NMR study of G.cntdot.A and A.cntdot.A pairing in (dGCGAATAAGCG)2

Abstract

One- and two-dimensional NMR, UV absorption experiments, and molecular mechanics calculations were conducted on an oligonucleotide duplex (dGCGAATAAGCG)2 which will be referred to as the T-11-mer. This oligonucleotide forms a duplex that is primarily B-form and contains two adjacent G.A and A.A base pairs and two 3' unpaired guanosines. The adjacent mismatch base pairs have an unusual structure which includes overwinding the helix and stacking with the base from the complementary strand (A4 with A8 and G3 with A7) instead of stacking with the base which is sequential on the strand. The exchangeable and nonexchangeable proton NMR spectra of the duplex have been characterized in H2O and D2O solution at neutral and acidic pH. The duplex is stabilized upon protonation; however, no additional hydrogen bonds are formed. We have observed the amino protons of adenosines A4 and A8 and guanosine G3 as a function of temperature and pH. These amino protons are involved in hydrogen bonds with the purine N3 or N7 acting as acceptors. Through the observation of a variety of NOE signals, the structure of the G.A and A.A mismatch base pairs has been defined.

Sheared purine·purine pairing in biology

“…In simple PyGAPu contexts with no intervening nucleotide, directly adjacent GÁ A and A Á G pairs form rather stable sheared (GA) 2 motifs. Similar stable PyGAPu:PyAAPu motifs with tandem sheared GÁA and AÁA pairs have been reported (Maskos et al, 1993).…”

Catalytic roles for proton transfer and protonation in ribozymes

“…144 Structure 8 involves a protonated adenine forming a base pair with an unprotonated adenine, as reported for a DNA duplex. 145,146 Structure 9 involves protonated adenine engaged in Hoogsteen pairing with guanine, as reported for a DNA duplex. 146 backbone, it does offer the possibility for the existence of local regions with enormous negative surface potential.…”

“…145,146 Structure 9 involves protonated adenine engaged in Hoogsteen pairing with guanine, as reported for a DNA duplex. 146 backbone, it does offer the possibility for the existence of local regions with enormous negative surface potential. Indeed, nonlinear Poisson-Boltzmann (NLPB) calculations have revealed a number of such regions in RNAs with tertiary structure, and several of these regions have been shown to correlate with Mg 2ϩ binding sites.…”

The detailed structure of tandem G·A mismatched base-pair motifs in RNA duplexes is context dependent

“…GÁA mismatches in the socalled sheared base-pair con®guration, in which both nucleotides are in the anti conformation, and in which hydrogen bonds are formed between the guanine 2-amino to the adenine N7 and the guanine N3 to the adenine 6-amino were originally found in a DNA duplex (Li et al, 1991) and an RNA hairpin loop (Heus & Pardi, 1991), and have been observed in RNA at loop helix junctions (Szewczak et al, 1993;Szewczak & Moore, 1995;Biou et al, 1994;Pley et al, 1994a,b;Scott et al, 1995;Cate et al, 1996;Huang et al, 1996;Fountain et al, 1996;Jucker et al, 1996), within internal loops in RNA (SantaLucia & Turner, 1993;Katahari et al, 1994;Szewczak et al, 1993;Szewczak & Moore, 1995) as well as in DNA (Chou et al, 192;Lane et al, 1992;Katahari et al, 1993;Ebel et al, 1994;Maskos et al, 1993). Thermodynamic studies have revealed that the stabilities of tandem GÁA basepairs in RNA can range over almost 5 kcal mol À1 , depending on the closing base-pair (Walter et al, 1994).…”