Highly Stable Pyrimidine-Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue

Sequence-specific DNA labelling for fluorescence microscopy

The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.

Selective attachment of a microtubule interacting peptide to plasmid DNA via a triplex forming oligonucleotide for transfection improvement

In nonviral gene therapy approaches, the linkage of signal molecules to plasmid DNA (pDNA) is of interest for guiding its delivery to the nucleus. Here, we report its linkage to a peptide (P_79-98) mediating migration on microtubules by using a triplex-forming oligonucleotide (TFO). pDNA of 5 kbp and 21 kbp containing 6 and 36 oligopurine • oligopyrimidine sites (TH), respectively, inserted outside the luciferase gene sequence were used. TFO with a dibenzocyclooctyl (DBCO) group in 3' end comprising some Bridged Nucleic Acid bases was conjugated by click chemistry with the peptide carrying an azide function in the C-terminal end. We found the formation of 6 and 18 triplex with pDNA of 5 kbp and 21 kbp, respectively. A twofold increase of the transfection efficiency was observed in the hind-limbs upon Hydrodynamic Limb Vein (HLV) injection in mice of naked P_79-98 -pDNA of 21 kbp. This work paves the way for the selective equipping of pDNA with intracellular targeting molecules while preserving the full expression of the encoded gene.

The ability of a triplex-forming oligonucleotide to recognize T-A and C-G base pairs in a DNA duplex is enhanced by incorporating N-acetyl-2,7-diaminoquinoline

A triplex-forming oligonucleotide (TFO) can recognize the homopurine-homopyrimidine sequence in DNA duplexes and inhibit the transcription of targeted mRNAs. Recently, we reported that N-acetyl-2,7-diamino-1,8-naphthyridine (^DAN_ac), incorporated into a TFO, has high binding ability and base recognition selectivity for the pyrimidine bases in the purine-rich chain of the DNA duplex at pH 7.4. However, it was found in this study that the difference in the T_m values between the pyrimidine bases and purine bases decreased by more than 4 °C at pH 6.0-7.0. To improve the low base recognition selectivity of the TFO, we designed a new artificial base, ^DAQ_ac, with a quinoline skeleton. The T_m values of the triplexes containing ^DAQ_ac:T-A or ^DAQ_ac:C-G were more than 13 °C higher than those of the triplexes containing ^DAQ_ac:A-T or ^DAQ_ac:G-C at pH 7.4. We also observed that under more acidic conditions (pH 6.0-7.0), the base recognition selectivity of ^DAQ_ac in a triplex was higher than that of ^DAN_ac, although the binding ability of ^DAQ_ac in a triplex was similar to that of ^DAN_ac. Additionally, we found that ^DAQ_ac, incorporated into the TFO, could accurately recognize the ^MeC-G base pair in the hairpin DNA, similar to the C-G base pair.

Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex-Forming Abilities and Fluorescence Properties

1,3-Diaza-2-oxophenoxazine ("phenoxazine"), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π-π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex-forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9-triaza-2-oxophenoxazine (9-TAP), could improve triplex-forming abilities. A triplex-forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double-stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9-TAP-containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9-TAP moiety was maintained even in triplex (9-TAP:AT) formation, so 9-TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.

Bridged Nucleic Acids Reloaded

Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.

Effective syntheses of 2',4'-BNANC monomers bearing adenine, guanine, thymine, and 5-methylcytosine, and the properties of oligonucleotides fully modified with 2',4'-BNANC

We efficiently synthesized 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNA^NC) monomers bearing the four nucleobases, guanine, adenine, thymine, and 5-methylcytosine and incorporated these monomers into oligonucleotides. Initially, we carried out the transglycosylation reaction on several 2'-O-substituted 5-methyluridines to evaluate the effects of 2'-substitutions on this reaction. Under the optimized conditions, purine nucleobases were successfully introduced, and 2',4'-BNA^NC monomers bearing adenine or guanine were obtained over several steps. In addition, the improved synthesis of the 2',4'-BNA^NC monomers bearing thymine or 5-methylcytosine was also achieved. The obtained 2',4'-BNA^NC monomers were subsequently incorporated into oligonucleotides and the duplex-forming abilities of the modified oligonucleotides were investigated. Duplexes containing 2',4'-BNA^NC monomers in both or either strands were found to possess excellent thermal stabilities.

