Olga Amosova

Repairing the Sickle Cell Mutation I. SPECIFIC COVALENT BINDING OF A PHOTOREACTIVE THIRD STRAND TO THE MUTATED BASE PAIR

A DNA third strand with a 3′-psoralen substituent was designed to form a triplex with the sequence downstream of the T·A mutant base pair of the human sickle cell β-globin gene. Triplex-mediated psoralen modification of the mutant T residue was sought as an approach to gene repair. The 24-nucleotide purine-rich target sequence switches from one strand to the other and has four pyrimidine interruptions. Therefore, a third strand sequence favorable to two triplex motifs was used, one parallel and the other antiparallel to it. To cope with the pyrimidine interruptions, which weaken third strand binding, 5-methylcytosine and 5-propynyluracil were used in the third strand. Further, a six residue “hook” complementary to an overhang of a linear duplex target was added to the 5′-end of the third strand via a T4 linker. In binding to the overhang by Watson-Crick pairing, the hook facilitates triplex formation. This third strand also binds specifically to the target within a supercoiled plasmid. The psoralen moiety at the 3′-end of the third strand forms photoadducts to the targeted T with high efficiency. Such monoadducts are known to preferentially trigger reversion of the mutation by DNA repair enzymes.

Self-catalyzed site-specific depurination of G-residues mediated by cruciform extrusion in closed circular DNA plasmids

Background: Self-catalyzed depurination of G residues occurs readily in single-stranded stem-loops of appropriate sequence. Results: The catalysis occurs in duplex DNA of comparable sequence upon cruciform extrusion, but not in relaxed circular plasmids. Conclusion: The catalytic reaction for self-depurination can occur under essentially in vivo conditions. Significance: Mutagenic consequences of the error-prone repair of resultant apurinic sites should be manifest in vivo. A major variety of “spontaneous” genomic damage is endogenous generation of apurinic sites. Depurination rates vary widely across genomes, occurring with higher frequency at “depurination hot spots.” Recently, we discovered a site-specific self-catalyzed depurinating activity in short (14–18 nucleotides) DNA stem-loop-forming sequences with a 5′-G(T/A)GG-3′ loop and T·A or G·C as the first base pair at the base of the loop; the 5′-G residue of the loop self-depurinates at least 105-fold faster than random “spontaneous” depurination at pH 5. Formation of the catalytic intermediate for self-depurination in double-stranded DNA requires a stem-loop to extrude as part of a cruciform. In this study, evidence is presented for self-catalyzed depurination mediated by cruciform formation in plasmid DNA in vitro. Cruciform extrusion was confirmed, and its extent was quantitated by digestion of the plasmid with single strand-specific mung bean endonuclease, followed by restriction digestion and sequencing of resulting mung bean-generated fragments. Appearance of the apurinic site in the self-depurinating stem-loop was confirmed by digestion of plasmid DNA with apurinic endonuclease IV, followed by primer extension and/or PCR amplification to detect the endonuclease-generated strand break and identify its location. Self-catalyzed depurination was contingent on the plasmid being supercoiled and was not observed in linearized plasmids, consistent with the presence of the extruded cruciform in the supercoiled plasmid and not in the linear one. These results indicate that self-catalyzed depurination is not unique to single-stranded DNA; rather, it can occur in stem-loop structures extruding from double-stranded DNA and therefore could, in principle, occur in vivo.

The Consensus Sequence for Self-catalyzed Site-specific G Residue Depurination in DNA

