PNA COMPLEXES OF POLYNUCLEOTIDES AND POLYAMIDES - STRUCTURE OF 2-STRANDED AND 3-STRANDED CHIMERIC HELICES REVEALED BY CONFORMATIONAL-ANALYSIS

We have performed a conformational analysis of double-stranded (dA:pT) (5) and triple-stranded (dA:pT.pT)(5) helices for all possible variant s of mutual orientation of oligoamide and oligonucleotide strands by m eans of AMBER 3.0. Computation results showed that the conformational flexibility of chimeric helices is practically like the DNA flexibilit y, although orientation of atoms around the amide bond is almost plana r. cis- and trans-orientations are close in energy. Permissible change s in helical parameters of chimeric helices practically coincide with the corresponding parameters of double- and triple-stranded DNA helice s. Double-stranded chimeric helices exhibit a tendency to twist accomp anied by helical pitch decreasing. Three-stranded chimeric complexes, on the contrary, exhibit a tendency to unwinding. Energy gain of chime ric helices is noticeable. Thus, double-stranded chimeras are characte rized by the energy of 20 kcal/mol per monomer unit lower than double- stranded DNAs. The energy gain of triple-stranded chimeric complexes i s about 40 kcal/mol per monomer unit. There is qualitative correlation between the experimentally obtained enthalpy of chimeric complexes an d their calculated potential energy. It fully explained the ability of oligoamides to interact with DNA following oligoamide strand invasion of the duplex through D-loop formation. The dependence of energy on m utual strand orientation in chimeric duplexes is weak. Energy penalty of duplexes with parallel orientation of 5' --> 3' and N --> C chain v ectors is about 0,7 kcal/mol per monomer unit. The dependence of energ y on mutual strand orientation in chimeric triplexes is much more appr eciable. The most advantageous is parallel orientation of 5' --> 3' an d N --> C vectors of Watson-Crick chains accompanied by antiparallel o rientation of the Hoogsteen oligoamide chain. It was shown that the st ability of double-stranded oligonucleotides may be increased as a resu lt of oligoamide insert of three or four monomer units in one of the o ligonucleotide chains. The length and base sequence in the insert allo wed one to modulate the degree of duplex stabilization. It is importan t that such stabilization may be obtained without any distortion in ve ctor character of nucleotide duplex formation. it is evident that this method of stabilization of helices is suitable also for triplexes. Mo reover, in this way, one can overcome the difficulties connected with the low penetration ability of PNA in living cells. (C) 1994 John Wile y & Sons, Inc.