Linear relationship between deformability and thermal stability of 2'-O-modified RNA hetero duplexes

We describe the relationship between the experimentally determined melting temperatures of 2′-O-modified-RNA/RNA duplexes and their deformability estimated from molecular dynamics simulations. To clarify this relationship, we synthesized several fully modified oligoribonucleotides such as 2′-O-cyanoethyl RNAs and 2′-O-methoxyethyl RNAs and compared the actual melting temperatures of the duplexes with their calculated deformabilities. An increase of the melting temperatures by 2′-O-modifications was found to correlate strongly with an increase of the helical elastic constants in U₁₄/A₁₄, (CU)₇/(AG)₇, and (GACU)₃/(AGUC)₃ sequences. Linear regression analyses could be used to estimate the melting temperature with an accuracy of ±2.0 °C in our model case. Although the strong correlation was observed in the same base sequence, the linear regression functions were different from each base sequence. Our results indicated the possibility of predicting the thermal stability of 2′-O-modified duplexes at the computer-aided molecular design stage.

Synthesis of 6-N-(benzothiazol-2-yl)deoxyadenosine and its exciton-coupled circular dichroism

6-N-(Benzothiazol-2-yl)deoxyadenosine (A(BT)) was synthesized and incorporated into DNAs. Although, the multipoint benzothiazole (BT) modification of oligodeoxynucleotides reduced the stability of duplexes with their complementary strands, it induced the strong exciton coupling between BT moieties. The circular dichroism (CD) spectra of this exciton coupling interaction were observed at wavelengths above 300nm and overlapping with the UV absorption bands of nucleotides could be avoided. The shapes of the CD spectra due to this interaction were strongly influenced by the helicity of two BT groups.

Fluorescence properties of pyrimidopyrimidoindole nucleoside dC(PPI) incorporated into oligodeoxynucleotides

A series of oligodeoxynucleotides labeled by a pyrimidopyrimidoindole deoxynucleoside (1a: dC(PPI)) and its derivatives 2a and 3a substituted with electron-donating and -withdrawing groups, respectively, were synthesized according to the phosphoramidite approach. The photophysical properties and quenching efficiencies of oligonucleotides incorporating dC(PPI) derivatives were studied in detail. The thermal denaturation experiments and molecular dynamics simulation of DNA duplexes incorporating dC(PPI) suggested that a modified base of dC(PPI) could form base pairs with guanine and adenine in canonical Watson-Crick and reverse-wobble geometries, respectively. The fluorescence of oligonucleotides incorporating dC(PPI) derivatives increased upon binding to the counter strands, except when dC(PPI) and guanine formed a base pair. It was revealed that dGMP quenched the fluorescence of the cyano derivative 3a most effectively, whereas it affected that of the methoxy derivative 2a least effectively. The involvement of the electron transfer from guanine to the dC(PPI) derivatives in the fluorescence quenching was supported by energy considerations.

Synthesis and hybridization of 2'-O-methyl-RNAs incorporating 2'-O-carbamoyluridine and unique participation of the carbamoyl group in U-G base pair

2'-O-Carbamoyluridine (U(cm)) was synthesized and incorporated into DNAs and 2'-O-Me-RNAs. The oligonucleotides incorporating U(cm) formed less stable duplexes with their complementary and U(cm)-U, U(cm)-C single-base mismatched DNAs and RNAs in comparison with those without the carbamoyl group. On the contrary, the T(m) analyses revealed that the duplexes with a mismatched U(cm)-G base pair showed almost the same thermostability as the corresponding unmodified duplexes. Molecular dynamics (MD) simulations of the U(cm)-modified 2'-O-Me-RNA/RNA duplexes with U(cm)-G mismatched base pair suggested that the carbamoyl group could participate in the U(cm)-G base pair by an additional intermolecular hydrogen bond between the carbamoyl oxygen and the H2 of the guanine base.

Efficient solid-phase synthesis of oligodeoxynucleotides having a 5'-terminal 2,2,7-trimethylguanosine pyrophosphate linkage

A 5'-terminal 2,2,7-trimethylguanosine (TMG) cap structure plays an important role in transport of TMG-capped snRNAs from the cytoplasm to the nucleus in living cells. This property can be expected to be used for carrying artificial nucleic acids into the nucleus in gene therapy. In this paper, a new TMG-capping reagent 1 was developed and used for the synthesis of oligodeoxynucleotides having a 5'-terminal TMG-capped pyrophosphate linkage (m(3)(2,2,7)G(5')pp-DNA) lacking one phosphate group using a silyl-type linker on polymer supports.

