence selective hybridization between oligonucleotide strands. It has long been known that base pairing fidelity at the termini is poor, as evidenced, e.g. by the degeneracy of the genetic code (Crick, F. H. C. J. Mol. Biol. 1966, 19, 548). These laboratories have declared the development of oligonucleotide derivatives with high base pairing fidelity throughout their length one of their goals. The bile acid-modified terminus shown on the left is one recent example where improved base discrimination has been achieved at the 5'-terminus. Some of the caps have been commercialized.

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  • J. Eyberg, C. Richert, Ethynylpyridone C-nucleoside phosphoramidite (dW): A high affinity replacement for thymidine. Glen Rep. 2019, 31.2, 1-3.
  • T.J. Walter, C. Richert, A strongly pairing fifth base: oligonucleotides with a C-nucleoside replacing thymidine. Nucleic Acids Res. 2018, 46, 8069-8078. [ Open Access ].
  • C. Kröner, M. Thunemann, S. Vollmer, M. Kinzer, R. Feil, C. Richert, Endless: A purine-binding motif that can be expressed in cells. Angew. Chem. 2014, 126, 9352-9356; Angew. Chem. Int. Ed. 2014, 53, 9198-9202.
  • M. Minuth, W. Frey, C. Richert, Improved synthesis of a salicylic aldehyde C-nucleoside for metallo base pairs via Heck reaction. Synlett, 2014, 10, 1438-1442.
  • M. Minuth, C. Richert, A nucleobase analog that pairs strongly with adenine. Angew. Chem., 2013, 125, 11074-11077; Angew. Chem. Int. Ed., 2013, 52, 10874-10877.

    highlighted on: [ ]
    also highlighted on: [ Pressebox | | VBio | innovations-report | | idw | Analytik News ]

  • C. Prestinari, C. Richert, Intrastrand locks increase duplex stability and base pairing selectivity. Chem. Comm. 2011, 47, 10824-10826.
  • S. Egetenmeyer, C. Richert, A 5'-cap for DNA probes binding RNA target strands. Chem. Eur. J.2011, 17, 11813-11827.
  • A. Patra, C. Richert, High fidelity base pairing at the 3'-terminus. J. Am. Chem. Soc. 2009, 131 , 12671-12681.
  • M. Printz, C. Richert, Optimizing the stacking moiety and linker of 2'-acylamido caps of DNA duplexes with 3'-terminal adenine residues. J. Combin. Chem. 2007, 9, 306-320.
  • L. Zhang, H. Zhu, M.C. Sajimon, J.A. Rojas Stütz, K. Siegmund, C. Richert, V. Shafirovich, F.D. Lewis, Stabilization of DNA hairpins by stilbene capping of the terminal base pair. J. Chin. Chem. Soc. 2006, 53, 1501-1507.
  • S. Al-Rawi, C. Ahlborn, C. Richert, 3'-Immobilized probes with 2'-caps: synthesis of oligonucleotides with 2'-N-methyl-2'-(anthraquinone carboxamido)uridine residues. Org. Lett. 2005, 7, 1569-1572.
  • J. Tuma, R. Paulini, J. A. Rojas Stütz, C. Richert, How much pi-stacking do DNA termini seek? Solution structure of a self-complementary DNA hexamer with trimethoxystilbenes capping the terminal base pairs. Biochemistry 2004, 43, 15680-15687.
  • S. Narayanan, J. Gall, C. Richert, Clamping down on weak terminal base pairs: oligonucleotides with molecular caps as fidelity-enhancing elements at the 5'- and 3'-terminal residues. Nucleic Acids Res. 2004, 32, 2901-2911.
  • W. H. Connors, S. Narayanan, O. P. Kryatova, C. Richert, Synthesis of oligonucleotides with a 2'-cap at the 3'-terminus via reversed phosphoramidites. Org. Lett. 2003, 5, 247-250.
  • J. Tuma, W.H. Connors, D.H. Stitelman, C. Richert, On the Effect of Covalently Appended Quinolones on Termini of DNA-Duplexes. J. Am. Chem. Soc. 2002, 124, 4236-4246.
  • O.P. Kryatova, W.H. Connors, C.F. Bleczinski, A.A. Mokhir, C. Richert, A 2'-acylamido cap that increases the stability of oligonucleotide duplexes. Org. Lett. 2001, 3, 987-990.
  • Bleczinski, C. F.; Richert, C. Steroid-DNA interactions increasing stability, sequence-selectivity, DNA/RNA discrimination, and hypochromicity of oligonucleotide duplexes. J. Am. Chem. Soc.1999, 121,10889-10894.

