Structure of an Oligodeoxynucleotide Containing a 1,N²-Propanodeoxyguanosine Adduct Positioned in a Palindrome Derived from the Salmonella typhimurium hisD3052 Gene:  Hoogsteen Pairing at pH 5.2

Abstract

The structure of the 1,N(2)-Propanodeoxyguanosine (PdG) adduct was determined at pH 5.2 in the oligodeoxynucleotide duplex 5'-d(CGCGGTXTCCGCG)3'.5'-d(CGCGGACACCGCG)-3' (X = PdG). This sequence, referred to as the -TXT- sequence, is contained within the Salmonella typhimurium hisD3052 gene and contains a palindrome, representing a potential hotspot for frameshift mutagenesis. PdG provides a model for the primary adduct induced in DNA by malondialdehyde, the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-a]-purin-10(3H)-one (M(1)G) lesion. The solution structure was refined by molecular dynamics calculations restrained by a combination of NMR-derived distances and dihedral angles, using a simulated annealing protocol. PdG introduced a localized perturbation into the sequence at base pair X(7).C(20), which was pH-dependent. At neutral pH, conformational exchange resulted in spectral line broadening, and it was not possible to determine the structure. A stable structure was observed at pH 5.2 in which PdG rotated about the glycosyl bond into the syn conformation. This placed the exocyclic moiety into the major groove of the duplex. PdG formed a protonated Hoogsteen pair with nucleotide C(20) in the complementary strand. The pseudorotation of the deoxyribose at C(20) was altered to an approximately equal blend of C2'-endo and C3'-endo structures. However, these made little difference in the overall structure of the modified oligodeoxynucleotide. The structure was compared to that of PdG in the 5'-d(CGCXCGGCATG)-3'.5'-(CATGCCGCGCG)-3' sequence (the -CXC- sequence) at pH 5.8 [Singh, U. S., Moe, J. G., Reddy, G. R., Weisenseel, J. P., Marnett, L. J., and Stone, M. P. (1993) Chem. Res. Toxicol. 6, 825-836]. A sequence effect was observed. When PdG was placed into the -TXT- sequence at low pH, the structural perturbation was limited to the X(7).C(20) base pair. In contrast, when PdG was placed into the -CXC- sequence at low pH, both the modified base pair and its 3'-neighbor base pair were disrupted. The results are discussed in the context of differential outcomes for site-specific mutagenesis and replication bypass experiments when PdG was placed in the -TXT- and -CXC- sequences, respectively.

Replication past a trans-4-Hydroxynonenal Minor-Groove Adduct by the Sequential Action of Human DNA Polymerases ι and κ

“…1). Nuclear magnetic resonance studies of the ring-closed form, 1,N 2 -propano-2Ј-deoxyguanosine (PdG), have shown that, in duplex DNA, the adducted base assumes a syn conformation and forms a PdG (syn) · dC ϩ (anti) Hoogsteen base pair with a C (22,29). The ring-open form of ␥-HOPdG, N 2 -(3-hydroxypropyl), remains in the anti conformation and retains the ability to form a normal Watson-Crick base pair with the C (4,13,14).…”

“…Since ␥-HOPdG is expected to be in the closed cyclic form when it is the templating residue (15,21), Pol can incorporate a C or a T opposite this adduct because of its ability to accommodate the closed cyclic form and utilize the Hoogsteen edge of the modified base that would be in a syn conformation (22,29). Pol proficiently extends from the dCMP residue, but not from the dTMP residue, incorporated by Pol opposite ␥-HOPdG, presumably because the incorporation of dCMP but not of dTMP favors the ringopening reaction of ␥-HOPdG (4,16), and the ability of the ring-opened adduct to form a normal Watson-Crick pair with the C (4) enables Pol to extend from such a primer terminus.…”

Human DNA Polymerase ι Promotes Replication through a Ring-Closed Minor-Groove Adduct That Adopts a syn Conformation in DNA

“…1). The nuclear magnetic resonance studies of a PdG present in the duplex DNA have shown that the adducted base adopts a syn conformation and forms a PdG(syn) · dC ϩ (anti) Hoogsteen base pair with the opposing C (18,27).…”

Bulge Migration of the Malondialdehdye OPdG DNA Adduct When Placed Opposite a Two-Base Deletion in the (CpG)3 Frameshift Hotspot of the Salmonella typhimurium hisD3052 Gene

“…The saturated analogue 1,N 2 -propanodG (PdG adduct) (49) was used by our laboratory (30,(50)(51)(52)(53)(54) as well as by other laboratories (55-58) as a stable structural surrogate for exocyclic 1,N 2 -dG adducts such as the M 1 dG adduct and the acrolein γ-OH-PdG adduct. The PdG adduct reduced the thermal stability, transition enthalpy, and transition free energy of duplex DNA when positioned opposite dC or dA (59).…”