An alternative way of thinking about stem-loops in DNA. A case study of the human G0S2 gene.

Single strands extruded from duplex DNA have the potential to form stem-loop structures, which may be involved in the homology search preceding recombination. The total stem-loop potential in a sequence window can be analysed in terms of the relative contributions of base composition and base order. There are at least 10 base composition-determined parameters of relevance to the energetics of stem-loop formation. These are the quantities of the four bases themselves, and six derived parameters: ATmin, CGmin, Chargaff differences for the W and S bases, and two base products. The quantities of the least represented base of a Watson-Crick base pair (ATmin, CGmin) might provide an index of the total stem potential of a widow. The degrees to which one base of a Watson-Crick pair exceeds the other (the Chargaff differences for the W bases and for the S bases) might provide an index of the total loop potential of a window. Base products (A x T, C x G) might provide an index both of stem and of loop potentials. Multiple regression analysis of the relationship of the 10 parameters to the energetics of stem-loop formation in the G0S2 gene reveals major roles of S bases, and of base products. While base composition may primarily serve genome or genome sector "strategies", it becomes of local relevance in the case of CpG islands. Base order serves many local "strategies", whose demands may conflict. Base order serves the encoding of protein or of recognition motifs for regulatory factors. On the other hand there appear to be circumstances under which base order synergizes with, or antagonises, base composition in determining total stem-loop potential. Antagonism is evident when the base composition-dependent component of the stem-loop potential of a region is greater than the total stem-loop potential of that region.