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    Binding Motifs for Nucleosides, Nucleotides and Cofactors

  • T. Feldner, M. Wolfrum, C. Richert, Turning DNA binding motifs into a material for flow cells. Chem. Eur. J. 2019, 25, 15288-15294.
  • Cover: [Link]
  • S. Vollmer, C. Richert, DNA triplexes that bind several cofactor molecules (cover). Chem. Eur. J. 2015, 21, 18613-18622.
  • A. Göckel, C. Richert, Synthesis of an oligonucleotide with a nicotinamide mononucleotide residue and its molecular recognition in DNA helices. (inside front cover). Org. Biomol. Chem. 2015, 13, 10303 - 10309.
  • S. Vollmer, C. Richert, Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands. Org. Biomol. Chem. 2015, 13, 5734 - 5742.
  • C. Kröner, A. Göckel, W. Liu, C. Richert, Binding cofactors with triplex-based DNA motifs (Inside Cover). Chem. Eur. J. 2013, 19, 15879-15887.
  • C. Kröner, M. Röthlingshöfer, C. Richert, Designed nucleotide binding motifs. J. Org. Chem. 2011, 76, 2933-2936.

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    Enzyme-free Copying and Replication

    The template-directed extension of primers is the pivotal reaction of DNA replication and transcription. It is also the basis of key biotechnological and diagnostic applications, including, but not limited to, the polymerase chain reaction (PCR), DNA sequencing by the dideoxy method, and most SNP-genotyping techniques. Traditionally, these reactions can only be performed with polymerases as catalysts. Elegant work from L. Orgel's lab and several other research groups has shown that replication can also be induced without enzymes. However, these non-enzymatic reactions are very slow and stop, if several weak base pairs are encountered. We have an interest in performing non-enzymatic primer extension reactions where the rate and specificity of the reactions are enhanced through affordable, non-biological catalysts, as well as biomedical applications for the chemically catalyzed primer extension.

