A5010094521- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- RNA Interference and Gene Delivery
- Click Chemistry and Applications
- Chemical Synthesis and Analysis
- RNA and protein synthesis mechanisms
- Alzheimer's disease research and treatments
- HIV/AIDS drug development and treatment
- Cholinesterase and Neurodegenerative Diseases
- Computational Drug Discovery Methods
- Advanced Biosensing Techniques and Applications
- Photochromic and Fluorescence Chemistry
- Sulfur-Based Synthesis Techniques
- Synthesis and Characterization of Heterocyclic Compounds
- MicroRNA in disease regulation
- Free Radicals and Antioxidants
- Amino Acid Enzymes and Metabolism
- Biosensors and Analytical Detection
- Carbohydrate Chemistry and Synthesis
- Chemical Reaction Mechanisms
- Adenosine and Purinergic Signaling
- Monoclonal and Polyclonal Antibodies Research
- Neuroscience and Neuropharmacology Research
Karolinska Institutet
2013-2022
Integrated Cardio Metabolic Centre
2015
Södertörn University
2014
Uppsala University
2005-2010
Institute of Molecular Biology
2009
KU Leuven
2009
Goethe University Frankfurt
2009
University of Southern Denmark
2009
Max Planck Institute of Molecular Cell Biology and Genetics
2009
The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method choice to manipulate gene expression in mammalian cell culture, yet improvements siRNA design expectably required for successful application vivo. Several studies have aimed at improving performance through introduction chemical modifications but a direct comparison these results difficult. We directly compared effect 21 types on activity and toxicity total 2160 duplexes. demonstrate that primarily...
The amyloid-β hypothesis of Alzheimer's Disease (AD) focuses on accumulation peptide (Aβ) as the main culprit for myriad physiological changes seen during development and progression AD including desynchronization neuronal action potentials, consequent aberrant brain rhythms relevant cognition, final emergence cognitive deficits. aim this study was to elucidate cellular synaptic mechanisms underlying Aβ-induced degradation gamma oscillations in AD, identify aggregation state(s) Aβ that...
The 2'-deoxy-2'-N,4'-C-ethylene-bridged thymidine (aza-ENA-T) has been synthesized using a key cyclization step involving 2'-ara-trifluoromethylsufonyl-4'-cyanomethylene 11 to give pair of 3',5'-bis-OBn-protected diastereomerically pure aza-ENA-Ts (12a and 12b) with the fused piperidino skeleton in chair conformation, whereas pentofuranosyl moiety is locked North-type conformation (7° < P 27°, 44° φm 52°). origin chirality two was found be due endocyclic chiral 2'-nitrogen, which axial N−H...
The 2-(4-tolylsulfonyl)ethoxymethyl (TEM) as a new 2'-OH protecting group is reported for solid-supported RNA synthesis using phosphoramidite chemistry. usefulness of the 2'-O-TEM exemplified by 12 different oligo-RNAs various sizes (14-38 nucleotides long). stepwise coupling yield varied from 97-99% with an optimized time 120 s. all four pure building blocks also described. Two reliable parameters, delta(C2')-delta(C3') and delta(H2')-delta(H3'), have been suggested characterization...
The DNA probes (ODNs) containing a 2'-N-(pyren-1-yl)-group on the conformationally locked nucleosides [2'-N-(pyren-1-yl)carbonyl-azetidine thymidine, Aze-pyr (X), and 2'-N-(pyren-1-yl)carbonyl-aza-ENA Aza-ENA-pyr (Y)], show that they can bind to complementary RNA more strongly than DNA. (X) ODNs with duplexes showed an increase in fluorescence intensity (measured at λem ≈ 376 nm) depending upon nearest neighbor 3'-end X [dA (∼12−20-fold) > dG (∼9−20-fold) dT (∼2.5−20-fold) dC (∼6−13-fold)]....
The synthesis of novel 1',2'-aminomethylene bridged (6-aza-2-oxabicyclo[3.2.0]heptane) "azetidine" pyrimidine nucleosides and their transformations to the corresponding phosphoramidite building blocks (20, 39, 42) for automated solid-phase oligonucleotide is reported. bicyclonucleoside monomers were synthesized by two different strategies starting from known sugar intermediate 6-O-benzyl-1,2:3,4-bis-O-isopropylidene-d-psicofuranose. Conformational analysis performed molecular modeling (ab...
The RNase H cleavage potential of the RNA strand basepaired with complementary antisense oligonucleotides (AONs) containing North−East conformationally constrained 1',2'-methylene-bridged (azetidine-T and oxetane-T) nucleosides, North-constrained 2',4'-ethylene-bridged (aza-ENA-T) nucleoside, 2'-alkoxy modified nucleosides (2'-O-Me-T 2'-O-MOE-T modifications) have been evaluated compared under identical conditions. When to native AON, aza-ENA-T AON/RNA hybrid duplexes showed an increase...
Improving oligonucleotide delivery is critical for the further development of oligonucleotide-based therapeutics. Covalent attachment reporter molecules one most promising approaches toward efficient therapies. An methods a variety groups Cu(I)-catalyzed Huisgen azide–alkyne 1,3-dipolar cycloaddition. However, majority potential (ON) therapeutics in clinical trials are carrying phosphorothioate (PS) linkages, and this robust conjugation method not yet established these ONs due to general...
In order to understand how the chemical nature of conformational constraint sugar moiety in ON/RNA(DNA) dictates duplex structure and reactivity, we have determined molecular structures dynamics conformationally constrained 1',2'-azetidine- 1',2'-oxetane-fused thymidines, as well their 2',4'-fused thymine (T) counterparts such LNA-T, 2'-amino ENA-T, aza-ENA-T by NMR, ab initio (HF/6-31G** B3LYP/6-31++G**), simulations (2 ns explicit aqueous medium). It has been found that, depending upon...
