BEYOND GUANINE QUARTETS - CATION-INDUCED FORMATION OF HOMOGENOUS AND CHIMERIC DNA TETRAPLEXES INCORPORATING ISO-GUANINE AND GUANINE

Background: iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By compar ing the abiotic molecular recognition properties of iso-G and its comp lement, ; iso-cytosine (iso-C), with those of genomic nucleotide bases , it may be possible to explain the exclusion of the iso-G-iso-C base pair from modern genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically , tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by ex panding the range of bases that can form the quartet motif. Results: N ative polyacrylamide gel electrophoresis of oligonucleotides bearing r uns of iso-G provides strong support for tetraplex formation via catio n-promoted DNA strand association. In particular, when strands of diff erent lengths bearing the same iso-G tetrad recognition element were c ombined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetr ad recognition domains supports the existence of mixed iso-GIG tetrapl exes with antiparallel strand alignment at chimeric junctions, iso-G t etraplex and quartet structure has also been probed by a photo-crossli nking experiment, ultra-violet spectroscopy and theoretical calculatio ns. Conclusions: As iso-G and G both have a marked tendency to form te traplexes, their tandem inclusion in genetic material may be problemat ic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases c ould undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.