Project

Back to overview

Chemically modified oligonucleotides - properties and applications

English title Chemically modified oligonucleotides - properties and applications
Applicant Leumann Christian
Number 165787
Funding scheme Project funding (Div. I-III)
Research institution Departement für Chemie und Biochemie Universität Bern
Institution of higher education University of Berne - BE
Main discipline Organic Chemistry
Start/End 01.04.2016 - 30.09.2018
Approved amount 700'000.00
Show all

All Disciplines (3)

Discipline
Organic Chemistry
Cellular Biology, Cytology
Biochemistry

Keywords (4)

RNA damage; chemically modified oligonucleotides; RNA therapeutics; antisense agents

Lay Summary (German)

Lead
Die Deoxyribonukleinsäure (DNA) enthält den genetischen Bauplan jeder lebenden Zelle. Kurze Stücke von DNA oder ihres Abbildes, der Ribonukleinsäure (RNA), haben aber auch regulatorische Funktionen. Sie können beispielsweise dafür verantwortlich sein, dass gewisse Gene an- oder abgestellt werden. Des weiteren hat die Natur einen komplexen Schutzmechanismus gegen chemische Schäden der DNA aufgebaut, doch ob und wie ihr Abbild RNA geschützt wird ist weitgehend unbekannt. Im Gebiete der synthetischen Biologie stellt sich des weiteren die Frage, ob es auch alternative molekulare Systeme gibt, welche als genetisches Material in Frage kämen. Gegenstand des vorliegenden Projektes ist die Synthese von chemisch veränderten Nukleosiden und Oligonukleotiden und deren Testung als potentielle Wirkstoffe in der Medizinalchemie, als alternative genetische Systeme oder deren Verwendung zur Untersuchung des biologischen Einflusses von RNA-Schäden.
Lay summary

Im ersten Teilprojekt werden neue chemische Modifikationen der von uns entwickelten Leitstruktur Tricyclo-DNA (tc-DNA) vorgeschlagen. Diese chemischen Modifikationen werden am tricyclo-Zuckergerüst durchgeführt und dienen der Verbesserung des Transports im Blutplasma sowie der zellulären Aufnahme. Zusätzlich sind Experimente zum besseren Verständnis der spontanen Bildung von tc-DNA Nanopartikel sowie deren Rolle in den biologischen Eigenschaften von tc-DNA geplant. Im zweiten Teilprojekt soll eine neue DNA-Modifikation auf ihre Eignung als alternatives genetisches Material untersucht werden. Die Modifikation leitet sich aus unseren früheren Arbeiten zur Bicyclo-DNA ab. In einer ersten Phase soll untersucht werden, ob natürliche oder genetisch veränderte DNA Polymerasen diese chemisch veränderten Nukleoside als Substrate akzeptieren und polymerisieren. In einer 2. Phase sollen mittels gezielter molekularer Evolutionsprozesse neue Aptamere und DNA-Enzyme gwonnen werden. Im dritten Teilprojekt befassen wir uns mit der Synthese und der chemischen Stabilität von RNA mit oxidierten Pyrimidinbasen wie zum Beispiel 5-Hydroxycytosin. Diese oxidierten Basen entstehen in der Natur durch 'reactive oxygen species'. Ausserdem untersuchen wir den Einfluss solcher RNA-Schädigungen auf die Funktion des Ribosms und der ribosomalen Translation.

Die vorgeschlagenen Teilprojekte stehen in Zusammenhang mit der Erschliessung neuer Therapeutika auf der Basis von Oligonuckleotiden, der Erschliessung neuer genetischer Systeme zur Verbesserung und Erweiterung von biotechnologischen Prozessen sowie dem Verständnis der Fogen von natürlicher, oxidativer Schädigung der RNA.