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. The sequence variation tolerated within the stem-loop-forming genomic consensus sequence for self-catalyzed site-specific depurination of G residues is explored. The variation in self-depurination kinetics with sequence changes in the loop residues and stem base pairs, as well as with pH, provides insights into the self-catalytic mechanism. The observations suggest that self-catalyzed depurination of the 5′ G residue of the loop consensus sequence 5′-G(T/A)GG-3′ probably involves formation of some intraloop hydrogen-bonded base pair with the 3′-terminal G residue; although the electronic structure of both these G residues is retained, their 2-amino substituents are not critical for that interaction. The strong dependence of the self-depurination kinetics on stem stability suggests that the lifetime of some strained form of the loop is controlled by the integrity of the stem. In addition to the effects of length and base pair sequence on stem stability, there is a base pair requirement at the base of the loop: self-depurination is suppressed by 5′-C·G-3′, 5′-A·T-3′, or a mismatch but is most favored by 5′T·A3′ and less so by 5′-G·C-3′. The occurrence in T and G of a similarly located carbonyl capable of hydrogen-bonding to the water molecule required for glycosyl bond hydrolysis may explain this sequence requirement. In toto, the more complete definition of the consensus sequence provided by this investigation enables a more accurate estimation of their number in the human genome and their distribution among different genes.

Self-catalytic DNA Depurination Underlies Human β-Globin Gene Mutations at Codon 6 That Cause Anemias and Thalassemias

Background: A self-catalytic depurination sequence centered at codon 6 in the β-globin gene creates a mutagenic apurinic site. Results: Unique codon 6 haplotypes, many anemia- and thalassemia-causing, far exceed haplotypes at other β-globin codons. Conclusion: Excessive mutagenicity at the only β-globin self-depurination site indicates a mechanism discovered in vitro that functions in vivo. Significance: In vivo functionality of self-depurination sites in genes can spontaneously cause diseases via somatic mutations. The human β-globin gene contains an 18-nucleotide coding strand sequence centered at codon 6 and capable of forming a stem-loop structure that can self-catalyze depurination of the 5′G residue of that codon. The resultant apurinic lesion is subject to error-prone repair, consistent with the occurrence about this codon of mutations responsible for 6 anemias and β-thalassemias and additional substitutions without clinical consequences. The 4-residue loop of this stem-loop-forming sequence shows the highest incidence of mutation across the gene. The loop and first stem base pair-forming residues appeared early in the mammalian clade. The other stem-forming segments evolved more recently among primates, thereby conferring self-depurination capacity at codon 6. These observations indicate a conserved molecular mechanism leading to β-globin variants underlying phenotypic diversity and disease.

Site-Specific Self-Catalyzed DNA Depurination, the Basis of a Spontaneous Mutagenic Mechanism of Wide Evolutionary Significance

This chapter focuses on the nature of site-specific self-catalyzed DNA depurination as a spontaneous mechanism inherent in the chemical structure and dynamics of DNA that has contributed to evolutionary change. It describes the essential molecular features of the mechanism, the short consensus sequence elements that form the catalytic intermediate, the basics of the reactions that lead to the creation of apurinic sites, and the means by which those sites give rise to substitution and short deletion mutations. The consensus sequences are widely distributed in double-stranded genomes across the phyla at high frequency that increases up the phylogenetic tree. In the human genome, they constitute >2 × 106 potential mutagenic sites, non-randomly scattered among very many genes, some containing multiple sites. Examples are presented of genes in which the mutations coincide with their self-depurination consensus sequences, the most striking being those in the β-globin gene that are responsible for six anemias and two β-thalassemias. Those of the olfactory receptor genes and the hypervariable regions of the immunoglobulin genes are shown to have utilized the mechanism to evolve their high degree of diversity and/or to develop their contemporaneous diversity for their present function.

Third strand-mediated psoralen-induced correction of the sickle cell mutation on a plasmid transfected into COS-7 cells.

A significant level of correction of the mutation responsible for sickle cell anemia has been achieved in monkey COS-7 cells on a plasmid containing a β-globin gene fragment. The plasmid was treated in vitro with a nucleic acid ‘third strand’ bearing a terminal photoreactive psoralen moiety that binds immediately adjacent to the mutant base pair. Following covalent attachment of the psoralen by monoadduct or diadduct formation to the mutant T-residue on the coding strand, the treated plasmid was transfected into the cells, which were then incubated for 48 h to allow the cellular DNA repair mechanisms to remove the photoadducts. Upon re-isolation and amplification of the transfected plasmid, sickle cell mutation correction, as determined by sequence analysis of both complementary strands, was established in a full 1%. This result encourages extension of the approach to correct the mutation directly on the chromosome.