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  • M. Sosson, D. Pfeffer, C. Richert, Enzyme-free Ligation of Dimers and Trimers to RNA Primers. Nucleic Acids Res. 2019, 47, 3836-3845. [ Open Access ].
  • D. Pfeffer, E. Hänle, M. Sosson, C. Richert, Replikation ohne Polymerase. GIT Lab. Fachz. 2018, (11), 18-21.
  • E. Hänle, C. Richert, Enzyme-Free Replication with Two or Four Bases. Angew. Chem. 2018, 130, 9049-9053; Angew. Chem. Int. Ed. 2018, 57, 8911-8915.
    highlighted on: [ | | idw | | ]
  • M. Sosson, C. Richert, Enzyme-free genetic copying of DNA and RNA sequences (Account). Beilstein J. Org. Chem. 2018, 14, 603-617.
  • E. Kervio, M. Sosson, C. Richert, The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA. Nucleic Acids Res. 2016, 44, 5504-5514.
  • M. Jauker, H. Griesser, C. Richert, Copying of RNA sequences without pre-activation. Angew. Chem. Int. Ed. 2015, 54, 14559-14563.
  • E. Kervio, B. Claasen, U. E. Steiner, C. Richert, The strength of the template effect attracting nucleotides to naked DNA. Nucleic Acids Res., 2014, 42, 7409-7420.
  • A. Kaiser, S. Spies, T. Lommel, C. Richert, Template-Directed Synthesis in 3'- and 5'-Direction with Reversible Termination. Angew. Chem. 2012, 124, 8424-8428; Angew. Chem. Int. Ed. 2012, 51. 8299-8303.
  • H. Vogel, C. Richert, Labeling small RNAs through chemical ligation at the 5'-terminus - enzyme-free or combined with enzymatic 3'-labeling. ChemBioChem 2012, 13, 1474-1482.
  • C. Deck, H. Vogel, M. Jauker, C. Richert, Chemische Primerverlängerung - Technologie zur Sequenzabfrage und Potentiell Präbiotischer Prozess. GIT Lab. Fachz. 2011, (11), 778-780.
  • C. Deck, M. Jauker, C. Richert, Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nature Chem. 2011, 3, 603-608.
  • E. Kervio, A. Hochgesand, U. Steiner, C. Richert, Templating efficiency of naked DNA. Proc. Natl. Acad. Sci. USA, 2010, 107 , 12074-12079.
  • K. Gießler, H. Griesser, D. Göhringer, T. Sabirov, C. Richert, Synthesis of 3'-BODIPY-labeled active esters of nucleotides and a chemical primer extension assay on beads. Eur. J. Org. Chem. 2010, 19 , 3611-3620.
  • M. Röthlingshöfer, C. Richert, Chemical primer extension at submillimolar concentration of deoxynucleotides (featured article). J. Org. Chem. 2010, 75, 3945-3952. (cover) .
  • R. Eisenhuth, C. Richert, Convenient syntheses of 3'-amino-2',3'-dideoxynucleosides, their 5'-monophosphates, and 3'-aminoterminal oligodeoxynucleotide primers. J. Org. Chem. 2009, 74, 26-37.
  • M. Röthlingshöfer, E. Kervio, T. Lommel, U. Plutowski, A. Hochgesand, C. Richert, Chemical primer extension in seconds. Angew. Chem. 2008, 120, 6154-6157; Angew. Chem. Int. Ed. 2008, 47, 6065-6068.
  • U. Plutowski, S. R. Vogel, M. Bauer, C. Deck, M. Pankratz, C. Richert, Enzyme-free interrogation of RNA sites via primers and oligonucleotides 3'-linked to gold-surfaces. Org. Lett. 2007, 9, 2187-2190.
  • S.R. Vogel, C. Richert, Adenosine residues in the template do not block spontaneous replication steps of RNA. Chem. Comm. 2007, 1896-1898.
    Highlighted in: M. Spencelayh, RNA on ice. RSC Chemical Biolology, 2007, 2, B41 (cover story).
  • J. A. Rojas Stütz, E. Kervio, C. Deck, C. Richert, Chemical primer extension - individual steps of spontaneous replication (Account). Chem. Biodiv. 2007, 4, 784-802.
  • P. Baumhof, N. Griesang, M. Bächle, C. Richert, Synthesis of oligonucleotides with 3'-terminal 5-(3-acylamidopropargyl)-3'-amino-2',3'-dideoxyuridine residues and their reactivity in single nucleotide steps of chemical replication. J. Org. Chem. 2006, 71, 1060-1067.
  • J. A. Rojas Stütz, C. Richert, Tuning the reaction site for enzyme-free primer extension reactions through small molecule substituents. Chem. Eur. J. 2006, 12, 2472-2481.
  • S.R. Vogel, C. Deck, C. Richert, Accelerating chemical replication steps of RNA involving activated ribonucleotides and downstream-binding elements. Chem. Comm. 2005, 4922-4924.
    For news highlights on this paper, see: Chemical Science and Hahn, U. Raschere enzymfreie RNA-Replikationsschritte. Nachr. Chem. 2005, 53, 1109.
  • P. Hagenbuch, E. Kervio, A. Hochgesand, U. Plutowski, C. Richert, Chemical primer extension: efficiently determining single nucleotides in DNA. Angew. Chem., 2005, 117, 6746-6750; Angew. Chem. Int. Ed. Engl. 2005, 44, 6588-6592.
    (Highlighted in: H.-A. Wagenknecht, Nachr. Chem. 2006, 54, 245-246.)
  • J.A. Rojas Stütz, C. Richert, A steroid cap adjusts the selectivity and accelerates the rates of non-enzymatic single nucleotide extensions of an oligonucleotide. J. Am. Chem. Soc. 2001, 123, 12718-12719.

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    DNA-Based Nanostructuring

    We study DNA-Nanoparticle, DNA-Nanotube, and DNA-DNA-interactions with the longterm goal of creating molecular electronics circuits based on sequence-selective recognition events. This work is supported by the Center Of Functional Nanostructures (CFN) at the University of Karlsruhe.

