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K. Kowata et al. / Bioorg. Med. Chem. 24 (2016) 2108–2113
inhibitory activity has been reported to depend on the lengths of
the stems flanking a sequence complementary to miRNA,23 these
results suggest that three-stranded AMO (I/II/III) could not
maintain the stem structures due to the small number of base
pairs. On the other hand, it was revealed that CL-AMO could
involve a stable stem-loop structure via the cross-linked linkages.
It is not clear why HP-AMO exhibited the slightly higher activity
than CL-AMO. Since HP-AMO involves two types of stable hairpin
loops, it might be superior to CL-AMO in nuclease resistance or
binding affinity against miRNA. Further experiments to reveal
them are ongoing. We confirmed that the cross-links between
50-ssH and 30-revH are able to provide functional long ONTs
conveniently.
Table S1. The results of molecular-weight analyses of the decom-
posed products (P1–P5) are listed in Table S2.
4.4. Labeling of amino-modified ONTs
The 30-amino-modified ONT (150 pmol) was reacted with FITC
(150 nmol) or biotin succinimidyl ester (15 nmol) in a solution
(100 lL) containing 250 mM phosphate buffer (pH 8.0) and 10%
dimethylformamide (DMF) at 25 °C. After 30 min (for biotin suc-
cinimidyl ester) or 60 min (for FITC), the reaction mixture was
desalted with a cartridge column (NAP5) and the products were
analyzed by HPLC equipped with a reversed-phase column and a
photodiode array detector (Waters). The percentage of the product
was determined by HPLC analysis.
Labeling with PEG-NHS (75 nmol) was carried out as described
for the reaction with biotin-NHS but in the absence of DMF. We
used branched PEG (SUNBRIGHTGL 2-400GS2, NOF Corp.).
3. Conclusion
N-(2-Aminoethyl)carbamate (revH) and 2-aminoethyl carba-
mate (ssH) linkers were synthesized for 30-terminal modification
of ONTs. Both the carbamate-containing linkers could exhibit effi-
cient reactivity toward active esters compared to the aminoalkyl
linker. Importantly, the revH was more stable in alkaline treat-
ments than the ssH. This high stability was attributed to the sym-
metrical ethylene diamine structure in the revH. These results
indicate the high potential of the revH as 30-amino-linker.
4.5. Cross-linking reaction between amino linkers on a blunt
end of a duplex
Amino-modified duplexes of complementary 25 bases (25-
revH/ssH-25 or 25-C6/C6-25; 200 pmol) were dissolved in
150 mM phosphate buffer (pH 8; 200 lL). The solution was heated
at 90 °C for 1 min and then cooled to room temperature. A 0.4 mM
solution of disuccinimidyl glutarate (Thermo) dissolved in DMF
(50 lL) was added, and the reaction solution was incubated at
27 °C. After 5 min, the reaction mixtures were analyzed as
described for the analysis of labeled ONTs.
We proved that the combination of 50-ssH and 30-revH linkers
enable the efficient cross-links at the blunt ends of duplexes in
the presence of a bifunctional reagent. An anti-microRNA ONT
(CL-AMO) was prepared via the cross-linking of three ONT pieces,
and it efficiently inhibited miRNA function compared to
a
noncross-linked ONT. In conclusion, the revH linker containing a
carbamate linkage is very useful for various 30-terminal modifica-
tions of ONTs and its combined use with a cognate ssH linker as
a 50-amino linker further enables versatile applications.
4.6. Preparation of a CL-AMO from cross-links of amino linkers
Oligo-I (1.0 nmol), oligo-II (1.2 nmol), and oligo-III (1.2 nmol)
were dissolved in 156 mM phosphate buffer (200 lL), heated at
90 °C for 1 min, and then annealed to room temperature. The solu-
tion was placed on an ice bath for 5 min, followed by the addition
4. Experimental
of 2 mM DSG dissolved in DMF (5 lL). The reaction solution was
4.1. Synthesis of 30-amino-linker CPG units
incubated at 17 °C for 3 h, and CL-AMO was purified by reversed-
phase HPLC. The molecular weight of CL-AMO, which was mea-
sured using liquid chromatography–mass spectrometry, was
observed to be nearly identical to the calculated value: calcd
17,815.48, found 17,818.06.
The syntheses of ssH-, revH-, revMe-, and revPro-CPG units are
presented in the Supplementary data.
4.2. Synthesis of 30-amino-modified ONTs
4.7. Luciferase assays
All ONTs were chemically synthesized using standard phospho-
ramidite chemistry. 30-Amino-modified oligoribonucleotides were
synthesized using 20-O-TBDMS-amidite units (Glen Research) with
the trityl-off mode. Cleavage from the support and removal of the
protecting groups were carried out in AMA solution at 65 °C for
10 min. The deprotection of TBDMS groups was carried out in a
A target sequence complementary to mature miR-21 was
inserted into the 30 untranslated region of the Renilla luciferase
(hRluc) gene of psiCHECK-2 vector (Promega), providing the plas-
mid of psiCHECK-2-miR21, which contained both hRluc and firefly
luciferase genes. HeLa cells were seeded at densities of 2 ꢀ 104
solution containing 3HF/TEA (75
(60
lL), DMSO (115 lL), and TEA
cells per well in 96 well plates in DMEM (200
l
L) containing 10%
L) was
removed from each well, the cells were transfected in triplicate
with DMEM solution (10 L) containing Lipofectamine 2000 (Invit-
rogen; 0.3 L), psiCHECK-2-miR21 (100 ng), and AMOs. The con-
l
L) at 65 °C for 2.5 h. After the reaction solution was desalted
FBS the day before transfection. After an aliquot (100
l
with NAP10, 30-modified oligoribonucleotides were purified by
HPLC using a reversed-phase column.
l
l
4.3. HPLC analyses of T5-X treated with alkaline solutions
centrations of the AMOs were varied from 0 to 10 nM.
Assays were performed 48 h post-transfection according to the
manufacturer’s instructions. Renilla luciferase/firefly luciferase
(Rluc/Fluc) values are the average of triplicate wells. All values
were normalized by the ratio of the plasmid signal to the control
plasmid (psiCHECK-2) signal.
After T5-X (1.5 nmol) were incubated in various alkaline sol-
vents (100 lL; condition 1: AMA at 65 °C for 10 min; condition 2:
conc. NH4OH at 55 °C or 65 °C for 16 h), each solvent was evapo-
rated under reduced pressure. The residues were dissolved in
water and subjected to HPLC analyses using a reversed-phase col-
umn. Figure 2a and Figure S1 show the chromatograms of the HPLC
analyses before and after the alkaline treatments (AMA at 65 °C,
conc. NH4OH at 55 °C). Percentages of each peaks generated from
the incubations in conc. NH4OH at 55 °C and 65 °C are listed in
Acknowledgments
We thank Drs. Yu Hirano and Yasuhiro Mie (Bioproduction
Research Institute, National Institute of Advanced Industrial