CD Studies of Double-Stranded Polydeoxynucleotides Composed of Repeating Units of Contiguous Homopurine Residues z SATYANARAYANAR. GUDIBANDE,SUMEDHA D. JAYASENA, and MICHAEL J. BEHE,* zyxw Department zyx of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015 Synopsis Double-stranded synthetic polydeoxynucleotides of the general zyx form poly[d(G,C,)] zy . poly[d(G,C,], poly[d(G,C)] . poly[d(GC,], and poly[d(A,T,)] . poly[d(A,T,)] have been synthe- sized. When zyxwvut n = zyxwvu 4 or larger, the CD spectra of polymers of the form poly[d(G,C,)] . poly[d(G,,C,)] or poly[d(G,C)] . poly[d(GC,)] closely resemble the spectrum of poly[dG] . poly[dC], suggesting that a string of four continguous guanosine residues is sufficient to induce a conformation resembling that of the polypurine . polypyrimidine. With polymers of the form poly[d(A,T,)] . poly[d(A,T,)], however, the CD spectrum only gradually approaches that of poly[dA] . poly[dT]. INTRODUCTION Double-stranded synthetic polydeoxynucleotides in which one strand con- sists entirely of purine residues and the other entirely of pyrimidine residues are known to have conformations different from that of polymers in which purine and pyrimidine residues occur on both complementary strands. X-ray fiber diffraction studies have shown that poly[dA] poly[dT], poly[dI] . poly[dC], and poly[d(A-I)] * poly[d(C-T)] all have different helical parameters from those of the classical B-form,' and the CD spectra of poly[dA] . poly[dT], poly[dG] . poly[dC], and poly[d(A-G)] . poly[d(C-T)] are quite distinctive and different from the expected CD spectra for polymers in a normal B-conforma- tion.2 The conformations of polyEdG] . poly[dC] and poly[dA] . poly[dT] are al- tered enough to be discriminated from normal DNA in protein binding. Although almost all natural and synthetic DNAs form recognizable nucleo- some complexes when reconstituted with histones, the above-mentioned poly- mers do n ~ t . ~ - ~ When an oligo[dA]. oligo[dT] tract was cloned and the recombinant plasmid reconstituted with histones, nucleosomes were excluded from the region.6 A similar result apparently was seen when a large number of chicken nucleosome core DNAs were sequenced and [dA], . [dT], regions were found to be underrepresented in the interior region of the nu~leosome.~ Apparently the structural differences occur because these polymers have a large number of contiguous purine residues. A question that then arises concerns the minimum number of contiguous purines necessary to observe an *To whom correspondence should be addressed. Biopolymers, Vol. 27, 1905-1915 (1988) zyxwv 0 1988 John Wiley & Sons, Inc. CCC 0006-3525/88/121905-11$04.00