Nucleic Acid Chemistry
Beilstein Organic Chemistry Symposium 2016

5 – 7 October 2016
Yachthotel Chiemsee, Prien (Chiemsee), Germany


Scientific Program:
Hans-Achim Wagenknecht / Karlsruhe Institute of Technology, Germany



The symposium  has been inspired by the thematic issue “Nucleic Acid Chemistry” in the Open Access Beilstein Journal of Organic Chemistry, edited by Hans-Achim Wagenknecht.


The Beilstein Organic Chemistry Symposium 2016 was inspired by the Thematic Series “Nucleic acid chemistry” in the Beilstein Journal of Organic Chemistry. Organized by Professor Hans-Achim Wagenknecht (Karlsruhe Institute of Technology), the symposium took place with 51 participants in Prien am Chiemsee (Germany, Bavaria) from 5th to 7th October 2016.

Since the discovery of solid-phase DNA (and later RNA) synthesis by methods of organic chemistry, the field of nucleic acid chemistry exploded. Natural and artificial functionalities as well as probes, markers or other biologically active molecules can be introduced synthetically into DNA, and in the meantime also into RNA, by preparing the corresponding artificial DNA building blocks. More recently, the chemistry was further developed for the case that building blocks are synthetically not obtainable. The so-called postsynthetic methodologies allow the modification of oligonucleotides even for those cases. This is especially important for functionalities, probes or biologically relevant molecules that are not compatible with the routinely applied phosphoramidite chemistry. Although nucleic acid chemistry seems to be already a mature part of organic and bioorganic chemistry, actual questions that are raised by research in biology and chemical biology give enough reasons to synthesize new nucleic acid probes and thereby further develop nucleic acid chemistry. Moreover, beside its biological functionality, DNA and RNA are considered as an increasingly important architecture and scaffold for two- and three-dimensional objects, networks and materials for nanosciences.

These broad aspects of nucleic acid chemistry were covered by the topics of five different sessions that included 21 invited speakers. In the first session “new nucleic acid building blocks”, Annemieke Madder reported on modified nucleic acids for crosslinks and Elmar Weinhold talked about sequence-specific labeling of DNA by methyltransferases. Sabine Müller described trinucleotide phosphoramidites and Michal Hocek allowed an insight into polymerase-assisted synthesis of modified nucleic acids. The second session on Wednesday covered “nucleic acid analogs and lipids”. The lipid aspect was discussed by Helmut Rosemeyer and Tirayut Vilaivan showed how the constrained pyrrolidinyl PNA binds to DNA. Hiroyuki Asanuma followed this path by a report on threolinol and serinol nucleic acid analogs and Jesper Wengel extended the topic by peptide-nucleic acid conjugates. In the evening, a poster session with 21 presentations took place – the first time within the Beilstein Organic Chemistry Symposia. The open end timeline in the evening after dinner allowed intense discussions about all aspects of nucleic acids by PhD researchers, postdocs and junior professors together with the invited speakers. It became clear that a poster session is not only important but a crucial part of the program for this type of conference.

The single session on Thursday was focused on light-driven and fluorescent functionalities and started with Nathan Luedtke talking about biorthogonal fluorescent reporters for nucleic acids in cells and Oliver Seitz focusing on enhanced hybridization probes for RNA imaging. Heiko Ihmels described DNA-binding cationic heteroarenes and Robert Häner left the classic biological purpose of DNA by describing supramolecular materials with optoelectronic functions. Hans-Achim Wagenknecht wrapped up the session by a report on light-driven functionalities in DNA. In the afternoon, the social program included a boat trip across the Chiemsee to the “Herreninsel” and a visit of King’s Ludwig II great castle “Herrenchiemsee”. Although the weather forecast was absolutely terrible, it stayed dry and the group was lucky to experience a great afternoon with intense social discussions.

The program on Friday started with the session “new nucleic acid architectures and base pairs” and comprised a presentation by Jens Müller on metal-mediated base pairing and a lecture by Clemens Richert on prebiotic aspects of peptido RNA formation. Tom Brown presented the chemical ligation of DNA by “click”-type chemistry and Thomas Carell talked about unusual bases in our genome and their epigenetic functions. The afternoon session turned the focus on RNA and was entitled “RNA and catalytically active nucleic acids”. Andrea Rentmeister gave a chemical biology perspective on the 5’-cap and Snorri Sigurdsson described strategies for site-directed spin labeling of nucleic acids. In the last two presentations of this conference, Claudia Höbartner gave insights in the structural basis of DNA catalysis and Ronald Micura showed modified RNA for the exploration of riboswitch and ribozyme functions.

I am very thankful to the speakers for the great contributions and to all the registered participants for fruitful and lively discussions not only during the sessions but also during coffee, lunch and dinner breaks. The program was not tightly packed to give enough room for such discussions. Thereby, the conference completely fulfilled its purpose: A market place of new scientific developments and results in a relaxed atmosphere to allow speaking with scientific friends. The Yachthotel at the Chiemsee represents the perfect setting of such a conference with a mixture of local Bavarian tradition and superior modern hotel style. Great thanks also to the Beilstein-Institut for financial support and in particular to Dr. Michael Penk and Dr. Peter Dietel for organizing this conference just perfectly and thereby giving a Beilstein Organic Chemistry Symposium 2016 that was scientifically fruitful and memorable.


