A self-catalyzed, site-specific guanine-depurination activity has been found to occur in short gene sequences with a potential to form a stem-loop structure. The critical features of that catalytic intermediate are a 5 -G-T-G-G-3 loop and an adjacent 5 -T⅐A-3 base pair of a short duplex stem stable enough to fix the loop structure required for depurination of its 5 -G residue. That residue is uniquely depurinated with a rate some 5 orders of magnitude faster than that of random ''spontaneous'' depurination. In contrast, all other purine residues in the sequence depurinate at the spontaneous background rate. The reaction requires no divalent cations or other cofactors and occurs under essentially physiological conditions. Such stem-loops can form in duplex DNA under superhelical stress, and their critical sequence features have been found at numerous sites in the human genome. Self-catalyzed stem-loop-mediated depurination leading to flexible apurinic sites may therefore serve some important biological role, e.g., in nucleosome positioning, genetic recombination, or chromosome superfolding.DNA self-catalysis ͉ guanine depurination ͉ stem-loop structure D epurination in DNA has been recognized as a spontaneous form of intracellular DNA damage that affects both G and A residues in an essentially random way (1). In mammalian cells, such damage has been estimated to occur with a k obs of 3 ϫ 10 Ϫ9 min Ϫ1 (2). A complex and elaborate cellular DNA repair machinery has evolved to repair apurinic sites (3, 4). It has long been known that some G residues are more prone to depurination than others (5, 6), and such depurination hot spots have been associated with elevated mutation rates (6, 7). Notwithstanding these insights, notions to account for DNA depurination that go beyond recognition that hydrolysis of the purine-deoxyribose glycosyl bond is acid-catalyzed have not been forthcoming.In the course of studies using a 29-residue single-stranded coding strand fragment encompassing the mutation site of the sickle cell ␤-globin gene (8-10), we found that this 29-nt oligomer as well as its shortened 18-nt segment self-catalyze site-specific depurination of a singular G residue adjacent to the mutation site. In this report, we identify the precise location of the depurination site, the reaction mechanism and its immediate products, the structure of the catalytic intermediate, and some of the sequence requirements and their tolerance for variation within the intermediate. We also note the wide distribution of such putative self-depurinating sequences in the human genome. Results Specific Backbone Cleavage Is the Result of Site-Specific Depurination.It is as a consequence of slow spontaneous backbone cleavage at apurinic sites that the self-catalyzed site-specific depurination we report here was discovered. At the outset, it was observed that this cleavage occurs whether or not 10 Ϫ3 M EDTA is present, indicating that divalent cations are not required for the cleavage. Incubation of the highly purified and homogeneous 29-nt ol...

3-Nitropyrrole (M) was introduced as a non-discriminating 'universal' base in nucleic acid duplexes by virtue of small size and a presumed tendency to stack but not hydrogen bond with canonical bases. However, the absence of thermally-induced hyperchromic changes by single-stranded deoxyoligomers in which M alternates with A or C residues shows that M does not stack strongly with A or C nearest neighbors. Yet, the insertion of a centrally located M opposite any canonical base in a duplex is sometimes even less destabilizing than that of some mismatches, and the variation in duplex stability is small. In triplexes, on the other hand, an M residue centrally located in the third strand reduces triplex stability drastically even when the X.Y target base pair is A.T or G. C in a homopurine. homopyrimidine segment. But, when the target duplex opposition is M-T and the third strand residue is T, the presence of M in the test triplet has little effect on triplex stability. Therefore, a lack of hydrogen bonding in an otherwise helix-compatible test triplet cannot be responsible for triplex destabilization when M is the third strand residue. Thus, M is non-discriminating and none-too-destabilizing in a duplex, but in a triplex it is extremely destabilizing when in the third strand.

A systematic study of agarose gel electrophoresis of double-stranded RNA in the kilobase range of sizes was performed. The dsRNA to dsDNA relative mobility was found to depend on gel concentration: in low density gels RNA moves slower and in high density gels - faster than DNA of the same molecular size. The electrophoretic differences were interpreted within the reptation theory to be mainly due to the molecular stiffness differences. The dsRNA persistence length was roughly estimated to be about twice as great as that of DNA.

Three identical deoxyoligonucleotide third strands with a 3'-terminal psoralen moiety attached by linkers that differ in length (N = 16, 6 and 4 atoms) and structure were examined for their ability to form triplex-directed psoralen photoproducts with both the mutant T residue of the Sickle Cell beta-globin gene and the comparable wild-type sequence in linear duplex targets. Specificity and yield of UVA (365 nm) and visible (419 nm) light-induced photoadducts were studied. The total photoproduct yield varies with the linker and includes both monoadducts and crosslinks at various available pyrimidine sites. The specificity of photoadduct formation at the desired mutant T residue site was greatly improved by shortening the psoralen linker. In particular, using the N-4 linker, psoralen interaction with the residues of the non-coding duplex strand was essentially eliminated, while modification of the Sickle Cell mutant T residue was maximized. At the same time, the proportion of crosslink formation at the mutant T residue upon UV irradiation was much greater for the N-4 linker. The photoproducts formed with the wild-type target were fully consistent with its single base pair difference. The third strand with the N-4 linker was also shown to bind to a supercoiled plasmid containing the Sickle Cell mutation site, giving photoproduct yields comparable with those observed in the linear mutant target.

Background: Certain stem-loop-forming sequences self-catalyze site-specific DNA depurination of G residues. Results: The catalytic intermediate is highly sequence-specific. Conclusion: Like other catalytic mechanisms inherent in macromolecules, self-catalyzed DNA-depurination involves critical sequence and structural elements. Significance: Because the resultant apurinic sites are subject to highly error-prone repair, knowledge of the sequence requirements enables location of potential spontaneous mutagenic sites within genes and other genomic elements.