Adenine Monomers Research Articles

ChemInform Abstract: Synthesis and Characterization of Oligodeoxyribonucleotides Modified with 2′‐Amino‐α‐L‐LNA Adenine Monomers: High‐Affinity Targeting of Single‐Stranded DNA.

The development of conformationally restricted nucleotide building blocks continues to attract considerable interest because of their successful use within antisense, antigene, and other gene-targeting strategies. Locked nucleic acid (LNA) and its diastereomer α-l-LNA are two interesting examples thereof. Oligonucleotides modified with these units display greatly increased affinity toward nucleic acid targets, improved binding specificity, and enhanced enzymatic stability relative to unmodified strands. Here we present the synthesis and biophysical characterization of oligodeoxyribonucleotides (ONs) modified with 2′-amino-α-l-LNA adenine monomers W–Z. The synthesis of the target phosphoramidites 1–4 is initiated from pentafuranose 5, which upon Vorbruggen glycosylation, O2′-deacylation, O2′-activation and C2′-azide introduction yields nucleoside 8. A one-pot tandem Staudinger/intramolecular nucleophilic substitution converts 8 into 2′-amino-α-l-LNA adenine intermediate 9, which after a series of nontrivia...

Synthesis and Characterization of Oligodeoxyribonucleotides Modified with 2′-Amino-α-l-LNA Adenine Monomers: High-Affinity Targeting of Single-Stranded DNA

The development of conformationally restricted nucleotide building blocks continues to attract considerable interest because of their successful use within antisense, antigene, and other gene-targeting strategies. Locked nucleic acid (LNA) and its diastereomer α-L-LNA are two interesting examples thereof. Oligonucleotides modified with these units display greatly increased affinity toward nucleic acid targets, improved binding specificity, and enhanced enzymatic stability relative to unmodified strands. Here we present the synthesis and biophysical characterization of oligodeoxyribonucleotides (ONs) modified with 2'-amino-α-L-LNA adenine monomers W-Z. The synthesis of the target phosphoramidites 1-4 is initiated from pentafuranose 5, which upon Vorbrüggen glycosylation, O2'-deacylation, O2'-activation and C2'-azide introduction yields nucleoside 8. A one-pot tandem Staudinger/intramolecular nucleophilic substitution converts 8 into 2'-amino-α-L-LNA adenine intermediate 9, which after a series of nontrivial protecting-group manipulations affords key intermediate 15. Subsequent chemoselective N2'-functionalization and O3'-phosphitylation give targets 1-4 in ~1-3% overall yield over 11 steps from 5. ONs modified with pyrene-functionalized 2'-amino-α-L-LNA adenine monomers X-Z display greatly increased affinity toward DNA targets (ΔTm/modification up to +14 °C). Results from absorption and fluorescence spectroscopy suggest that the duplex stabilization is a result of pyrene intercalation. These characteristics render N2'-pyrene-functionalized 2'-amino-α-L-LNAs of considerable interest for DNA-targeting applications.

Structures of Alkali Metal Ion−Adenine Complexes and Hydrated Complexes by IRMPD Spectroscopy and Electronic Structure Calculations

Complexes between adenine and the alkali metal ions Li(+), Na(+), K(+), and Cs(+) have been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy between 2800 and 3900 cm(-1), as have some singly hydrated complexes. The IRMPD spectra clearly show the N-H stretching and the NH(2) symmetric and asymmetric stretching vibrations of adenine; and for the solvated ions, the O-H stretching vibrations are observed. These experimental spectra were compared with those for a variety of possible structures, including both A9 (A9 refers to the tautomer where hydrogen is on the nitrogen in position 9 of adenine, see Scheme 1) and A7 adenine tautomers, computed using B3-LYP/6-31+G(d,p). By comparing the experimental and the simulated spectra it is possible to rule out various structures and to further assign structures to the species probed in these experiments. Single-point calculations on the B3-LYP/6-31+G(d,p) geometries have been performed at MP2/6-311++G(2d, p) to obtain good estimates of the relative thermochemistries for the different structures. In all cases the computed IR spectrum for the lowest energy structure is consistent with the experimental IRMPD spectrum, but in some cases structural assignment cannot be confirmed based solely upon comparison with the experimental spectra so computed thermochemistries can be used to rule out high-energy structures. On the basis of the IRMPD spectra and the energy calculations, all adenine-M(+) and adenine-M(+)-H(2)O are concluded to be composed of the A7 tautomer of adenine, which is bound to the cations in a bidentate fashion through N3 and N9 (see Scheme 1 for numbering convention). For the hydrated ions water binds directly to the metal ion through oxygen, as would be expected since the metal contains most positive charge density. For the hydrated lithium cation-bound adenine dimer, the water molecule is concluded to be hydrogen bonded to a free basic site of one of the adenine monomers, which is also bound to the lithium cation. Experimental and theoretical results on adenine-Li(+)-H(2)O suggest that the electrosprayed adenine-Li(+) resembles the lowest-energy solution phase ion rather than the lowest-energy gas-phase ion, which is the imine form.

