Dipyrido[3,2-#alpha#:2',3'-clphenazine-Tethered Oligo-DNA:Synthesis and Thermal Stability of Their DNA.DNA and DNA.RNA Duplexes and DNA.DNA.DNA Triplexes

摘要

Dipyrido[3,2-#alpha#:2'3'-c]phenazine (dppz) derivatives were conjugated to 9-mer and 18-mer DNA(ODN) a site without nucleobase,either at the 5'-or 3'-end or at a internucleotied position,vi#alpha# linkers of 7,12,or 18 atoms lengths,These dppz-linked ODNs were synthesized using novel backbone glycerol phosphoramidites:Glycerol,serving as artificial nucleoside without nucleobase,was modified to amines 10,23,and 24,which were suitable for the subsequent key reaction with dppz-carboxylic acld 3(Schemes 2 and 3).The products of these reactions (see 5-7) were then transformed to the standard phosphoramidite derivatives (see 2,29,and 30) or used for loading on a CPG support (see 28,31, and 32). The dppz-modified ODNs were subsequently assembled in the usual manner using automated solid-phase DNA synthesis.The 9-mer ODN-dppz conjugates 35-43 were tested for their ability to form stable duplexes with target DNA or RNA strands (D11(60) or R11 (61)),while the 18-mer ODN-dppz conjugates 48-56 were tested for their ability to form stable triqlexes with a DNA target duplex D24.D24(62)(see t#alpha#bles 1 and 2).The presence of the conjugated dppz derivative increases the stability of DNA.DNA and DNA.RNA duplexes,typically by a #DELTA#T_m of 7.3-10.9deg and 4.5-7.4deg,respectively,when the dppzis tethered at the 5'-or3'-terminal(T#alpha#ble 2).The dppz derivatives also stabilize triplexes when attached to the 5'-or 3'-end,with a #DELTA#T_m varying from 3.8-11.1deg (T#alpha#ble 3).The insertion of a dppz building block at the center of a 9-mer results in a considerably poorer stability of the corresponding DNA.DNA duplexes(#DELTA#T_m=0.5 to 4.2deg )and DNA.RNA duplexes (#DELTA#T_m=-1.5 to 0.9deg).while the replacement of one interior nucleotide by a dppz building unit in the corresponding 8-mer ODN does not reveal the formation of any duplex at all.Different types of modifications in the middle of the 18-mer ODN,in general,do not lead to any triplex fomation,except when the dppz derivative is tethered to the ODN through a 12-atom-ling linker(Entry 9 in T#alpha#ble3).