Biological applications of xeno nucleic acids

Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.

The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA

It has been confirmed by our previous studies that a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer displays high affinity and selectivity to the target RNA strand, promising mRNA inhibitory activity and excellent nuclease resistance. Herein, we have obtained a crystal structure that provides insights into these excellent antisense properties.

Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs

A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (d^gC) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2’-OMe-4N-(2-guanidoethyl)-5-methylcytidine (_2’-OMe^gC), 2’-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (_2’-OMe^gC_s), d^gC and 4S-(2-guanidoethyl)-4-thiothymidine (^gsT). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine (^DAN_ac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing ^DAN_ac, d^gC, 2’-OMe-2-thiothymidine (_2’-OMe^sT) and 2’-OMe-8-thioxoadenosine (_2’-OMe^sA) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions.

2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability

We present the synthesis and characterization of 2′-N-guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligo-DNA that forms a stable triplex (ΔT_m +9.5 °C) with exceptional nuclease stability.

Polymerase-mediated high-density incorporation of amphiphilic functionalities into DNA: enhancement of nuclease resistance and stability in human serum

Modified oligodeoxyribonucleotides (mdODNs) bearing multiple copies of an amphiphilic functional group were enzymatically synthesized by simultaneous incorporation of base-modified 5'-triphosphate analogs of 2'-deoxyguanosine (dG(am)TP), 2'-deoxyuridine (dU(am)TP), 2'-deoxyadenosine (dA(am)TP), and 2'-deoxycytosine (dC(am)TP). The amphiphilic functionality, that is, (E)-38,53-dioxo-2,5,8,11,14,17,20,23,26,29,32,35-dodecaoxa-39,52-diazapentapentacont-54-en-55-yl group, consists of the water soluble dodeca(ethylene glycol) chain and the hydrophobic dodecyl chain. An enzymatically synthesized ODN, composed of a 20-mer 5'-terminal segment containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotide (B/L nucleotide) and a 12-mer 3'-terminal segment containing the nucleobase-modified analogs, exhibits very high resistance against phosphodiesterase I and is stable in human serum for a longer period when compared with ODN, where the 12-mer 3'-terminal segment contains unmodified nucleotides.

In vitro selection of BNA (LNA) aptamers

Recently, we achieved the first in vitro selection of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5'-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5'-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses.

Fluorescent intercalator displacement replacement (FIDR) assay: determination of relative thermodynamic and kinetic parameters in triplex formation--a case study using triplex-forming LNAs

Triplex forming oligonucleotides (TFOs) are the most commonly used approach for site-specific targeting of double stranded DNA (dsDNA). Important parameters describing triplex formation include equilibrium binding constants (K(eq)) and association/dissociation rate constants (k(on) and k(off)). The 'fluorescent intercalator displacement replacement' (FIDR) assay is introduced herein as an operationally simple approach toward determination of these parameters for triplexes involving TC-motif TFOs. Briefly described, relative rate constants are determined from fluorescence intensity changes upon: (i) TFO-mediated displacement of pre-intercalated and fluorescent ethidium from dsDNA targets (triplex association) and (ii) Watson-Crick complement-mediated displacement of the TFO and replacement with ethidium (triplex dissociation). The assay is used to characterize triplexes between purine-rich dsDNA targets and TC-motif TFOs modified with six different locked nucleic acid (LNA) monomers, i.e. conventional and C5-alkynyl-functionalized LNA and α-L-LNA pyrimidine monomers. All of the studied monomers increase triplex stability by decreasing the triplex dissociation rate. LNA-modified TFOs form more stable triplexes than α-L-LNA-modified counterparts owing to slower triplex dissociation. Triplexes modified with C5-(3-aminopropyn-1-yl)-LNA-U monomer Z are particularly stable. The study demonstrates that three affinity-enhancing features can be combined into one high-affinity TFO monomer: conformational restriction of the sugar ring, expansion of the pyrimidine π-stacking surface and introduction of an exocyclic amine.