Photoinduced Dynamics of Hydrated Adenine Clusters

We studied the photoinduced dynamics of hydrated adenine clusters by multiphoton ionization techniques. The majority of the hydrated adenine monomers are found to experience dissociative ionization, where the adenine monomer ions are produced due to the fragmentation of the water solvents by three-photon process. Due to fast internal conversion from the electronic states reached by the first photon, the fragmentation takes place in the vibrationally excited electronic ground state and in the vibrationally excited ionic states. Thus, the abundance of the hydrated adenine monomer ion depends on the excitation photon energy, possibly because the lifetime of the intermediate states is different and an internal conversion competes with direct ionization. In addition, a significant amount of protonated adenine monomer is observed. This indicates that the proton transfer is followed by the fragmentation in the hydrated adenine clusters. The abundance of the protonated adenine monomer also depends on the excitation photon energy mainly due to the ionization efficiency of the parent species.

Atom Transfer Radical Polymerization of Adenine, Thymine, Cytosine, and Guanine Nucleobase Monomers

Methacrylate monomers functionalized with thymine, adenine, cytosine, and guanine were prepared by alkylation of the nucleobases with 3-bromopropyl methacrylate. Application of atom transfer radical polymerization in deuterated DMSO allowed controlled polymerization of the adenine-, thymine-, and for the first time, also of the cytosine- and guanine-modified monomers. The guanine and cytosine monomers appeared to form a complex with the copper catalyst, as could be observed with 1H NMR spectroscopy. In the case of guanine, this did not cause any problems for the polymerization process, while in the case of cytosine, a stronger copper binding ligand, PMDETA, needed to be applied to gain control over polymerization.

Unusual rate enhancement in the thymine assisted ATRP process of adenine monomers

Thymine and adenine monomers were synthesized and polymerized using ATRP in a controlled fashion. In addition a thymine functionalized block copolymer was prepared using ATRP, starting from a poly(ethylene glycol) macro initiator. Polymerization of adenine monomer in DMSO-d6 showed a significant increase in polymerization rate when polymeric thymine template was present, while thymine monomer did not show a polymerization rate enhancement. Varying the template to monomer ratio demonstrated that the polymerization rate increased even further if an excess of template was applied. Surprisingly, the addition of monomeric complementary moieties resulted in an even greater rate enhancement. These findings led to our conclusion that non-covalent interaction between adenine and thymine in DMSO-d6 protects the adenine monomer from interaction with the copper catalyst, thus resulting in a faster polymerization.

Synthesis of pyrrolidine-based oxy-peptide nucleic acids that contain four bases and their properties

Adenine, guanine, thymine and cytosine monomers of oxy-peptide nucleic acid that contain a pyrrolidine ring in the main chain have been synthesized for use in the synthesis of novel peptide nucleic acid.

Synthesis of (3R,6R)- and (3S,6R)-piperidinone PNA

Two new conformationally restricted piperidinone PNA adenine monomers 12 and 13 have been synthesised using a stereoselective synthesis strategy analogous to a previously published strategy for pyrrolidinone analogues. In contrast to the pyrrolidinone case, epimerisation occurred during the final hydrolysis step. However, the diastereomeric mixture could be separated by RP-HPLC to give small amounts of pure 12 and 13. These were built into a PNA dodecamer (once in a central position), and the thermal stability (Tm) of the modified oligomers hybridised to complementary DNA, RNA and PNA were measured. PNA modified with either 12 or 13 resulted in a decrease of the Tm compared to unmodified PNA and to pyrrolidinone modified PNA. Thus, any preorganisation for duplex formation of PNA with a six-membered piperidinone ring seems to be inferior to preorganisation with a five-membered ring in the pyrrolidinone PNA analogues studied earlier.

LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition

LNA (Locked Nucleic Acids), consisting of 2′- O,4′- C-methylene bicyclonucleoside monomers, is efficiently synthesized and its nucleic acid recognition potential evaluated for six different nucleobases, namely adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil. Unprecedented increases (+3 to +8 °C per modification) in the thermal stability of duplexes towards both DNA and RNA were obtained when evaluating mixed sequences of partly or fully modified LNA. Studies of mis-matched sequences show that LNA obey the Watson-Crick base pairing rules with generally improved selectivities compared to the corresponding unmodified reference strands.

Synthesis and properties of DNA-PNA chimeric oligomers.

Adenine, thymine and cytosine PNA monomers have been prepared using 3-amino-1,2-propanediol as a starting material. The benzoyl group was used to protect the exocyclic amines of the heterocyclic bases of A and C PNA monomers and the backbone primary amine was protected with the monomethoxytrityl group. The thymine and cytosine PNA monomers were used in conjunction with standard DNA synthesis monomers to produce chimeric PNA DNA (PDC) oligomers. Ultraviolet melting studies confirmed that these oligomers form stable hybrids with complementary DNA strands and that mismatches in the DNA but more so in the PNA sections lead to duplex destabilisation.