DNA structure in which an adenine-cytosine mismatch pair forms an integral part of the double helix

• Published in: Biochemistry (Easton) 1987-12, Vol.26 (24), p.7707-7715
• Main Authors: Sarma, Mukti H, Gupta, Goutam, Sarma, Ramaswamy H, Bald, Rolf, Engelke, Ute, Oei, Shiao Li, Gessner, Reinhard, Erdmann, Volker A
• Format: Article
• Language: English
• Subjects: Adenosine; Base Composition; Cytosine; DNA; Magnetic Resonance Spectroscopy - methods; Models, Molecular; Nucleic Acid Conformation; Oligodeoxyribonucleotides
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00398a026

Extensive studies using one- and two-dimensional 1H NMR at 500 MHz revealed that the oligonucleotide d(CGCCGCAGC) in solution at 5 degrees C forms a double helix under conditions of high salt (500 mM in NaCl, 1 mM sodium phosphate), low pH (pH 4.5), and high DNA concentration (4 mM in duplex). The presence of very strong nuclear Overhauser effects (NOEs) from base H8/H6 to sugar H2',H2" and the absence of NOE from base H8/H6 to sugar H3' suggested that the oligomer under these solution conditions forms a right-handed B-DNA double helix. The following lines of experimental evidence were used to conclude that C4 and A7 form an integral part of the duplex: (i) the presence of a NOESY cross-peak involving H8 of A7 and H8 of G8, (ii) the presence of a two-dimensional NOE (NOESY) cross-peak between H6 of C3 and H6 of C4, (iii) base protons belonging to C4 and A7 forming a part of the H8/H6---H1' cross-connectivity route, and (iv) the pattern of H8/H6---H2',H2" NOESY cross-connectivity based upon a B-DNA model requiring that both C4 and A7 form an integral part of the duplex. The possibility of an A-C pair involving H bonds was also examined. Two possible structural models of the duplex at pH 4.5 are proposed: in one model A-C pairing involves two H bonds, and in the other A-C pairing involves a single H bond.