Sequence-specific base pair mimics are efficient topoisomerase IB inhibitors

Topoisomerase IB controls DNA topology by cleaving DNA transiently. This property is used by inhibitors, such as camptothecin, that stabilize, by inhibiting the religation step, the cleavage complex, in which the enzyme is covalently attached to the 3'-phosphate of the cleaved DNA strand. These drugs are used in clinics as antitumor agents. Because three-dimensional structural studies have shown that camptothecin derivatives act as base pair mimics and intercalate between two base pairs in the ternary DNA-topoisomerase-inhibitor complex, we hypothesized that base pairs mimics could act like campthotecin and inhibit the religation reaction after the formation of the topoisomerase I-DNA cleavage complex. We show here that three base pair mimics, nucleobases analogues of the aminophenyl-thiazole family, once targeted specifically to a DNA sequence were potent topoisomerase IB inhibitors. The targeting was achieved through covalent linkage to a sequence-specific DNA ligand, a triplex-forming oligonucleotide, and was necessary to position and keep the nucleobase analogue in the cleavage complex. In the absence of triplex formation, only a weak binding to the DNA and topoisomerase I-mediated DNA cleavage was observed. The three compounds were equally active once conjugated, implying that the intercalation of the nucleobase upon triplex formation is the essential feature for the inhibition activity.

2'-O,4'-C-methyleneoxymethylene bridged nucleic acids (2',4'-BNA(COC))

The synthesis of 2'-O,4'-C-methyleneoxymethylene bridged nucleoside (2',4'-BNA(COC)) phosphoramidites and oligonucleotides containing 2',4'-BNA(COC) are described. 2',4'-BNA(COC) phosphoramidites bearing natural nucleobases, such as thymine, cytosine, 5-methylcytosine, adenine, and guanine were synthesized. Moreover, fully or partially 2',4'-BNA(COC)-modified oligonucleotides can be prepared by using a standard protocol except for a prolonged coupling time on an automated DNA synthesizer.

Antisense drug discovery and development

Numerous chemically modified oligonucleotides have been developed so far and show their own unique chemical properties and pharmacodynamic/pharmacokinetic characteristics. Among all non-natural nucleotides, to the best of our knowledge, only five chemistries are currently being tested in clinical trials: phosphorothioate, 2´-O-methyl RNA, 2´-O-methoxyethyl RNA, 2´,4´-bridged nucleic acid/locked nucleic acid and the phosphorodiamidate morpholino oligomer. Since phosphorothioate modification can improve the pharmacokinetics of oligonucleotides, this modification is currently used in combination with all other modifications except phosphorodiamidate morpholino oligomer. For the treatment of metabolic, cardiovascular, cancer and other systemic diseases, the phosphorothioate class of drugs is obviously helpful, while superior efficacies can be observed in phosphorodiamidate morpholino oligomer compared to other classes of oligonucleotides for the treatment of Duchenne muscular dystrophy. Which properties of antisense molecules are actually essential for clinical applications? In this article, we provide an overview of the medicinal chemistry of existing non-natural antisense molecules, as well as their clinical applications, to discuss which properties of antisense oligonuculeotides affect therapeutic potency.

Formation of stable DNA triplexes

Triple-helical nucleic acids are formed by binding an oligonucleotide within the major groove of duplex DNA. These complexes offer the possibility of designing oligonucleotides which bind to duplex DNA with considerable sequence specificity. However, triple-helix formation with natural nucleotides is limited by (i) the requirement for low pH, (ii) the requirement for homopurine target sequences, and (iii) their relatively low affinity. We have prepared modified oligonucleotides to overcome these limitations, including the addition of positive charges to the sugar and/or base, the inclusion of cytosine analogues, the development of nucleosides for recognition of pyrimidine interruptions and the attachment of one or more cross-linking groups. By these means we are able to generate triplexes which have high affinities at physiological pH at sequences that contain pyrimidine interruptions.

Interrupted 2'-o,4'-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition

Due to instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex formation-based strategies in vivo, such as regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis. To this end, we investigated the effect of our previously reported chemical modification, 2'-O,4'-C-aminomethylene bridged nucleic acid (2',4'- BNA(NC)) modification, introduced into interrupted and continuous positions of triplex-forming oligonucleotide (TFO) on pyrimidine motif triplex formation at physiological pH. The interrupted 2',4'-BNA(NC) modifications of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold, and significantly increased the nuclease resistance of TFO. On the other hand, the continuous 2',4'-BNA(NC) modification of TFO showed lower ability to promote the triplex formation at physiological pH than the interrupted 2',4'-BNA(NC) modifications of TFO, and did not significantly change the nuclease resistance of TFO. Selection of the interruptedly 2',4'-BNA(NC)-modified positions in TFO was more favorable for achieving the higher binding affinity of the pyrimidine motif triplex formation at physiological pH and the higher nuclease resistance of TFO than that of the continuously 2',4'-BNA(NC)-modified positions in TFO. We conclude that the interrupted 2',4'-BNA(NC) modification of TFO could be a key chemical modification to enhance pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition, and may eventually lead to progress in various triplex formation-based strategies in vivo.