Hans-Achim Wagenknecht
Karlsruhe, 2nd December 2016

Scientific Program


WEDNESday, 5 OCTOber


Welcome and Introduction 

Session chair: Nathan Luedtke

Modified nucleic acids for crosslinking and catalysis
Annemieke Madder / Ghent University, Belgium

Sequence-specific labeling of DNA with methyltransferases and cofactor analogues
Elmar Weinhold / RWTH Aachen University, Germany

Coffee break

Trinucleotide phosphoramidites: Superior building blocks for the synthesis of controlled randomized gene libraries
Sabine Müller / University of Greifswald, Germany

Polymerase synthesis of base-modified nucleic acids: New methods and new applications
Michal Hocek / Academy of Sciences, Prague, Czech Republic



Session chair: Oliver Seitz

Nucleolipids: Synthesis, biomedical activity, and hydrophobization tools for nucleic acids for their incorporation into artificial lipid membranes
Helmut Rosemeyer / University of Osnabrück, Germany

Pyrrolidinyl peptide nucleic acids with a/β-peptide backbone: Synthesis, properties and applications
Tirayut Vilaivan / Chulalongkorn University, Bangkok, Thailand

Coffee break

D-L-aTNA and SNA as a new class of acyclic XNA
Hiroyuki Asanuma / Nagoya University, Japan

Playing chemistry on nucleic acids and their peptide conjugates
Jesper Wengel / University of Southern Denmark, Odense, Denmark





Presentation and discussion of all posters


Thursday, 6 october


Session chair: Hiroyuki Asanuma

Bioorthogonal chemical reporters of DNA metabolism
Nathan Luedtke / University of Zurich, Switzerland

Enhanced hybridization probes for RNA imaging
Oliver Seitz / Humboldt University Berlin, Germany

Coffee break

Reversible in situ generation of DNA-binding cationic hetarenes
Heiko Ihmels / University of Siegen, Germany

DNA-inspired supramolecular materials
Robert Häner / University of Bern, Switzerland

Light-driven functions in DNA
Hans-Achim Wagenknecht / Karlsruhe Institute of Technology, Germany





FRIday, 7 OCTOber


Session chair: Hans-Achim Wagenknecht

Metal-mediated base pairing using 1H-imidazo[4,5-f][1,10]phenanthroline as artificial nucleobase
Jens Müller / University of Münster, Germany

Peptido RNA from ribonucleotides and amino acids
Clemens Richert / University of Stuttgart, Germany

Coffee break

Chemical ligation of DNA, biocompatibility and applications of artificial backbones
Tom Brown / University of Oxford, UK

Unusual DNA bases in our genomes
Thomas Carell / LMU Munich, Germany





Session chair: Jesper Wengel

A chemical biology perspective on the 5' cap
Andrea Rentmeister / University of Münster, Germany

Strategies for site-directed spin labeling of nucleic acids
Snorri Sigurdsson / University of Iceland, Reykjavik, Iceland

Coffee break

The structural basis of DNA catalysis
Claudia Höbartner / University of Göttingen, Germany

Modifying RNA to explore riboswitch and ribozyme function
Ronald Micura / University of Innsbruck, Austria




No. 1:
Manipulation of the mRNA 5’-cap at the N7 position as valuable platform for RNA labeling, translation and interaction studies
Lea Anhäuser / University of Münster

No. 2:
Distance dependency of thymine-thymine-dimer formation in benzophenone-modified DNA
Linda Antusch / Karlsruhe Institute of Technology

No. 3:
Alkene-tetrazine ligation as a tool for DNA labeling
Anna Bujalska / University of Zurich

No. 4:
Interstrand crosslinking of DNA using strain-promoted click chemistry
Zahra Harati Taji / University of Zurich

No. 5:
Developing emissive isomorphic nucleosides
Aaron Johnson / University of Zurich

No. 6:
Synthesis and structural elucidation of Formycin A-nucleolipids
Christine Knies / University of Osnabrück

No. 7:
Click-linked DNA for one-pot gene synthesis
Mikiembo Kukwikila / University of Southampton

No. 8:
Triazole-linked locked nucleic acids
Pawan Kumar / University of Oxford

No. 9:
Synthesis and genetic selection of acyclic oxomethylenephosphono oligonucleotides (ONA)
Min Luo / KU Leuven

No. 10:
Synthesis of chemical tools for targeted epigenetic modifications
Ha Phuong Nguyen / University College London

No. 11:
Double-headed nucleotides as new building blocks for nucleic acid architectures
Poul Nielsen / University of Southern Denmark

No. 12:
New strategies for the label-free optical detection of oliginucleotides or antibodies with surface plasmon fluorescence spectroscopy
Gilbert Nöll / University of Siegen

No. 13:
Electrochemically switchable protein-DNA layers
Gilbert Nöll / University of Siegen

No. 14:
Aggregation-inclined dyes as resource of multitarget-probes for DNA and RNA
Ivo Piantanida / Ruđer Bošković Institute

No. 15:
Structural basis of the mispairing of an artificially expanded genetic information system
Linus Reichenbach / University of Strathclyde

No. 16:
Kinetic and thermodynamic stabilities of T-HgII-T base pairs: Inhibition of DNA polymerases
Olivia Schmidt / University of Zurich

No. 17:
New insights into 8-Vinyl-2‘-Deoxyguanosine and 8-Vinyl-Guanosine
Julia Schneider / University of Göttingen

No. 18:
Synthesis and optical properties of cyanine dyes as wavelength-shifting fluorescent DNA and siRNA probes
Jeannine Steinmeyer / Karlsruhe Institute of Technology

No. 19:
Berberine dimer as a turn-on fluorescent G-quadruplex ligand by its conformational change
Masayuki Tera / Suntory Foundation for Life Sciences

No. 20:
Temperature-controlled and programmable fusion of liposomes
Stefan Vogel / University of Southern Denmark

No. 21:
Development of bright fluorescent base analogues for applications in FRET
Marcus Wilhelmsson / Chalmers University of Technology

Gruppenfoto Org Chem Symposium 2016