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  • N. L. Wenz, S. Piasecka, M. Kalinowski, A. Schneider, C. Richert, C. Wege, Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein. Nanoscale 2018, 10, 6496-6510.
  • M. Kramer, C. Richert, Enzyme-free ligation of 5'-phosphorylated oligodeoxynucleotides in a DNA nanostructure. Chem. Biodiv. 2017, 14, e1700315. [ Open Access ].
  • R. J. Schwarz, C. Richert, A four-helix bundle DNA nanostructure with binding pockets for pyrimidine nucleotides. Nanoscale, 2017, 9, 7047-7054.
  • M. Kalinowski, R. Haug, H. Said, S. Piasecka, M. Kramer, C. Richert, Phosphoramidate ligation of oligonucleotides in nanoscale structures. ChemBioChem 2016, 17, 1150-1155.
  • H. Said, V. Schueller, F. Eber, C. Wege, T. Liedl, C. Richert, M1.3 - A small scaffold for DNA origami, Nanoscale, 2013, 5, 284-290.
  • Singh, A.; Tolev, M.; Schilling, C. Bräse, S.; Griesser, H.; Richert, C. Solution-phase synthesis of branched DNA hybrids via H-phosphonate dimers. J. Org. Chem., published online February 27, 2012, DOI: 10.1021/jo202508n.
  • Griesser, H.; Tolev, M.; Singh, A.; Sabirov, T.; Gerlach, C.; Richert, C. Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. J. Org. Chem., published online February 27, 2012, DOI: 10.1021/jo202505h.
  • A. Singh, M. Tolev, M. Meng, K. Klenin, O. Plietzsch, C. I. Schilling, T. Muller, M. Nieger, S. Bräse, W. Wenzel, C. Richert, Branched DNA that forms a solid at 95 °C. Angew. Chem. 2011, 123, 3285-3289; Angew. Chem. Int. Ed. 2011, 50, 3227-3231.
  • K.J.C. Heimann, C. Richert, DNA-Mediated site-specific deposition of gold nanoparticles on silicon wafers. Nanoscale 2010, 2, 2579-2582.
  • K. Müller, S. Malik, C. Richert, Sequence-Specifically Addressable Hairpin DNA-SWCNT Complexes for Nanoconstruction. ACS Nano 2010, 4, 649-656.
  • C. Richert, M. Meng, A. Singh, Designed DNA crystals: Assembling triangles with short sticky ends (Highlight). Small 2009, 5, 2782-2783.
  • M. Meng, C. Ahlborn, M. Bauer, O. Plietzsch, S. A. Soomro, A. Singh, T. Muller, W. Wenzel, S. Bräse, C. Richert, Two base pair duplexes suffice to build a novel material. ChemBioChem 2009, 10 , 1335-1339.
  • C. Richert, M. Meng, K. Müller, K. Heimann, The third dimension: DNA-driven formation of nanoparticle crystals (Highlight). Small 2008, 4, 1040-1042.
  • S. R. Vogel, K. Müller, U. Plutowski, M. M. Kappes, C. Richert, DNA-carbon nanotube interactions and nanostructuring based on DNA. Phys. Stat. Sol. B, 2007, in press (DOI 10.1002/pssb.200776108).
  • U. Plutowski, S.S. Jester, S. Lenhert, M.M. Kappes, C. Richert, DNA-based self-sorting of nanoparticles on gold surfaces. Adv. Mat. 2007, 19, 1951-1956.
    Highlighted in: M. Berger,The long road to molecular electronics could be paved with DNA.Nanowerk Spotlight, 2007, August 6.
  • S. R. Vogel, M. M. Kappes, F. Hennrich, C. Richert, An unexpected new optimum in the structure space of DNA solubilizing single-walled carbon nanotubes. Chem. Eur. J. 2007, 13, 1815-1820.
  • S. Malik, S. Vogel, H. Rösner, K. Arnold, F. Hennrich, A.-K. Köhler, C. Richert, M.M. Kappes, Physical chemical characterisation of DNA-SWNT suspensions and associated composites. Comp. Sci. Tech. 2007, 67, 916-921.