2'-O,4'-C-aminomethylene-bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH

Due to the instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex-formation-based strategies in vivo, such as gene expression regulation, genomic DNA mapping, and gene-targeted mutagenesis. To this end, we investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNA(NC)) modification of triplex-forming oligonucleotide (TFO), on triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA(NC) modification of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold. The number and position of the 2',4'-BNA(NC) modification in TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity and the increased degree of hydration of the 2',4'-BNA(NC)-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant. Kinetic data demonstrated that the observed increase in the binding constant by the 2',4'-BNA(NC) modification resulted mainly from the considerable decrease in the dissociation rate constant. The TFO stability in human serum showed that the 2',4'-BNA(NC) modification significantly increased the nuclease resistance of TFO. Our results support the idea that the 2',4'-BNA(NC) modification of TFO could be a key chemical modification to achieve higher binding affinity and higher nuclease resistance in the triplex formation under physiological conditions, and may lead to progress in various triplex-formation-based strategies in vivo.

Study on suitability of KOD DNA polymerase for enzymatic production of artificial nucleic acids using base/sugar modified nucleoside triphosphates

Recently, KOD and its related DNA polymerases have been used for preparing various modified nucleic acids, including not only base-modified nucleic acids, but also sugar-modified ones, such as bridged/locked nucleic acid (BNA/LNA) which would be promising candidates for nucleic acid drugs. However, thus far, reasons for the effectiveness of KOD DNA polymerase for such purposes have not been clearly elucidated. Therefore, using mutated KOD DNA polymerases, we studied here their catalytic properties upon enzymatic incorporation of nucleotide analogues with base/sugar modifications. Experimental data indicate that their characteristic kinetic properties enabled incorporation of various modified nucleotides. Among those KOD mutants, one achieved efficient successive incorporation of bridged nucleotides with a 2′-ONHCH₂CH₂-4′ linkage. In this study, the characteristic kinetic properties of KOD DNA polymerase for modified nucleoside triphosphates were shown, and the effectiveness of genetic engineering in improvement of the enzyme for modified nucleotide polymerization has been demonstrated.

Reversible circularization of an anthracene-modified DNA conjugate through bimolecular triplex formation and its analytical application

We prepared an oligodeoxyribonucleotide conjugate (5-3ant(2)18) carrying two anthracenes, each of which was tethered to both ends of the conjugate through hexamethylene linker chains. The conjugate has a mirror repeat of two heptamer sequences, such that it forms a bimolecular triplex with the single stranded target, forming a two-fold U-shaped conformation. The conformation of the conjugate in its triplex structure could be frozen instantaneously by circularization through photodimerization of the anthracenes. Compared with the duplex formation of linear probes with relevant sequences, bimolecular triplex formation of 5-3ant(2)18 shows a unique feature in its target recognition; it binds the target tightly, yet still retains high sequence selectivity. Circularization of 5-3ant(2)18 by UV photoirradiation was verified as the probe reaction for a DNA assay. The probe reaction could be performed in a few seconds over a wide range of temperatures, at least between 0 and 25 °C. In addition, the reaction could be regarded as a reversible method for the preparation of circular DNA that shows higher affinity for the target.

