CONFORMATIONAL CHANGES OF SINGLE-STRANDED DNA

The conformation of intact, essentially monodisperse, single-stranded T7 DNA was studied in solutions between 0.001 and 1 m-NaCl at neutral and alkaline pH and temperatures between 5 and 35 °C. Over-all shape is assessed by measurement of S20,w0, and base stacking by absorbance at 260 mμ. The results are interpreted in terms of intrastrand interactions between the bases: stacking which occurs in the absence of H-bonding is referred to as free stacking; associations which involve H-bonding (as well as stacking) are referred to as folding. Folding has large effects on both absorbance and S20,w0; free stacking has a much smaller effect on absorbance and essentially no effect on S20,w0. Folding is sensitive to change in ionic strength, temperature, and pH; free stacking depends mainly on temperature and is affected to a lesser extent, if at all, by alkaline titration or by changes in ionic strength. The transition between unfolded and folded forms can be measured by changes in either absorbance or sedimentation coefficient; the two measurements give broadly similar results but do not agree exactly. The differences are interpreted in terms of short-range and long-range folding, the former involving associations between bases which are near each other in the chain, the latter involving associations between bases which are widely separated along the contour length of the chain. Knowledge of the conformational state of single-stranded T7 DNA over the above range of conditions allows study of the effects of conformation on reactions which might have biological significance. The succeeding paper (Studier, 1969) shows that folding is a major influence on the renaturation and aggregation of single-stranded DNA. © 1969.