Evaluation of thermodynamic properties of irreversible protein thermal unfolding measured by DSC

Summary We assessed the applicability of the extrapolation procedure at infinite scanning rate to differential scanning calorimetry (DSC) data related to irreversible protein unfolding. To this aim, an array of DSC curves have been simulated on the basis of the Lumry-Eyring model N↔U→F. The results obtained confirmed that when the apparent equilibrium constant K_{app (T=T1/2)} is lower than 3, the application of the extrapolation procedure provides accurate thermodynamic parameters. Although this procedure applies only to monomeric proteins for which the Lumry-Eyring model is a reasonable approximation, it will hopefully contribute to increase the potential of DSC in obtaining reliable thermodynamic information regarding the folding/unfolding equilibrium.     

Diverse polymorphism of G-quadruplexes as a kinetic phenomenon

Knowledge of forces that drive conformational transitions of G-quadruplexes is crucial for understanding the molecular basis of several key cellular processes. It can only be acquired by combining structural, thermodynamic and kinetic information. Existing biophysical and structural evidences on polymorphism of intermolecular G-quadruplexes have shown that the formation of a number of these structures is a kinetically controlled process. Reported kinetic models that have been used to describe the association of single strands into quadruplex structures seem to be inappropriate since the corresponding model-predicted activation energies turn out to be negative. By contrast, we propose here a novel kinetic model that successfully describes experimentally monitored folding/unfolding transitions of G-quadruplexes and gives positive activation energies for all elementary steps, including those describing association of two single strands into bimolecular quadruplex structures. It is based on a combined thermodynamic and kinetic investigation of polymorphic behavior of bimolecular G-quadruplexes formed from d(G4T4G4) and d(G4T4G3) strands in the presence of Na(+) ions, monitored by spectroscopic (UV, CD) and calorimetric (DSC) techniques. According to our experiment and model analysis the topology of the measured G-quadruplexes is clearly flexible with the conformational forms that respond to the rate of temperature change at which global unfolding/folding transitions occur.     

Mechanistic investigations of the palladium-catalyzed aerobic oxidative kinetic resolution of secondary alcohols using (-)-sparteine

The mechanistic details of the Pd(II)/(-)-sparteine-catalyzed aerobic oxidative kinetic resolution of secondary alcohols were elucidated, and the origin of asymmetric induction was determined. Saturation kinetics were observed for rate dependence on [(-)-sparteine]. First-order rate dependencies were observed for both the Pd((-)-sparteine)Cl(2) concentration and the alcohol concentration at high and low [(-)-sparteine]. The oxidation rate was inhibited by addition of (-)-sparteine HCl. At low [(-)-sparteine], Pd-alkoxide formation is proposed to be rate limiting, while at high [(-)-sparteine], beta-hydride elimination is proposed to be rate determining. These conclusions are consistent with the measured kinetic isotope effect of k(H)/k(D) = 1.31 +/- 0.04 and a Hammett rho value of -1.41 +/- 0.15 at high [(-)-sparteine]. Calculated activation parameters agree with the change in the rate-limiting step by increasing [(-)-sparteine] with DeltaH(++) = 11.55 +/- 0.65 kcal/mol, DeltaS(++) = -24.5 +/- 2.0 eu at low [(-)-sparteine], and DeltaH(++) = 20.25 +/- 0.89 kcal/mol, DeltaS() = -5.4 +/- 2.7 eu at high [(-)-sparteine]. At high [(-)-sparteine], the selectivity is influenced by both a thermodynamic difference in the stability of the diastereomeric Pd-alkoxides formed and a kinetic beta-hydride elimination to maximize asymmetric induction. At low [(-)-sparteine], the selectivity is influenced by kinetic deprotonation, resulting in lower k(rel) values. A key, nonintuitive discovery is that (-)-sparteine plays a dual role in this oxidative kinetic resolution of secondary alcohols as a chiral ligand on palladium and as an exogenous chiral base.     

Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking

It has been shown that DNA oligonucleotides composed, in part, of G repeat sequences can adopt G-quadruplex structures in the presence of specific metal ions. In this work, we use a combination of spectroscopic and calorimetric techniques to determine the spectral and thermodynamic characteristics of two DNA aptamers, d(G2T2G2TGTG2T2G2), G2, and d(G3T2G3TGTG3T2G3), G3; a sequence in the promoter region of the c-MYC oncogene, d(TG4AG3TG4AG3TG4A2G2), NHE-III; and the human telomere sequence d(AG3T2AG3T2AG3T2AG3), 22GG. The circular dichroism spectra of these oligonucleotides in the presence of K+ indicate that all form G-quadruplexes with G-quartets in an antiparallel arrangement (G2), in a parallel arrangement (NHE-III and 22GG), or in a mixed parallel and antiparallel G-quartet arrangement (G3). Melting profiles show transition temperatures, TM, above 45 degrees C that are independent of strand concentration, consistent with the formation of very stable intramolecular G-quadruplexes. We used differential scanning calorimetry to obtain complete thermodynamic profiles for the unfolding of each quadruplex. Subtracting the thermodynamic folding profiles of G2 from those of G3 yielded the following thermodynamic profile for the formation of a G-quartet stack: DeltaG degrees 20 = -2.2 kcal/mol, DeltaHcal = -14.6 kcal/mol, TDeltaScal = -12.4 kcal/mol, DeltanK+ = -0.3 mol of K+/mol, and DeltanW = 13 mol of H2O/mol. Furthermore, we used this profile to estimate the thermodynamic contributions of the loops and/or extra base sequences of each oligonucleotide in the G-quadruplex state. The average free energy contributions of the latter indicate that the incorporation of loops and base overhangs stabilizes quadruplex structures. This stabilization is enthalpy-driven and is due to base-stacking contributions.     

Kinetic Analysis of Non-isothermal DSC Data. Computer-aided test of its applicability

The applicability of the kinetic analysis of data obtained by non-isothermal differential scanning calorimetry (DSC) is discussed. The Johnson-Mehl-Avrami (JMA) model was used for the computer simulation of DSC traces subsequently analysed by common methods of kinetic analysis of non-isothermal data. For the temperature-independent kinetic exponent n of the JMA equation, the kinetic analysis was shown to provide correct results, e.g. a correct kinetic model and apparent activation energy. On the other hand, for the temperature-dependent kinetic exponent, there is a great possibility of erroneous determination of the correct kinetic model and apparent activation energy, especially at higher heating rates. Since the temperature dependence of n cannot be determined on the basis of non-isothermal DSC experiments, conclusions must be drawn with appropriate caution. This revised version was published online in August 2006 with corrections to the Cover Date.     

Calorimetric unfolding of intramolecular triplexes: length dependence and incorporation of single AT --> TA substitutions in the duplex domain

DNA triplexes have been the subject of great interest due to their ability to interfere with gene expression. The inhibition of gene expression involves the design of stable triplexes under physiological conditions; therefore, it is important to have a clear understanding of the energetic contributions controlling their stability. We have used a combination of UV spectroscopy and differential scanning calorimetric (DSC) techniques to investigate the unfolding of intramolecular triplexes, d(A(n)C5T(n)C5T(n)), where n is 5-7, 9, and 11, and related triplexes with a single AT --> TA substitution in their duplex stem. Specifically, we obtain standard thermodynamic profiles for the unfolding of each triplex in buffer solutions containing 0.1 M or 1 M NaCl. The triplexes unfold in monophasic or biphasic transitions (triplex --> duplex --> coil) depending on the concentration of salt used and position of the substitution, and their transition temperatures are independent of strand concentration. The DSC curves of the unsubstituted triplexes yielded an unfolding heat of 13.9 kcal/mol for a TAT/TAT base-triplet stack and a heat capacity of 505 cal/ degrees C.mol. The incorporation of a single substitution destabilizes triplex formation (association of the third strand) to a larger extent in 0.1 M NaCl, and the magnitude of the effects also depends on the position of the substitution. The combined results show that a single AT --> TA substitution in a homopurine/homopyrimidine duplex does not allow triplex formation of the neighboring five TAT base triplets, indicating that the in vivo formation of triplexes, such as H-DNA, is exclusive to homopurine/homopyrimidine sequences.     