Synthesis of terminally modified oligonucleotides and their hybridization dependence on the size of the target RNAs

We have developed new artificial oligonucleotide probes that show selective recognition for short RNA targets over long RNA targets. Our results suggested that modification of the termini of the oligonucleotide probes by bulky substituents such as cyclohexyl and 4-(3,6,9-trioxaundecylenedioxy)phenyl (Bzcr) groups significantly improved the selectivity of the probes toward the short RNA targets. The selectivity was further improved by the addition of a phosphate group on the cyclohexane ring. Although much improved selectivity toward short RNA targets is desirable in a general sense, it is particularly applicable to the selective detection of matured-miRNA over pre-miRNAs.

Synthesis and triplex formation of oligonucleotides containing 8-thioxodeoxyadenosine

For more effective DNA triplex formation under neutral conditions, we synthesized triplex-forming oligonucleotides containing 8-thioxodeoxyadenosine (s(8)dA) residues in place of the protonated deoxycytidines required for the third base pairing with DNA duplexes. Consequently, it was found that s(8)dA exhibited much stronger hybridization ability than dC under neutral conditions when four s(8)dA bases were arranged in a consecutive sequence.

Synthesis and properties of new RNA molecules incorporating 2'-O-aryluridine derivatives

A variety of 2'-O-arylnucleosides with functional groups were synthesized by the microwave-assisted reaction of 2,2'-anhydrouridine with phenol derivatives. The 2'-O-arylnucleosides thus obtained were incorporated into 2'-O-Me RNA or DNA oligomers and their hybridization properties were studied by T(m) measurements.

Development of new DNA triplex triads by using 5-substituted deoxycytidine

We developed a new artificial DNA triplex triad which has the adenine nucleobase in the first strand. This triplex triad (A-psi-C*) is composed of adenine, pseudouridine and 5-sudstituted cytosine as the 1st, 2nd and 3rd strand nucleobases, respectively. The molecular design and synthesis of the nucleobases for the 2nd and 3rd strand of the triplex are also described.

Synthesis of oligodeoxynucleotides incorporating 2-N-carbamoylguanine and evaluation of the hybridization properties

Previously, we reported 2-N-carbamoylguanine (cmG) as a guanine analog. We further studied the synthetic protocol and hybridization properties of oligodeoxynucleotides (ODNs) incorporating cmG. These ODNs were synthesized using the phosphoramidite of cmG without protection of the 6-O position. However, the isolated products were contaminated with deacylated products having guanine in place of cmG. The detailed analysis of the synthetic process suggested that the deacylation resulted from the reaction of the carbamoyl moiety with capping reagents. Protection of the 6-O position suppressed the side reaction. The thermal stability of the DNA duplexes incorporating cmG was analyzed. An analysis of T(m) values revealed that the base discrimination ability of cmG was comparable to or higher than that of the canonical guanine depending on the flanking bases.

New nucleotide pairs for stable DNA triplexes stabilized by stacking interaction

New nucleotide pairs applicable to formation of DNA triplexes were developed. We designed oligonucleotides incorporating 5-aryl deoxycytidine derivatives (dC5Ars) and cyclic deoxycytidine derivatives, dCPPP and dCPPI, having an expanded aromatic area, as the second strand. As pairing partners, two types of abasic residues (C3: propylene linker, phi: abasic base) were chosen. It was concluded that, when the 5-aryl-modified cytosine bases paired with the abasic sites in TFOs in a space-fitting manner, the stability of the resulting triplexes significantly increased. The recognition of C3 toward dC5Ars was selective because of the stacking interactions between their aromatic part and the nucleobases flanking the abasic site. These results indicate the potential utility of new nucleotide triplets for DNA triplex formation, which might expand the variety of structures and sequences and might be useful for biorelated fields such as DNA nanotechnologies.