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    High Fidelity DNA Microarrays

    Taking full advantage of the base pairing selectivity of arrayed oligonucleotide probes (DNA chips) requires duplex stabilities that are independent of G/C-content. Developing sequence independent high affinity/selectivity probes is one of the challenges in today's nucleic acid chemistry. Click here for a recent short essay (in German) and here for the pdf version of an older essay (in English) on this topic.

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  • M. Printz, C. Richert, Pyrenylmethyldeoxyadenosine: A 3'-cap for universal DNA hybridization probes. Chem. Eur. J. 2009, 15, 3390-3402.
  • C. Ahlborn, K. Siegmund, C. Richert, Isostable DNA. J. Am. Chem. Soc. 2007, 129, 15218-15232.
  • K. Siegmund, C. Ahlborn, C. Richert, ChipCheckII - Predicting binding curves for multiple analyte strands on small DNA microarrays, Nucleosides Nucleotides Nucl. Acids, 2008, 27, 376-388.
  • J. A. Rojas Stütz, C. Ahlborn, C. Richert, Ansätze zu "High Fidelity DNA-Microarrays". Bioforum 2006, 29 (5), 32-34.
  • K. Siegmund, U.E. Steiner, C. Richert, ChipCheck - A program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays. J. Chem. Inf. Comp. Sci. 2003, 43, 2153-2162.
  • T. Kottysch, C. Ahlborn, F. Brotzel, C. Richert, Stabilizing or destabilizing oligodeoxynucleotide duplexes containing single 2'-deoxyuridine residues with 5-alkynyl substituents. Chem. Eur. J. 2004, 10, 4017-4028.
  • Z. Dogan, R. Paulini, J.A. Rojas Stütz, S. Narayanan, C. Richert, 5'-Tethered stilbene derivatives as fidelity- and affinity-enhancing modulators of DNA duplex stability. J. Am. Chem. Soc. 2004, 126, 4762-4763.
  • C. Richert, M. Pankratz, DNA-Chips: Kleine Plättchen, mit denen sich die Aktivität des Genoms verfolgen lässt. Fridericiana 2004, 62, 19-32.
  • K.L. Dombi, N. Griesang, C. Richert, Oligonucleotide arrays from aldehyde-bearing glass with coated background. Synthesis 2002, 816-824.

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    Immunostimulatory Nucleic Acids

    Oligonucleotides (both DNA and RNA) stimulate the innate immune system, presumably through signalling by Toll-like receptors (TLRs). We study the structural basis of this phenomenon through chemical synthesis. Biological evaluation (in collaboration with the groups of profs. Dalpke and Heeg at the University of Heidelberg). This work is supported by the Landesstiftung Baden-Württemberg.

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  • F. Eberle, K. Giessler, C. Deck, K. Heeg, M. Peter, C. Richert, A. H. Dalpke, Modifications in siRNA that separate immunostimulation from RNA interference. J. Immunol. 2008, 180, 3229-3237.
  • G. He, A. Patra, K. Siegmund, M. Peter, K. Heeg, A. Dalpke, C. Richert, Immunostimulatory CpG oligonucleotides form defined three-dimensional structures: results from an NMR study. ChemMedChem 2007, 2, 549-560.
  • S. Narayanan, A.H. Dalpke, K.H. Siegmund, K. Heeg, C. Richert,CpG Oligonucleotides with modified termini and nicked dumbbell structure show enhanced immunostimulatory activity.J. Med. Chem. 2003, 46, 5031-5044.

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    Structure Elucidation of non-natural RNA Analogs and Peptide-Nucleic Acid Hybrids

    Our NMR-based structural work has several motivations. First, we want to gain structural insight into new modes of interaction between potential therapeutic agents and their targets. Particularly, we are interested in the duplexes formed between antisense oligonucleotides and their genetic targets. Second, we want to better understand ligand-nucleic acid and particularly protein-nucleic acid interactions. To this end, we use peptide-nucleic acid hybrid molecule. Linking entropically favors complex formation and provides structural preorientation. Structure elucidation starts with the acquisition of two- and, if necessary, three-dimensional NMR spectra, followed by peak assignments and generation of distance constraints. Restrained molecular dynamics are performed with both simulated annealing and the distance geometry algorithms. We employ the GIFA and XPLOR program packages, the most recent version of CNS (by A. Bruenger, Yale University), along with some software developed in-house. Spectroscopic work is performed both at U. Constance and at the Francis Bitter Magnet Labs at the MIT.
    Key Techniques: Multidimensional NMR, Restrained molecular dynamics

