A cyclic dinucleotide with a four-carbon 5'-C-to-5'-C connection; synthesis by RCM, NMR-examination and incorporation into secondary nucleic acid structures

Double-headed nucleosides: Synthesis and applications

Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.

Three pyrene-modified nucleotides: synthesis and effects in secondary nucleic acid structures

Synthesis of three pyrene-modified nucleosides was accomplished using the CuAAC reaction. Hereby, pyrene is attached either to the 5'-position of thymidine or to the 2'-position of 2'-deoxyuridine through triazolemethylene linkers, or to the 2'-position of 2'-deoxyuridine through a more rigid triazole linker. The three nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes and other secondary structures, which were analyzed by thermal stability and fluorescence studies. The three monomers were found to have different impacts on the nucleic acid complexes. Hence, pyrene attached to the 5'-position shows a tendency for intercalation into the duplex as indicated by a general decrease in fluorescence intensity followed by an increase in duplex thermal stability. Pyrene attached to the 2'-position through a rigid triazole linker also shows a tendency for intercalation but with decrease in duplex stability, whereas the pyrene attached to the 2'-position through a triazolemethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence but here in most cases leading to increase in duplex stability. All three pyrene nucleotides lead to thermal stabilization of bulged duplexes and three-way junctions. In some cases when two pyrenes were introduced into the core of these complexes, the formation or disappearance of a fluorescence excimer band can be used to indicate the hybridization process. Hereby these oligonucleotides can act as specific recognition probes.

Configuration of the 5'-methyl group modulates the biophysical and biological properties of locked nucleic acid (LNA) oligonucleotides

As part of a program aimed at exploring the structure- activity relationships of 2',4'-bridged nucleic acid (BNA) containing antisense oligonucleotides (ASOs), we report the synthesis and biophysical and biological properties of R- and S-5'-Me LNA modified oligonucleotides. We show that introduction of a methyl group in the (S) configuration at the 5'-position is compatible with the high affinity recognition of complementary nucleic acids observed with LNA. In contrast, introduction of a methyl group in the (R) configuration reversed the stabilization effect of LNA. NMR studies indicated that the R-5'-Me group changes the orientation around torsion angle γ from the +sc to the ap range at the nucleoside level, and this may in part be responsible for the poor hybridization behavior exhibited by this modification. In animal experiments, S-5'-Me-LNA modified gapmer antisense olignucleotides showed slightly reduced potency relative to the sequence matched LNA ASOs while improving the therapeutic profile.

Synthesis of functionalized carbocyclic locked nucleic acid analogues by ring-closing diene and enyne metathesis and their influence on nucleic acid stability and structure

A series of bicylic 2'-deoxynucleosides that are locked in the N-type conformation due to three-carbon linkages between the 2'- and 4'-positions have been prepared by ring-closing diene or enyne metathesis. The alkene or 1,3-diene hereby introduced in the bicyclic system is further derivatized, the latter showing the expected potential for Diels-Alder reactions. Four derivatives that are saturated or unsaturated as well as functionalized at the 2'-4'-linkage are incorporated into oligodeoxynucleotides, and the affinity of these for complementary RNA and DNA is studied. Substantially increased affinity for complementary RNA is observed, especially with additional hydroxyl groups attached to the bicyclic system. On the other hand, decreased affinity for complementary single-stranded DNA is obtained, whereas only a very small influence on a triplex-forming oligonucleotide sequence is found. Hence, a strong RNA-selective nucleic acid recognition is seen, and it can be concluded that the 2'-oxygen atom is less important for the formation of DNA:RNA duplexes than for the formation of DNA:DNA duplexes. However, the lack of a 2'-oxygen in the duplex formation can be partly compensated by other hydrophilic moieties around the 2'-4'-linkages indicating structural water binding to be of significant importance.

Nucleic acid secondary structures containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine

Oligodeoxynucleotides containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine were prepared by standard solid phase synthesis. The synthetic building block for incorporating the double-headed moiety was prepared from thymidine, which was stereoselectively converted to a protected 5'(S)-C-hydroxyethyl derivative and used to alkylate the additional thymine by a Mitsunobu reaction. The oligodeoxynucleotides were studied in different nucleic acid secondary structures: duplexes, bulged duplexes, three-way junctions and artificial DNA zipper motifs. The thermal stability of these complexes was studied, demonstrating an almost uniform thermal penalty of incorporating one double-headed nucleoside moiety into a duplex or a bulged duplex, comparable to the effects of the previously reported double-headed nucleoside 5'(S)-C-(thymin-1-yl)methylthymidine. The additional base showed only very small effects when incorporated into DNA or RNA three-way junctions. The various DNA zipper arrangements indicated that extending the linker from methylene to ethylene almost completely removed the selective minor groove base-base stacking interactions observed for the methylene linker in a (-3)-zipper, whereas interactions, although somewhat smaller, were observed for the ethylene linker in a (-4)-zipper motif.