Hybridization-dependent fluorescence of oligodeoxynucleotides incorporating new pyrene-modified adenosine residues

We report the synthesis and properties of oligonucleotides incorporating N(6)-[N-(pyren-1-ylmethyl)carbamoyl]-deoxyadenosine (dA(pymcm)). We designed the ODN which incorporated two consecutive dA(pymcm) residues. It was revealed that on hybridization with the target DNA and RNA oligomers, the fluorescence spectra of ODNs having two consecutive dA(pymcm) molecules near the 5'-terminal position can change from the pyrene monomer emission to the excimer, depending on the chain length of the target DNA and RNA. These results indicated that dA(pymcm)-modified ODNs can be used as interesting hybridization sensors that are sensitive to the size of the target strand.

Synthesis and properties of oligodeoxynucleotides incorporating 5-carboxydeoxycytidine

We synthesized oligodeoxynucleotide derivatives containing 5-carboxydeoxycytidine (1) as a new deoxynucleoside derivative having an anionic residue at the base part. The base pairing properties of the 5-carboxycytosine base were evaluated by use of ab initio calculations at the MP2/6-31G++(2d,p)//HF/6-31G(d) level. These calculations suggest that the Hoogsteen-type hydrogen bond in DNA triplex is less stable than that of the canonical C(+)-G pair and that the Watson-Crick base pair of this modified base with G is slightly more stable than the natural G-C base pair. These expectations were confirmed by T(m) experiments of duplexes and triplexes formed by hybridization of an oligodeoxynucleotide 14mer incorporating 5-carboxydeoxycytidine with ssDNA and dsDNA oligomers, respectively.

Development of an N-unprotected phosphoramidite method for the chemical synthesis of aminoacylated RNAs

In the previous study, we developed a method for O-selective phosphorylation, i.e., "the activated phosphite method" for DNA synthesis without base protection. However, the O-selectivity was low in RNA synthesis when the activated phosphite method was used. In this paper, we developed a new method for the O-selective phosphorylation available for the chemical synthesis of aminoacylated RNAs on polymer supports. As the result, it was found that the selectivity of the phosphorylation in RNA synthesis without base protection increased to more than 99% by treatment of the undesired N-P(III) bonds with 1-hydroxyl-6-nitorobenzotriazole, independent of the kind of protecting groups at the 2' position. Moreover, we succeeded in synthesizing a 21 mer oligoRNA without base protection.

Short-step chemical synthesis of DNA by use of MMTrS group for protection of 5'-hydroxyl group

4-methoxytrithylthio (MMTrS) group was applied for the appropriately protected four canonical nucleosides. We prepared the phosphoroamidite units by use of these nucleosides and developed the synthesis of oligodeoxynucleotides without any acidic treatment. Moreover, the new DNA synthesis protocol was applied to an automated DNA synthesizer for the synthesis of longer oligodeoxynucleotides.

Recognition of triplex forming oligodeoxynucleotides incorporating abasic sites by 5-arylcytosine residues in duplex DNAs

In this paper, we reported our attempt to use a 5arylcytosine (dC(ar)) and the abasic site () as an artificial base pair for DNA triplex. The idea was confirmed by the molecular modeling studied in which the aromatic group of (ph) which protrudes in the major groove was buried into the cleft formed by the residue in the TFO. We synthesized three kinds of dC(ar) and the oligonucleotides incorporating them. Our UV-melting experiments revealed that the DNA triplex containing the dC(ph).phi was more stable than that containing dC.phi pair. Moreover, the dC.phi pair was more stable than any other dC.Y pairs such as dC(ph).G, dC(ph).C, dC(ph).T and dC(ph).A. These results indicated the possibility that the appropriate pair of dC(Ar) and could be the new sequence code of DNA triplex. We also carried out the Tm analyses of other TFOs incorporating dC(Ar) and , and clarified the stability of these triplexes.

Development of a new method for the synthesis of oligodeoxynucleotides by use of carbamoyl-type protecting groups

Previously, we observed thermal elimination of a quinolylcarbamoyl group from N-quinolylcarbamoylated nucleobase residues. In this paper, we examined the thermal stability of several carbamoyl groups on nucleobases and developed new carbamoyl-type protecting groups for base protection that can be removed by "heating". Particularly, the phenylsulfonylcarbamoyl group was found to be rapidly removed from three kinds of nucleobases, cytosine, adenine, and guanine bases. Moreover, we could carry out the synthesis of oligodeoxynucleotides by using the thermolytic protecting group for base protection.