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Dipyrido[3,2‐ a :2′,3′‐ c ]phenazine‐Tethered Oligo‐DNA: Synthesis and Thermal Stability of Their DNA⋅DNA and DNA⋅RNA Duplexes and DNA⋅DNA⋅DNA Triplexes
Author(s) -
Ossipov Dimitri,
Zamaratski Edouard,
Chattopadhyaya Jyoti
Publication year - 1999
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/(sici)1522-2675(19991215)82:12<2186::aid-hlca2186>3.0.co;2-1
Subject(s) - chemistry , phenazine , dna , nucleobase , stereochemistry , nucleotide , nucleic acid , rna , phosphoramidite , duplex (building) , nucleoside , a dna , oligonucleotide , combinatorial chemistry , biochemistry , gene
Dipyrido[3,2‐ a :2′,3′‐ c ]phenazine (dppz) derivatives were conjugated to 9‐mer and 18‐mer DNA (ODN) at a site without nucleobase, either at the 5′‐ or 3′‐end or at a internucleotide position, via 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 acid 3 ( Schemes 2 and 3 ). The products of these reactions (see 5 – 7 ) were then transformed to the standard phosphoramidite derivatives (see 27 , 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 triplexes with a DNA target duplex D24⋅D24 ( 62 ) (see Tables 1 and 2 ). The presence of the conjugated dppz derivative increases the stability of DNA⋅DNA and DNA⋅RNA duplexes, typically by a Δ T m of 7.3 – 10.9° and 4.5 – 7.4°, respectively, when the dppz is tethered at the 5′‐ or 3′‐terminal ( Table 2 ). The dppz derivatives also stabilize triplexes when attached to the 5′‐ or 3′‐end, with a Δ T m varying from 3.8 – 11.1° ( Table 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 ( Δ T m =0.5 to 4.2°) and DNA⋅RNA duplexes ( Δ T m =−1.5 to 0.9°), 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 formation, except when the dppz derivative is tethered to the ODN through a 12‐atom‐long linker ( Entry 9 in Table 3 ).