Torsten Bryld

LNA (locked nucleic acid) and the diastereoisomeric alpha-L-LNA: conformational tuning and high-affinity recognition of DNA/RNA targets.

The remarkable binding properties of LNA (Locked Nucleic Acid) and α-L-LNA (the α-L-ribo configured diastereoisomer of LNA) are summarized, and hybridization results for LNA/2′-O-Me-RNA chimera and LNAs with a “dangling” nucleotide are introduced. In addition, results from NMR investigations on the furanose conformations of the individual nucleotide monomers in different duplexes are presented. All these data are discussed with focus on the importance of conformational steering of unmodified nucleotides in partly modified LNA and α-L-LNA sequences in relation to the unprecedented binding properties of LNA and α-L-LNA.

Oligonucleotides Containing Novel 4′‐C‐ or 3′‐C‐(Aminoalkyl)‐Branched Thymidines

The synthesis of four novel 3′-C-branched and 4′-C-branched nucleosides and their transformation into the corresponding 3′-O-phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′-C-branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′-O-methyl and 2′-deoxy-2′-fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′-C-(aminomethyl)-2′-O-methyl monomer X and 4′-C-(aminomethyl)-2′-deoxy-2′-fluoro monomer Y (Schemesu20052 and 3). In general, increased binding affinity towards complementary single-stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Tableu20051). The presence of monomer X or monomer Y in a 2′-O-methyl-RNA oligonucleotide had a negative effect on the binding affinity of the 2′-O-methyl-RNA oligonucleotide towards DNA and RNA. Starting from the 3′-C-allyl derivative 28, 3′-C-(3-aminopropyl)-protected nucleosides and 3′-O-phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′-C-(3-aminopropyl)thymidine monomer Z or the corresponding 3′-C-(3-aminopropyl)-2′-O,5-dimethyluridine monomer W (Schemesu20054 and 5). Incorporation of the 2′-deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′-O-methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Tableu20052).

At Tachment of Cholesterol to Amino-LNA: Synthesis and Hybridization Properties

Here, we present our synthesis of amino-LNA with a C6-linker and hybridization studies of these. A cholesterol moiety was attached at the end of the C6-linker. This resulted in drastic drops against DNA of the modified oligonucleotide.

Parallel nucleic acid recognition by the LNA (locked nucleic acid) stereoisomers β-L-LNA and α-D-LNA; studies in the mirror image world

Two LNA (locked nucleic acid) stereoisomers (β-L-LNA and α-D-LNA) are evaluated in the mirror-image world, that is by the study of two mixed sequences of LNA and α-L-LNA and their L-DNA and L-RNA complements. Both are found to display high-affinity RNA-recognition by the formation of duplexes with parallel strand orientation.

N-Methylpiperazinocarbonyl-2′,3′-BcNA and 4′-C-(N-methylpiperazino)methyl-DNA: introduction of basic functionalities facing the major groove and the minor groove of a DNA:DNA duplex

Piperazino-functionalized 2,3-BcNA and 4-C-hydroxymethyl-DNA are appropriate molecular architectures for the introduction of basic functionalities facing the major groove and the minor groove of nucleic acid duplexes, respectively. 4-C-(N-Methylpiperazino)methyl-DNA monomers induce significantly increased thermal stability of a DNA:DNA duplex.

Synthesis and structural characterization of piperazino-modified DNA that favours hybridization towards DNA over RNA

We report the synthesis of two C4′-modified DNA analogues and characterize their structural impact on dsDNA duplexes. The 4′-C-piperazinomethyl modification stabilizes dsDNA by up to 5°C per incorporation. Extension of the modification with a butanoyl-linked pyrene increases the dsDNA stabilization to a maximum of 9°C per incorporation. Using fluorescence, ultraviolet and nuclear magnetic resonance (NMR) spectroscopy, we show that the stabilization is achieved by pyrene intercalation in the dsDNA duplex. The pyrene moiety is not restricted to one intercalation site but rather switches between multiple sites in intermediate exchange on the NMR timescale, resulting in broad lines in NMR spectra. We identified two intercalation sites with NOE data showing that the pyrene prefers to intercalate one base pair away from the modified nucleotide with its linker curled up in the minor groove. Both modifications are tolerated in DNA:RNA hybrids but leave their melting temperatures virtually unaffected. Fluorescence data indicate that the pyrene moiety is residing outside the helix. The available data suggest that the DNA discrimination is due to (i) the positive charge of the piperazino ring having a greater impact in the narrow and deep minor groove of a B-type dsDNA duplex than in the wide and shallow minor groove of an A-type DNA:RNA hybrid and (ii) the B-type dsDNA duplex allowing the pyrene to intercalate and bury its apolar surface.

Triplex-forming ability of modified oligonucleotides.

We present our studies on the ability of several different nucleotide analogs as triplex-forming oligonucleotides. The modifications tested include 4′-C-hydroxymethyl, LNA, 2′-amino-LNA and N2′-functionalized 2′-amino-LNA. Triplexes containing monomers of N2′-glycyl-functionalized 2′-amino-LNA are particularly stable.

DNA-selective hybridization and dual strand invasion of short double-stranded DNA using pyren-1-ylcarbonyl-functionalized 4?-C-piperazinomethyl-DNAElectronic supplementary information (ESI) available: short description of synthesis of the phosphoramidites 1 and 2 and procedure used to record fluorescence emission spectra. See http://www.rsc.org/suppdata/cc/b4/b402414a/

Incorporation of a novel pyren-1-ylcarbonyl-functionalized 4-C-piperazinomethyl-DNA monomer into oligodeoxynucleotides leads to increased thermal stability of duplexes with DNA complements but reduced thermal stability of duplexes with RNA complements. This DNA-selective hybridization is explored for recognition of double-stranded DNA by a novel dual strand invasion approach.

Synthesis and antiviral evaluation of novel conformationally locked nucleosides and masked 5′-phosphate derivatives thereof

As part of a programme towards evaluating the potential of conformationally locked 3′-deoxy- and 3′-azido-3′-deoxy-nucleoside derivatives as prodrugs of potential 5′-O-triphosphorylated anti-HIV drugs, novel nucleoside derivatives with locked N-type (north-type, C3′-endo) furanose conformation were prepared using convergent synthetic strategies. In addition, masked 5′-monophosphate derivatives of these, and of a conformationally restricted 3′-azido-3′-deoxynucleoside with E-type (eastern-type, O4′-endo) furanose conformation, were prepared in order to potentially circumvent the first phosphorylation step. However, neither the free 5′-hydroxy derivatives nor the masked 5′-monophosphates showed anti-HIV activity in MT-4 cells.

Synthesis of a Base-Protected xylo-LNA Adenine Nucleoside

Abstract Synthesis of (1S,3R,4R,7R)-7-hydroxy-1-hydroxymethyl-3-(6-N-benzoyl-adenin-9-yl)-2,5-dioxabicyclo[2.2.1]heptane (2), a base-protected xylo-LNA adenine nucleoside, has been accomplished using a convergent synthetic strategy starting from 1,2-di-O-acetylfuranose 3.