TRIPLEX FORMATION AT PHYSIOLOGICAL PH BY 5-ME-DC-N-4-(SPERMINE) [X] OLIGODEOXYNUCLEOTIDES - NON PROTONATION OF N3 IN X OF X-ASTERISK-G-C TRIAD AND EFFECT OF BASE MISMATCH IONIC-STRENGTH ON TRIPLEX STABILITIES

Oligodeoxynucleotide (ODN) directed tripler formation has therapeutic importance and depends on Hoogsteen hydrogen bonds between a duplex DN A and a third DNA strand, TA:T triplets are formed at neutral pH and C(+)G:C are favoured at acidic pH, It is demonstrated that spermine c onjugation at N-4 Of 5-Me-dC in ODNs 1-5 (sp-ODNs) imparts zwitterioni c character, thus reducing the net negative charge of ODNs 1-5, sp-ODN s form triplexes with complementary 24mer duplex 8:9 show foremost sta bility at neutral pH 7.3 and decrease in stability towards lower pH, u nlike the normal ODNs where optimal stability is found at an acidic pH 5.5, At pH 7.3, control ODNs 6 and 7 carrying dC or 5-Me-dC, respecti vely, do not show any triple helix formation, The stability order of t ripler containing 5-Me-dC-N-4-(spermine) with normal and mismatched du plex was found to be XG:C similar to X*A:T > X*C:G > X*T:A. The hyste resis curve of sp-ODN tripler 38:9 indicated a better association wit h complementary duplex 8:9 as compared to unmodified ODN 6 in tripler 68:9, pH-dependent UV difference spectra suggest that N3 protonation is not a requirement for tripler formation by sp-ODN and interstrand i nteraction of conjugated spermine more than compensates for loss in st ability due to absence of a single Hoogsteen hydrogen bond, These resu lts may have importance in designing oligonucleotides for antigene app lications.