Solid-phase synthesis of oligodeoxyribonucleoside boranophosphates by the boranophosphotriester method.
Oligodeoxyribonucleoside boranophosphates (BH3-ODNs), containing four kinds of nucleobases, were synthesized by the solid-phase boranophosphotriester method. The 2'-deoxyribonucleoside 3'-boranophosphate monomers having 2-cyanoethyl (CE) groups as the phosphorus protecting groups were synthesized in good yields. A new condensing reagent, 1,3-dimethyl-2-(3-nitro-1,2,4-triazol-1-yl)-2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate, was found to be highly effective for the condensation reaction on the solid support. We also found that 1,8-bis(N,N-dimethylamino)naphthalene could accelerate the condensation reaction without causing beta-elimination of the CE groups from the boranophosphate triesters. The internucleotidic CE groups were selectively removed by treatment with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) under anhydrous conditions. The acetylation of the terminal 5'-hydroxy group was found to be effective to suppress the decomposition of the BH3-ODNs during the DBU treatment on the solid support. Under optimized conditions for the solid-phase synthesis and the deprotection reactions, BH3-ODNs (4mers and 12mers) containing four kinds of nucleobases were synthesized in good yields. The hybridization properties of the BH3-ODN 12mers with the complementary native DNAs and RNAs were determined by the thermal denaturing studies. In contrast to the low thermal melting (Tm) value of the duplex composed of T((PB)T)11 and native dA12 (12.8 degrees C), the duplex consisting of d(C(PB)A(PB)G(PB)T)3 and d(ACTG)3 showed a higher Tm value (44.7 degrees C) under high-salt conditions. Furthermore, d(C(PB)A(PB)G(PB)T)3 formed a more stable duplex with the complementary RNA, r(ACUG)3 with a Tm value of 50.5 degrees C. Thus, we first demonstrated that the binding affinity of BH3-ODN to a complementary DNA or RNA is dramatically increased, owing to the inclusion of the four kinds of nucleobases.
Shimizu
Mamoru
M
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building 702, Kashiwa, Chiba 277-8562, Japan.
Saigo
Kazuhiko
K
Wada
Takeshi
T
D001880:Boranes / Q000737:chemistry*; D015394:Molecular Structure; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry*
D001880:Boranes; D009838:Oligodeoxyribonucleotides; D010710:Phosphates; C510710:boranophosphate