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  • J. Tuma, W.H. Connors, D.H. Stitelman, C. Richert, On the Effect of Covalently Appended Quinolones on Termini of DNA-Duplexes. J. Am. Chem. Soc. 2002, 124, 4236-4246.
  • W.C. Ho, C. Steinbeck, C. Richert, Solution Structure of the Aminoacyl-Capped Oligodeoxyribonucleotide Duplex (W-TGCGCAC)2, Biochemistry, 1999, 38, 12597-12606.
  • C. Steinbeck, C. Richert, The Role of Ionic Backbones in RNA Structure: An Unusually Stable non-Watson-Crick Duplex of a Non-Ionic Analog in an Apolar Medium. J. Am. Chem. Soc., 1998, 120, 11576-11580.
  • C. Steinbeck, C, Richert, Solution structure of a backbone-modified UC-dimer: An unusual recognition motif. Poster to be presented at the Conference "Multidimensional NMR in Structural Biology", Lucca (Italy), August 17-21, 1997.

  • Other Completed Projects

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    Combinatorial Synthesis and in Vitro Selection:
    Searching Structure Space Efficiently

    These experiments are being employed to search structure space for oligonucleotide derivatives with high affinity for single- and double-stranded targets, and have been shown to allow rapid genotyping of DNA from patient samples.

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    Spectrometrically monitored selection experiments (SMOSE)

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  • K.L. Dombi, U.E. Steiner, C. Richert, Rapidly Measuring Reactivities of Carboxylic Acids to Generate Equireactive Building Block Mixtures: A Spectrometric Assay. J. Combin. Chem. 2003, 5, 45-60.
  • J. Störker, C.N. Tetzlaff, J. Mayo, D.A. Sarracino, I. Schwope, C. Richert, Rapid genotyping via MALDI-monitored nuclease selection from probe libraries. Nature Biotechn. 2000, 18, 1213 - 1216.
  • Jay Störker, Jason Mayo, Charles N. Tetzlaff, David A. Sarracino, and Clemens Richert, Rapid Genotyping Using Spectrometrically Monitored Nuclease Selections, presented at the Conference Mass Spectrometry for Pharmaceutical Research, Orlando, FL, December 9-10, 1999.
  • R.K. Altman, I. Schwope, D.A. Sarracino, C.N. Tetzlaff, C.F. Bleczinski, C. Richert, Selection of modified oligonucleotides with increased target affinity via MALDI-monitored nuclease survival assays, J. Combin. Chem., 1999, 1, 493-508.
  • C. F. Bleczinski, C. Richert, Monitoring the hybridization of the components of oligonucleotide mixtures to immobilized DNA via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Rapid Comm. Mass Spectrom., 1998, 12, 1737-1743.
  • K. Berlin, D.A. Sarracino, R.K. Jain, C. Steinbeck, C. Richert, MALDI-TOF analysis of combinatorial libraries of porphyrins. Poster presented at ASMS, Orlando, May 31-June 4, 1998.
  • K. Berlin, R.K. Jain, C. Tetzlaff, C. Steinbeck, C. Richert, Spectrometrically monitored selection experiments: quantitative laser desorption mass spectrometry of small chemical libraries. Chemistry & Biology 1997, 4, 63-77; 1997, 4, 237- 238.

  • MASP - a program predicting mass spectra of combinatorial libraries

    In order to search structure space efficiently for new functional molecules, our lab has developed monitored selection assays. These involve small chemical libraries and a spectrosc opic technique for detecting the library components simultaneously. We find MALDI-TOF mass spectrometry to be particularly useful in this context, as it produces essentially fragmentation-free spectra or, in the case of isotopically resolved spectra, one peak cluster of minimal spectral width. The size of libraries that can be employed in such experiments is limited, among other things, by the spectral overlap, i.e. by the number of isobaric library components. Optimization of mass spectrometrically mo nitored selection experiments therefore called for a computational tool that would facilitate the choice of library components. MASP, a computer program that scans meta-library space, is such a tool.

