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

Abstract

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.

Structure and bonding of Ag(I)–DNA base complexes and Ag(I)–adenine–cytosine mispairs: An ab Initio study

“…14,15,[62][63][64] The NMR studies have shown that two possible a-c mispairs may coexist in the duplex at pH 4.5: the reverse Wobble and the reverse Hoogsteen pairing models, which involve two hydrogen bonds rather than just a single hydrogen bond. 62 Compared to the Watson-Crick binding, such mispairing is energetically not favorable. 15,16 This picture changes dramatically when metals ions are involved.…”

The Hairpin Elements of Nucleic Acid Structure: DNA and RNA Folding

“…The -UNCG-loops are also highly abundant, as the -GNRA-loops in the aforementioned systems. In DNA studies, the choice of heteronucleotide loop sequences Sarma et al 1987;Hiroa et al 1989) was guided by the discovery of unexpectedly stable "minihairpins" (Orbons et al 1986) and by theoretical considerations that four-membered loops would be most stable and that stability would be increased by formation of a base pair between the first and the last base of the loop. In this situation it was expected that this base pair formation is favored with a pyrimidine at the 5'-and the complementary purine at the 3'-end of the loop Blommers et al 1989).…”

Translational Regulation of Cloned Genes

“…1. This structure includes atypical A-G base pairs (at nucleotides 14 and 22) and A-C base pairs (at nucleotides 20 and 24) ; both of these base pairs have been reported to occur in the context of double-helical regions of RNA or synthetic oligonucleotides (23)(24), and the structure shown agrees with nuclease SI sensitivity mapping of single and double-stranded regions of this hairpin (7,25). Fig.…”