Direct link to Lay Summary Last update: 01.04.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA
Frei Sibylle, Katolik Adam K, Leumann Christian J (2019), Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA, in Beilstein Journal of Organic Chemistry, 15, 79-88.
6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations
Frei Sibylle, Istrate Andrei, Leumann Christian J (2018), 6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations, in Beilstein Journal of Organic Chemistry, 14, 3088-3097.
Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center
Willi Jessica, Küpfer Pascal, Evéquoz Damien, Fernandez Guillermo, Katz Assaf, Leumann Christian, Polacek Norbert (2018), Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center, in Nucleic Acids Research, 46(4), 1945-1957.
2′β-Fluoro-Tricyclo Nucleic Acids (2′F-tc-ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation
Istrate Alena, Katolik Adam, Istrate Andrei, Leumann Christian J. (2017), 2′β-Fluoro-Tricyclo Nucleic Acids (2′F-tc-ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation, in Chemistry - A European Journal, 23(43), 10310-10318.
Enzymatic Synthesis of 7′,5′-Bicyclo-DNA Oligonucleotides
Diafa Stella, Evéquoz Damien, Leumann Christian J., Hollenstein Marcel (2017), Enzymatic Synthesis of 7′,5′-Bicyclo-DNA Oligonucleotides, in Chemistry - An Asian Journal, 12(12), 1347-1352.
Probing the Backbone Topology of DNA: Synthesis and Properties of 7′,5′-Bicyclo-DNA
Evéquoz Damien, Leumann Christian J. (2017), Probing the Backbone Topology of DNA: Synthesis and Properties of 7′,5′-Bicyclo-DNA, in Chemistry - A European Journal, 23(33), 7953-7968.
Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates
Roethlisberger Pascal, Kaliginediand Veerabhadrarao, Leumann Christian J. (2017), Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates, in Chemistry - A European Journal, 23(9), 2022-2025.
3CAPS – a structural AP–site analogue as a tool to investigate DNA base excision repair
Schuermann David, Scheidegger Simon P., Weber Alain R., Bjørås Magnar, Leumann Christian J., Schär Primo (2016), 3CAPS – a structural AP–site analogue as a tool to investigate DNA base excision repair, in Nucleic Acids Research, 44(5), 2187-2198.
X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Roethlisberger P., Istrate A., Marcaida Lopez M. J., Visini R., Stocker A., Reymond J.-L., Leumann C. J. (2016), X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair, in Chemical Communications, 52(26), 4749-4752.

Collaboration

Group / person Country
Types of collaboration
Synthena AG Switzerland (Europe)
- Industry/business/other use-inspired collaboration
Dr. Kariem Ezzat, Karolinska Institut, Stockholm Sweden (Europe)
- Publication
Prof.Norbert Polacek/University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Dr. Luis Garcia, Dr. Aurélie Goyenvalle, Université de Versailles France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. R. Sigel, UniZH Switzerland (Europe)
- Publication

Associated projects

Number Title Start Funding scheme
130373 Chemically modified Oligonucleotides for Biotechnology and Material Sciences 01.04.2010 Project funding (Div. I-III)

Abstract

In this grant application we present three projects that are situated in the area of oligonucleotide chemistry and biology and that address questions of current interest in the fields of oligonucleotide therapy, artificial genetic systems and RNA damage and its biological consequences.In the first project which is grouped into sub-projects A-D we will focus mostly on understanding and improving the molecular properties of tricyclo-DNA (tc-DNA) which has been developed in our laboratory and is currently in consideration for clinical trials. The goal of sub-project A is to obtain high resolution NMR structures on tc-DNA/RNA duplexes and on other modified tc-DNA duplexes. This is necessary because we have been unsuccessful in the past to obtain high resolution structures of tc-DNA by X-ray crystallography. Knowing the structure in detail, however, is an important prerequisite to determine potential sites for further chemical modification. In sub-project B we will focus on tc-DNA modifications carrying fluorine substituents in various positions. This work is inspired by recent reports in which differential protein binding of fluorinated nucleic acids is described. Furthermore, due to conformational control of the ribose unit in tc-DNA, we expect to overcome current limitations in the use of tc-DNA/DNA mixmers, and may be able to generate a tc-DNA version that is able to elicit RNase H activity. In sub-project C we propose novel tc-DNA modifications that vary in their degree of hydrophobicity. With this we aim at improving cellular uptake and, eventually, at generating therapeutically active oligonucleotides that need no phosphorothioate backbone. Sub-project D is overarching all activities in this project by collecting all modifications and determine their plasma protein binding pereferences as well as their propensity to form nanoparticles. This will shed light on the importance of nanoparticle formation with respect to cellular uptake which is of great current interest.In the second project we want to develop an artificial genetic system based on 7’-5’-bc-DNA. This modification has previously been investigated in our group and shows the required chemical properties. Preliminary experiments show that this modification is successfully processed by DNA polymerases. We therefore propose to perform molecular evolution by SELEX with this modification. We expect the emergence of different folding patters for single strands which may be beneficial for the binding properties of corresponding aptamers and DNAzymes.The third project deals with questions on the biological consequences of oxidative RNA base damage. In two sub-projects we will determine the mechanism of base decay of 5-hydroxy-pyrimidines that are the primary products of oxidation by reactive oxygen species and will investigate the consequences of site-specific oxidative base lesions in the ribosome on translation (in collaboration with Prof. N. Polacek in or department).
-