Possible Molecular Detent in the DNA Structure at Regulatory Sequences

Abstract

A common feature that appears in a number of DNA sites where proteins interact is the sequence GTG/CAC. In the lac operator this sequence leads to a region with a higher imino proton exchange rate well below the optical melting temperature. It is suggested that this reflects a structural feature recognized by proteins that bind specific sites on the DNA molecule.

Correlation of lac operator DNA imino proton exchange kinetics with its function.

“…Its intensity decreases more rapidly than the resonance intensities of its two neighbors, imino protons of G-5 and G-7. This is consistent with the interpretation of our observations of sequence I that we have previously reported (20). There is also a hint of this lower temperature-dependent melting of the TEA between positions 23 In both cases, a number of ANT imino proton resonances are clearly visible at elevated temperatures, suggesting that a juxtaposition of the T-A pair between two G-C pairs in this manner increases its imino proton exchange rate.…”

“…Initially we synthesized a 13-bp DNA corresponding to sequences -2 to + 11 (20), from which we observed the anticipated early disappearance of the T-6 imino proton resonance. However, the saturation recovery experiments indicated that the high exchange rates at both ends, presumably due to fraying, obscured the marked maximum that we see here for the 17-bp DNA fragment II, even though the GTG/CAC sequence was 6 bp from the nearest end in our 13-bp fragment.…”

“…The imino proton region (19) of the NMR spectrum of the 36-bp lac operator fragment shows a nonsequential loss of resonance intensity occurs as the temperature is elevated (20); i.e., melting does not only start from the ends of the double helix. To simplify the examination of this DNA sequence, three 17-bp subsections were synthesized (Fig.…”

“…The imino proton resonances of the subsections were assigned by nuclear Overhauser enhancement (NOE) and their exchange kinetics were examined by saturation recovery methods developed to probe the structure and dynamics of tR.NA in solution (20,21). Similar kinds of observations have been applied to short DNA fragments obtained from both restriction endonuclease digestion (22,23) and chemical synthesis (24)(25)(26)(27)(28).…”

“…There is an interesting dynamic heterogeneity with a maximal opening rate centered about a GTG/CAC sequence that appears frequently and often symmetrically in a number of other prokaryotic and eukaryotic systems where a specific interaction occurs between protein and DNA. Our suggestion is that this sequence is a common feature used often as part of the protein-DNA recognition mechanism (20) for gene regulation or recombination. EXPERIMENTAL Sequence I, Fig.…”