A click chemistry approach to pleuromutilin conjugates with nucleosides or acyclic nucleoside derivatives and their binding to the bacterial ribosome

Pleuromutilin and its derivatives are antibacterial drugs that inhibit protein synthesis in bacteria by binding to ribosomes. To promote rational design of pleuromutilin based drugs, 19 pleuromutilin conjugates with different nucleoside fragments as side chain extensions were synthesized by a click chemistry protocol. Binding was assessed by chemical footprinting of nucleotide U2506 in 23S rRNA, and all conjugates bind to varying degree reflecting their binding affinity to the peptidyl transferase center. The side chain extensions also show various protections at position U2585. Docking studies of the conjugates with the highest affinities support the conclusion that despite the various conjugations, the pleuomutilin skeleton binds in the same binding pocket. The conjugated triazole moiety is well accommodated, and the nucleobases are placed in different pockets in the 50S ribosomal subunit. The derivative showing the highest affinity and a significantly better binding than pleuromutilin itself contains an adenine-9-ylpropylene triazole conjugate to pleuromutilin C-22.

Thermodynamic analysis of nylon nucleic acids

The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 degrees C increase in the thermal transition temperature (T(m)) for five linkages) and RNA (around 15 degrees C increase in T(m) for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised T(m) from less to slightly greater than T(m) of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2'-position of ribose and recovery of stability upon linkage of the side chains.

Synthetic nucleic acid secondary structures containing the four stereoisomers of 1,4-bis(thymine-1-yl)butane-2,3-diol

The four stereoisomers of the double-headed acyclic nucleoside 1,4-bis(thymine-1-yl)butane-2,3-diol were incorporated in the central position of four 13-mer oligonucleotides. The phosphoramidite building blocks were synthesized in four or six steps from either D- or L-2,3-O-isopropylidenethreitol. Two epimeric and fully deprotected double-headed nucleosides were analyzed by X-ray crystallography. The incorporation into oligonucleotides was hampered by steric hindrance and formation of a cyclic phosphate. The use of pyridinium chloride as the activator and a kinetic analysis based on 31P NMR of the coupling and detritylation processes led to improved yields of the oligonucleotides. In comparison with the (S)-GNA monomer, one of the four stereoisomers was found to show a similar destabilization of a DNA duplex, indicating that the additional base can be introduced without a thermal penalty. Another stereoisomer was found to induce a thermal stabilization of a DNA:RNA three-way junction. Thus, the stereochemistry of this acyclic double-headed nucleoside motif is important, indicating potential for the design of artificial nucleic acid secondary structures.

Recent highlights in modified oligonucleotide chemistry

The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.

Synthesis and modelling of DNA junction and minor groove zipper motifs incorporating the double-headed nucleoside 5'(S)-C-(thymine-1-ylmethyl)thymidine

A nucleoside with two nucleobases, a so-called double-headed nucleoside, 5'(S)-C-(thymine-1-ylmethyl)thymidine 3, is synthesised and incorporated into oligonucleotides. The additional nucleobase is hereby positioned in the minor groove of the duplexes, which are formed with complementary DNA and RNA-sequences. Slight thermal destabilisation of these duplexes as compared to unmodified duplexes is observed. With other target sequences forming bulged duplexes or three-way junctions, no additional influence of the additional base on the thermal stability is observed. On the other hand, a base-base stacking interaction and subsequent stabilisation is observed when two double-headed nucleotide moieties are positioned in two complementary DNA-sequences forming a DNA-zipper motif.

Synthesis and antiviral activities of new acyclic and "double-headed" nucleoside analogues

To develop an understanding of the structure-activity relationships for the inhibition of orthopoxviruses by nucleoside analogues, a variety of novel chemical entities were synthesized. These included a series of pyrimidine 5-hypermodified acyclic nucleoside analogues based upon recently discovered new leads, and some previously unknown "double-headed" or "abbreviated" nucleosides. None of the synthetic products possessed significant activity against two representative orthopoxviruses; namely, vaccinia virus and cowpox virus. They were also devoid of significant activity against a battery of other DNA and RNA viruses. So far as the results with the orthopoxviruses and herpes viruses, the results may point to the necessity for nucleoside analogues 5'-phosphorylation for antiviral efficacy.