2′-<italic>O</italic>-AECM modified oligonucleotides provide a combination of remarkable properties, such as high stability towards degradation, stable duplexes with RNA and enhanced cellular uptake.
Oligonucleotide (ON) conjugates are increasingly important tools for various molecular diagnostics, nanotechnological applications, and the development of nucleic acid-based therapies. Multiple labeling ONs can further equip ON-conjugates provide improved or additional tailored properties. Typically, preparation ON multiconjugates involves synthetic steps and/or manipulations in post-ON assembly. This report describes simplified methodology allowing multiple on a solid support is compatible...
We here show that the pKa (error limit: 0.01 to 0.03 unit) of a nucleobase in nucleotide can be modulated by chemical nature 2′-substituent at sugar moiety. This has been evidenced measurement 47 different model nucleoside 3′,5′-bis- and 3′-mono-ethylphosphates. The fact electronic character each 2′-substituents (Fig. 1) alters shift H2′ proton, also nucleotides correlation plot N3 pyrimidine (T/C/U) or N7 9-guaninyl with corresponding δH2′ shifts neutral pH, which shows linear high...
An efficient method for the synthesis of multiply functionalized oligonucleotides (ONs) utilizing a novel H-phosphonate alkyne-based linker multiple functionalization (LMF) is developed. The strategy allows conjugation various active entities to oligonucleotide through postsynthetic attachment LMF at 5'-terminus ONs using chemistry followed by via [3 + 2] copper(I) catalyzed cycloaddition in stepwise manner. Each cycle composed click reaction with azido-containing units. Sequential...
During the F – -promoted deprotection of oligo–RNA, synthesized using our 2′-O-(4-tolylsulfonyl)ethoxymethyl (2′-O-TEM) group [Org. Biomol. Chem. 5, 333 (2007)], p-tolyl vinyl sulphone (TVS) is formed as a by-product. The TVS has been shown to react with exocyclic amino functions adenosine (A), guanosine (G), and cytidine (C) fully deprotected oligo–RNA give undesirable adducts, which are then purified by HPLC unambiguously characterized 1 H, 13 C Heteronuclear Multiple Bond Correlation...
A new generation of ligands designed to interact with the α-helix/β-strand discordant region amyloid-β peptide (Aβ) and counteract its oligomerization is presented. These are stabilize Aβ central helix (residues 13–26) in an α-helical conformation increased interaction by combining properties several first-generation ligands. The peptide-like aim at extended hydrophobic polar contacts across part Aβ, that is, "clamping" target. Molecular dynamics (MD) simulations stability presence a set...
Abstract Working towards the synthesis of 2′‐ O ‐[ N ‐(aminoethyl)carbamoyl]methyl‐modified di‐ and oligonucleotides, we have synthesised a protected adenosine where modification is introduced in convenient one‐pot three‐step procedure. The corresponding H‐phosphonate building block was also synthesised, from this intermediate, ‐(aminoethyl)carbamoyl]methyl‐containing dinucleotide could be made. We performed studies on chemical enzymatic stability dinucleotide. subjected to different...
2'-O-(N-(Aminoethyl)carbamoyl)methyl (2'-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2'-O-methyl (2'-OMe ONs) phosphodiester linkers as well partial full phosphorothioate (PS) inclusion were synthesized functionally evaluated splice-switching in several different reporter cell lines originating from tissues. This was enabled by first preparing the AECM-modified A, C, G U, which required a strategy for each building block. The AECM modification has previously been shown to...
A new triamino acid enables synthesis of an amyloid-β peptide (Aβ) targeting ligand with additional Aβ–ligand interactions that gives protection towards Aβ-induced reduction gamma oscillations in hippocampal slice preparation.
This thesis is based on six original research publications describing synthesis, structure and physicochemical biochemical analysis of chemically modified oligonucleotides (ONs) in terms their potential diagnostic therapeutic applications. Synthesis two types bicyclic conformationally constrained nucleosides, North-East locked 1',2'-azetidine North 2',4'-aza-ENA, described. Study the molecular structures dynamics nucleosides showed that depending upon type fused system they fall into...
To obtain different amino acids with varying lipophilicity and that can carry up to three positive charges we have developed a number of new triamino acid building blocks. One set blocks was achieved by aminoethyl extension, via reductive amination, the side chain ortnithine, diaminopropanoic diaminobutanoic acid. A second extension having hydrocarbon chains synthesized from The aldehydes needed for amination were corresponding Fmoc-L-2-amino fatty in two steps. Reductive these compounds...
An efficient method for attachment of a variety reporter groups to oligonucleotides (ONs) is copper (I) [Cu(I)]-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition ("click reaction"). However, in the case ONs with phosphorothioate modifications as internucleosidic linkages (PS-ONs), this conjugation has be adjusted compatible sulfur-containing groups. The described here adapted PS-ONs, utilizes solid-supported ONs, and implements Cu(I) bromide dimethyl sulfide complex (CuBr × Me2 S)...
2′-O-(N-(Aminoethyl)carbamoyl)methyl-modified 5-methyluridine (AECM-MeU) and 5-methylcytidine (AECM-MeC) phosphoramidites are reported for the first time prepared in multigram quantities. The syntheses of AECM-MeU AECM-MeC nucleosides designed larger scales (approx. 20 g up until phosphoramidite preparation steps) using low-cost reagents minimizing chromatographic purifications. Several steps were screened best conditions, focusing on most crucial such as N3 and/or 2′-OH alkylations, which...