DNA photocleavage by DNA and DNA-LNA amino acid-dye conjugates

DNA photocleavage by triplex forming oligonucleotides (TFO) has potential implications in both biotechnology and medicine. We have synthesized a series of homopurine DNA and DNA/LNA 14-mers to which an amino acid (glycine or l-tryptophan) and a cyanine dye are covalently linked. Two cyanine dyes were examined that include a quinolinium ring linked to a benzothiazolium ring through a monomethine (TO1) or trimethine (TO2) linker. The 14-mer sequence was chosen to target mdm2, a ubiquitin ligase (E3) that regulates p53 by promoting its ubiquitylation and proteosomal degradation. Such inhibition has been previously proposed as a therapeutic approach to target wild-type p53-expressing cancers. To examine whether our TFO conjugates photocleave the mdm2 target, we incubated the various conjugates with the mdm2 plasmid and irradiated the samples with visible light. We show that only the TFO with the complementary sequence and with an intervening l-tryptophan leads to the linearization of the plasmid after a short irradiation time (10 min) exciting the dye (lambda(max)(TO1) = 500 nm and lambda(max)(TO2) = 630 nm) with visible light. Furthermore, the photoreactivity is more pronounced for the LNA/DNA conjugate, an observation that is consistent with improved hybridization to the DNA target. Sequence specificity of the photoreaction is further corroborated on a synthetic 44-mer duplex containing the TFO site. Evidence for a ROS-dependent mechanism is also given and discussed.

RNA interference with 2',4'-bridged nucleic acid analogues

In this study, a number of 2',4'-BNA- and 2',4'-BNA(NC)-modified siRNAs were designed and synthesized. Their thermal stability, nuclease resistance and gene silencing properties against cultured mammalian cells were evaluated and compared with those of natural siRNAs. The 2',4'-BNA- and 2',4'-BNA(NC)-modified siRNAs (named siBNA and siBNA(NC), respectively) showed very high T(m) values, were remarkably stable in serum sample and showed promising RNAi properties equal to those exhibited by natural siRNAs. Thermally stable siBNAs composed of slightly modified sense and antisense strands were capable of suppressing gene expression equal to that of natural siRNA. A number of modifications on the sense strand by 2',4'-BNA or 2',4'-BNA(NC), either consecutively or separated by natural RNA nucleotides, is tolerable in RNAi machinery. Modifications at the Argonauate (Ago2) cleavage site of the sense strand (9-11th positions from the 5'-end of the sense strand) produced variable results depending on siRNA composition. Mostly, modification at the 10th position diminished siRNA activity. In moderately modified siRNAs, modification at the 11th position displayed usual RNAi activity, while modification at the 9th position showed variable results depending on siRNA composition.

Effect of 3'-end capping of aptamer with various 2',4'-bridged nucleotides: Enzymatic post-modification toward a practical use of polyclonal aptamers

The capping of the 3'-ends of thrombin binding aptamers (TBAs) with bridged nucleotides increased the nuclease resistances and the stabilities in human serum. The binding abilities of the aptamers were not affected by the capping. The capping could be simply executed via a one step enzymatic process using 2',4'-bridged nucleoside 5'-triphosphate and terminal deoxynucleotidyl transferase.

Optimized DNA-targeting using triplex forming C5-alkynyl functionalized LNA

Triplex forming oligonucleotides (TFOs) modified with C5-alkynyl functionalized LNA (locked nucleic acid) monomers display extraordinary thermal affinity toward double stranded DNA targets, excellent discrimination of Hoogsteen-mismatched targets, and high stability against 3?-exonucleases.

Synergistic stabilization of nucleic acid assembly by 2'-O,4'-C-methylene-bridged nucleic acid modification and additions of comb-type cationic copolymers

Stabilization of nucleic acid assemblies, such as duplex and triplex, is quite important for their wide variety of potential applications. Various stabilization methods, including molecular designs of chemically modified nucleotides and hybrid stabilizers, and combinations of different stabilization methods have been developed to increase stability of nucleic acid assemblies. However, combinations of two stabilizing methods have not always yielded desired synergistic effects. In the present study, to propose a strategy for selection of a rational combination of stabilizing methods, we demonstrate synergistic stabilization of triplex by 2'-O,4'-C-methylene-bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide and addition of poly(l-lysine)-graft-dextran copolymer [poly(l-lysine) grafted with hydrophilic dextran side chains]. Each of these methods increased the binding constant for triplex formation by nearly 2 orders of magnitude. However, their kinetic contributions were quite distinct. The copolymer increased the association rate constant, whereas the 2',4'-BNA modification decreased the dissociation rate constant for triplex stabilization. The combination of both stabilizing methods increased the binding constant by nearly 4 orders of magnitude. Kinetic analyses revealed that the successful synergistic stabilization resulted from kinetic complementarity between increased association rate constants by the copolymer and decreased dissociation rate constants by the 2',4'-BNA modification. The stabilizing effect of one stabilization method did not alter that of the other stabilization method. We propose that kinetic analyses of each stabilizing effect permit selection of a rational combination of stabilizing methods for successful synergy in stabilizing nucleic acid assemblies.