  • C. Steinbeck, K. Berlin, C. Richert, MASP - a program predicting mass spectra of combinatorial libraries. J. Chem. Inf. Comput. Sci., 1997, 37, 449-457.

  • Automaton - A program (perl) for analyzing MALDI-TOF monitored nuclease selection assays(1)

    DAS - a computer macro (aura) for integrating peaks in MALDI-TOF mass spectra of small libraries(1)

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    (1) R.K. Altman, I. Schwope, D.A. Sarracino, C.N. Tetzlaff, C.F. Bleczinski, C. Richert,
    Selection of modified oligonucleotides with increased target affinity via MALDI-monitored nuclease survival assays,
    J. Combin. Chem., 1999, 1, 493-508.

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    Natural Products

    Natural products are important building blocks for our combinatorial work and interesting synthetic targets in themselves. We synthesize and modify natural products.

  • D.L. Daniels, C. Richert, One-pot synthesis of L-felinine. Tetrahedron Lett. 1999, 40, 4463-4465.

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    Peptide-DNA Hybrids: Synthesis and Selection of Acyl-DNA Hybrids

    The long term goal of this research project is to use the combined DNA and peptide structure space to search for new therapeutic agents that bind to DNA or RNA targets. Presently, we focus on hybrids between single stranded DNA and short peptides with the underlying theme to tune the bioavailability and recognition properties of oligonucleotides by complexing them with ligands rather than by replacing atoms in their backbone. Peptide-DNA hybrids are "selectable" entities. This work uses combinatorial synthesis and in vitro selection to identify hybrids with increased stability against enzymatic degradation and with increased affinity for target strands. Critical positions in the hybrids are randomized to produce small libraries. The survival of the individual members of these libraries under selection conditions is monitored directly, using quantitative laser desorption mass spectrometry in a new form of assay established in these laboratories (Berlin, et al. & Richert Chemistry & Biology 4 (1997) 63).
    Covalently linking a peptide and an oligonucleotide entropically favors the formation of a complex. The hybrids proposed here are therefore ideal entities for studying interactions that may otherwise be too weak or too unspecific to be studied in solution. Our work will involve elucidation of the three-dimensional structure of selected peptide-DNA hybrids by multidimensional NMR and molecular dynamics.
    Key Techniques: Semi-automated synthesis of peptide-DNA hybrids, Quantitative MALDI-TOF mass spectrometry, Enzymatic in vitro selection and footprinting.

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  • D.A. Sarracino, C. Richert, Synthesis and Nuclease Stability of Trilysyl Dendrimer-Oligodeoxyribonucleotide Hybrids. Bioorg. Med. Chem. Lett. 2001, 11, 1733-1736.
  • C.F. Bleczinski, C. Richert, Solid-phase synthesis of cyclic peptide-DNA hybrids. Org. Lett. 2000, 2, 1697-1700.
  • I. Schwope, C.F. Bleczinski, and C. Richert, Synthesis of 3',5'-Dipeptidyl Oligonucleotides, J. Org. Chem., 1999, 64, 4749-4761.
  • D.A. Sarracino, J.A. Steinberg, M.T. Vergo, G.F. Woodworth, C.N. Tetzlaff, C. Richert, 5'-Peptidyl Substituents Allow a Tuning of the Affinity of Oligodeoxyribonucleotides for RNA. Bioorg. Med. Chem. Lett., 1998, 8, 2511-2516.
  • C.N. Tetzlaff, D.A. Sarracino, I. Schwope, J.A. Steinberg, C.F. Bleczinski, M.T. Vergo, W. Ho, C. Richert, 5'-Peptidyl-DNA:Synthesis and Binding Studies. Presented at the 216th ACS Meeting, Boston, August 23-27, 1998.
  • Charles N. Tetzlaff, Ina Schwope, Colleen F. Bleczinski, Joshua A. Steinberg, Clemens Richert, A convenient synthesis of 5'-amino-5'-deoxythymidine and preparation of peptide-DNA hybrids. Tetrahedron Lett., 1998, 39, 4215-4218.
  • K. Berlin, R.K. Jain, C. Tetzlaff, C. Steinbeck, C. Richert, Spectrometrically monitored selection experiments: quantitative laser desorption mass spectrometry of small chemical libraries. Chemistry & Biology 1997, 4, 63-77; 1997, 4, 237-238.
  • C. Tetzlaff, D. Sarracino, I. Schwope, C. Bleczinski & C. Richert, "Synthesis and in Vitro Selection of Peptide-DNA Hybrids: Towards Ligand-Shielded Oligonucleotides." presented at the Nature Biotechnology Conference "Antisense 97", Cambridge, Massachusetts, May 1-2, 1997

