Two-state model of conformational ¯uctuation in a DNA hairpin-loop Liming Ying, Mark I. Wallace, David Klenerman * Department of Chemistry, University of Cambridge, Lens®eld Road, Cambridge CB2 1EW, UK Received 22 August 2000; in ®nal form 17 October 2000 Abstract Stretched exponential kinetics have been observed in the conformational ¯uctuation of a DNA hairpin-loop under equilibrium conditions. In this paper, we employ a simple multiple-pathway two-state jump model to calculate single- molecule proximity ratio distributions. The simulation can reasonably reproduce the experimental single-molecule data of the conformational ¯uctuations in water, indicating that static disorder is dominant. In contrast, there exists sig- ni®cant discrepancy between the two-state simulation and experiment in buer (2.5 mM Tris-HCl, 250 lM EDTA, 100 mM NaCl), suggesting that both static and dynamic disorder may contribute to the non-exponential kinetics. Ó 2001 Elsevier Science B.V. All rights reserved. 1. Introduction The hairpin-loop is a secondary structural motif frequently observed in both DNA and RNA where there is self-complementarity in the sequence. DNA hairpin-loops are involved in various bio- logical functions, including gene expression and regulation [1]. Hairpin forming sequences have been found near the promoter region [2], enhancer binding site [3], receptor binding site [1] and in the origins of DNA replication [4]. Hairpin structure also exists in ligand-DNA aptamer complexes, which target cofactors, amino acids, peptides and proteins [5]. In addition, hairpin-loops were pro- posed as antisense drugs [6] and serve as DNA biosensors (e.g., molecular beacons) [7,8]. DNA hairpin structures ¯uctuate between dif- ferent conformations and are generally classi®ed as open or closed as shown in Fig. 1. Although the stability and thermodynamics of DNA hairpins have been investigated in detail [9], our under- standing of the kinetics of loop-to-coil transitions remains very limited [10,11]. Recently, Bonnet et al. [12] examined the kinetics of conformational ¯uctuations in DNA hairpin-loops using a com- bination of ¯uorescence quenching and ¯uores- cence correlation spectroscopy (FCS). A simple model of an all-or-none transition between open and closed states was supported by their experi- mental data. This model describes the open-to- closed transition as involving collision of the two arms of a hairpin, followed by the nucleation and the propagation of a base-paired region, whereas closed-to-open transition requires an energy ¯uc- tuation suciently large to unzip all the base pairs [12]. Statistical mechanical models have been proposed to describe the free energy cost of loop 2 February 2001 Chemical Physics Letters 334 (2001) 145±150 www.elsevier.nl/locate/cplett * Corresponding author. Fax: +44-01223-336362. E-mail address: dk10012@cam.ac.uk (D. Klenerman). 0009-2614/01/$ - see front matter Ó 2001 Elsevier Science B.V. All rights reserved. PII: S 0 0 0 9 - 2 6 1 4 ( 0 0 ) 0 1 4 2 5 - 1