Smart conferring of nuclease resistance to DNA by 3'-end protection using 2',4'-bridged nucleoside-5'-triphosphates

Incorporation of 2',4'-bridged nucleotides into the 3'-end of oligodeoxyribonucleotide (ODN) was examined using terminal deoxynucleotidyl transferase (TdT). The three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures used were incorporated efficiently into the 3'-end of DNA by TdT, although only single nucleotide incorporation was observed. Nuclease resistance was conferred on DNA, depending on the types of bridging nucleotides added.

[Overview of 40 years' chemical study]

1,6-Dihydro-3(2H)-pyridinone, designed as a common synthon for synthesis of various natural products, was found to be easily prepared in large scale and successfully used to synthesize a variety of alkaloids such as ibogamine, quinine and tecomanine. A tricyclo[3.3.0.0(2.8)]octane was also served as a common synthon for several sesquiterpenes such as pentalenene and quadrone. Synthetic studies by using sulfinyl chirality via an intramolecular Michael addition gave the novel route to construct spiro-ketal moiety in enantiomerically pure form. By applying this method, many natural spiro-ketal compounds were asymmetrically synthesized effectively. 3-Sulfinylated 1,4-dihydropyridine, a chiral NADH model compound, reduced activated ketones such as methyl benzoylformate to give the corresponding alcohols in excellent optical yields. A kind of 3-O-substituted pyridoxal chiral model compound was useful for preparation of alpha,alpha-dialkylated alpha-amino acids by asymmetric alpha-alkylation of alpha-amino acids. 2'-O,4'-C-Bridged nucleic acid analogs, BNAs, developed as novel type of artificial nucleic acids, showed an extraordinarily high binding affinity toward single stranded RNA and double stranded DNA complements along with excellent nuclease-resistant ability. Oligonucleotides containing BNA monomer units were proved to be very useful for various biotechnologies, such as antisense and antigene methodologies.

A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition

Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNA(COC)) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNA(COC) monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNA(COC)/BNA(COC) duplex possessed excellent thermal stability and that the BNA(COC) increased thermal stability with a complementary RNA strand. On the other hand, BNA(COC)/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.

Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides

In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2'-O,4'-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2',4'-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2',4'-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2',4'-bridged nucleotides into extending strands using 2',4'-bridged nucleoside-5'-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.

Design, synthesis, and properties of 2',4'-BNA(NC): a bridged nucleic acid analogue

The novel bridged nucleic-acid analogue 2',4'-BNA(NC) (2'-O,4'-C-aminomethylene bridged nucleic acid), containing a six-membered bridged structure with an N-O linkage, was designed and synthesized efficiently, demonstrating a one-pot intramolecular NC bond-forming key reaction to construct a perhydro-1,2-oxazine ring (11 and 12). Three monomers of 2',4'-BNA(NC) (2',4'-BNA(NC)[NH], [NMe], and [NBn]) were synthesized and incorporated into oligonucleotides, and their properties were investigated and compared with those of 2',4'-BNA (LNA)-modified oligonucleotides. Compared to 2',4'-BNA (LNA)-modified oligonucleotides, 2',4'-BNA(NC) congeners were found to possess: (i) equal or higher binding affinity against an RNA complement with excellent single-mismatch discriminating power, (ii) much better RNA selective binding, (iii) stronger and more sequence selective triplex-forming characters, and (iv) immensely higher nuclease resistance, even higher than the S(p)-phosphorthioate analogue. 2',4'-BNA(NC)-modified oligonucleotides with these excellent profiles show great promise for applications in antisense and antigene technologies.

N-Methyl substituted 2',4'- BNANC: a highly nuclease-resistant nucleic acid analogue with high-affinity RNA selective hybridization

Oligonucleotides modified with a novel BNA analogue, 2', 4'-BNA(NC)[N-Me], were synthesized, and in comparison to 2',4'-BNA (LNA), have similarly high RNA affinity, better RNA selectivity and much higher resistance to nuclease degradation, suggesting that the novel BNA analogue may be particularly useful for antisense approaches.