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    Porphyrin Synthesis

    Porphyrins are photoactive heterocyclic macro cycles with important biological functions. Our synthetic efforts focus on porphyrins that can be employed as sensitizers for photodynamic therapy and porphyrins that interact with nucleic acids. Among possible nucleic acid targets, single-stranded DNA and RNA are of particular interest to us. We have established combinatorial syntheses for a number of different tetraphenylporphyrin species and have also succeeded in incorporating an alkylporphyrin in the backbone of DNA.

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  • K.L. Dombi, C. Richert, Relative reactivities of activated carboxylic acids in amide-forming reactions employed for the synthesis of tetraphenylporphyrin libraries. Molecules 2000, 5, 1265-1280.
  • M.D. Simon, C. Richert, Synthesis and Selection of Peptidyl-Tetraphenylporphyrins: Toward Target-Specific Nucleic-Acid Ligands. Poster presented at the 217th American Chemical Society National Meeting, Anaheim, CA, March 1999: Abstr. Pap. Am. Chem. Soc. 1999, 217, 558.
  • K. Berlin, R. K. Jain, C. Richert, Are porphyrin mixtures favorable photodynamic anticancer drugs? A model study with combinatorial libraries of tetraphenylporphyrins. Biotechn. Bioengin.: Combin. Chem. 1998, 61, 107-118.
  • K. Berlin, R.K. Jain, M.D. Simon, C. Richert, A porphyrin embedded in DNA. J. Org. Chem, 1998, 63, 1527-1535.
  • Rishi K. Jain, David A. Sarracino, and Clemens Richert, A tetraphenylporphyrin-peptide hybrid with high affinity for single-stranded DNA. Chem. Comm., 1998, 423-424.

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    Photodynamic Therapy

    Photodynamic therapy is a binary treatment modality for neoplastic tissue. Photodynamic therapy of tumors has b een approved for treatment of esophageal cancer (USA), lung and esophageal cancer (France and Netherlands), esophageal and bladder cancer (Canada), and early-stage lung cancer, superficial and esophageal cancer, superficial and early stage gastric cancer, early stage cervical cancer, and cervical dysplasia (Japan) with photofrin, a porphyrin mixture as sensitizer. Our work in this area focuses on the chemical and physical principles that underlie tumor selective localization and site-selective action.

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  • K. Berlin, R. K. Jain, C. Richert, Are porphyrin mixtures favorable photodynamic anticancer drugs? A model study with combinatorial libraries of tetraphenylporphyrins. Biotechn. Bioengin.: Combin. Chem., 1998, 61, 107-118.
  • M. Dellian, C. Richert, F. Gamarra, A.E. Götz, Photodynamic eradication of amelanotic melanoma of the hamster with fast acting photosensitizers. Int. J. Cancer, 1996, 65, 246-248.
  • C. Richert, J.M. Wessels, M. Mller, M. Kisters, T. Benninghaus, A.E. Götz, Photodynamic antitumor agents: b-methoxyethyl groups give access to functionalized porphycenes and enhance cellular uptake and activity. J. Med. Chem., 1994, 37, 2797-2807.
  • M. Leunig, C. Richert, F. Gamarra, W. Lumper, E. Vogel, D. Jocham, A.E. Götz, Tumour localization kinetics of photofrin and three synthetic porphyrinoids in an amelanotic melanoma of the hamster. Br. J. Cancer, 1993, 68, 225-234.
  • F. Gamarra, F. Yuan, A.E. Götz, M. Leunig, C. Richert, R.K. Jain, K. Messmer, Monitoring extravascular transport of porphycenes. In P. Spinelli, M. Dal Fante, R. Marchesini (Eds.) "Photodynamic therapy and biomedical lasers", Elsevier, Amsterdam, Excerpta Med., 1992, 1011, 706-709.

  • Two of the structures frequently employed in our work:

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