J. Mol. Biol. (1976) 108, 665-682 Fluctuational Opening of the Double Helix as Revealed by Theoretical and Experimental Study of DNA Interaction with Formaldehyde ALEXANDER V. LVKASHrS, ALEXANDER V. VOLOGODSKII M~Yr~ D. FRANK-KAMENETSKII AND YURII L. LYUBCHENKO Department of Biology I. V. Kurchatov Institute of Atomic Energy, Moscow 123182, U.S.S.R. (Received 2 March 1976, and in revised form 7 July 1976) It follows from the theory of helix-coil transition that local opening of the double helix due to thermal fluctuations must take place at temperatures well below the melting range. Provided that formaldehyde can not react with hydro- gen-bonded bases and can react only with the exposed ones, such fluetuational opening of base-pairs may be probed by formaldehyde. To test the adequacy of the theory for describing the fluctuational opening of the double helix, the process of DNA interaction with formaldehyde has been simulated by the Monte Carlo method with the aid of a computer. On the basis of kinetic constants for the forward and reverse reactions of formaldehyde with all four nucleotides measured by McGhee &von Hippel (197 ha,b), the kinetic curves of DI~A unwind- ing by formaldehyde have been calculated theoretically without the use of any adjustable parameter. The calculations have demonstrated that the highly reversible but very fast reaction of formaldehyde with the imino group of thymine plays a very important role in the process as a whole. The results of computations of the characteristic time of the process of DNA unwinding by formaldehyde have been compared with experimental data obtained for bacteriophage T7 I)NA for different values of pH, temperature and concentration of formaldehyde. This comparison leads to the conclusion that the theory offers a correct general des- cription of fluctuational opening of the double helix. The main characteristics of this process calculated by the theory are as follows. At room temperatures only individual base-pairs are opened and the mean distance between adjacent unpaired bases is as great as 2 • 105 base-pairs. Each A.T pair is sho~-n to be opened with frequency about 10 ~ s -1 and each G.C pair with a frequency about 10 s-1. At elevated temperatures, in the DNA pre- melting region, the probability of fluctuational opening, as well as the average number of base-pairs in an opened region, increases considerably. A possible role of the results obtained from an analysis of the processes of DNA function in the cell is discussed. 1. Introduction During recent years interest has been aroused in the investigation of the conforma- tional motility of the DNA double helix (for references see review by Frank-Kamenet- skii & Lazurkin, 1974). Such conformational motility is believed to play an important role in DNA functioning in the cell and has been used recently to explain the DNA organization in ehromatin, in virus particles and so on (see, for example, Crick & Klug, 1975). However, investigation of these effects presents severe problems because 665