Thermochemical and kinetic study of the carbocation ring contraction of cyclohexylium to methylcyclopentylium

The isomerization of cyclohexylium to methylcyclopentylium is a model for a key step required in sterol and triterpene biosynthesis and is important in catalytic processes associated with ring-opening reactions in upgrading petroleum fractions. Using high-level, correlated wave function techniques based on QCISD, the mechanism for this isomerization was found to be very different from that first proposed more than 35 years ago. On the basis of our mechanism, a first-order rate constant expression was derived and used with complete basis set-extrapolated QCISD(T) energies to obtain Ea = 6.9 kcal/mol and A = 1011.18 s-1, in excellent agreement with values of 7.4 +/- 1 kcal/mol and A = 1012 +/- 1.3 s-1 measured in the gas phase. The B3LYP and MP2 methods, two commonly used computational approaches, were found to predict incorrect mechanisms and, in some cases, poor kinetic parameters. The PBE method, however, produced a reaction profile and kinetic parameters in reasonable agreement with those obtained with the complete basis set-extrapolated QCISD(T) method.     

Energetic contributions for the formation of TAT/TAT,TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks

We used a combination of spectroscopic and calorimetric techniques to determine complete thermodynamic profiles accompanying the folding of a set of triple helices and control duplexes. Specifically, we studied the sequences: d(A(7)C(5)T(7)C(5)T(7)), d(A(6)C(5)T(6)C(5)T(6)), d(A(6)C(5)T(6)), d(AGAGAGAC(5)TCTCTCTC(5)TCTCTCT), d(AGAGAC(5)TCTCTC(5)TCTCT), d(AGAGAC(5)TCTCTC(2)), d(AAGGAC(5)TCCTTC(5)TTCCT), d(AGGAAC(5)TTCCTC(5)TCCTT), and d(GAAAGC(5)CTTTCC(5)CTTTC). Circular dichroism spectroscopy indicated that all triplexes and duplexes are in the "B" conformation. DSC melting experiments revealed that the formation of triplexes is accompanied by a favorable free energy change, which arises from the compensation of a large and favorable enthalpic contribution with an unfavorable entropic contribution. Comparison of the thermodynamic profiles of these triplexes yielded enthalpic contributions of -24 kcal/mol, -23 kcal/mol, and -22 kcal/mol for the formation of TAT/TAT, TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks, respectively. UV melts as a function of sodium concentration show sodium ions stabilize the triplexes that contain only TAT triplets but destabilize the triplexes that contain CGC(+) triplets. UV melts as a function of pH indicate that the protonation of the third strand and loop cytosines stabilizes the triplexes that contain CGC(+) and TAT triplets, respectively. Our overall results suggest that the triplex to duplex transition of triplexes that contain CGC(+) triplets is accompanied by a release of protons and an uptake of sodium, while their duplex to random coil transition is accompanied by a release of sodium ions. A consequence of this opposite sodium dependence is that their coupled transitions are nearly independent of sodium concentration but are dependent on the experimental pH.     

Kinetics and thermodynamics of copper(II) binding to apoazurin

The binding of copper(II) to apoazurin has been probed by isothermal titration calorimetry in cholamine buffer at pH 7.0. The standard enthalpy change was determined to be -10.0 +/- 1.4 kcal/mol. Each calorimetric trace reveals an initial exothermic phase followed by an endothermic phase. The calorimetric data could be fit to a kinetic model involving a bimolecular combination of copper(II) and apoazurin in an exothermic process (k = 2 +/-1 x 103 M-1 s-1, DeltaH degrees = -19 +/- 3 kcal/mol) to form an intermediate that spontaneously converts to Cu(II)-azurin in an endothermic process (k = 0.024 +/- 0.01 s-1, DeltaH degrees = +9 +/- 3 kcal/mol). These data suggest that copper(II) first combines with apoazurin in an irreversible process to form an intermediate that converts to copper(II)-azurin in a process driven by the release of water. The overall standard free energy of copper(II) binding to apoazurin is estimated to be -18.8 kcal/mol.     

Dynamic unfolding of a regulatory subunit of cAMP-dependent protein kinase by capillary electrophoresis: Impact of cAMP dissociation on protein stability

Characterization of the unfolding dynamics of a recombinant type IA regulatory subunit (RIalpha) of cyclic adenosine monophosphate (cAMP)-dependent protein kinase (cAPK) was examined by CE with UV detection. Electrophoretic separation of RIalpha by CE in a buffer devoid of cAMP resulted in rapid dissociation of the complex from the original sample due to the high negative mobility of the ligand relative to receptor. This process enabled in-capillary generation of cAMP-stripped RIalpha, which was used to estimate the apparent dissociation constant (Kd) of 0.6 +/- 0.2 microM. A comparison of RIalpha dynamic unfolding processes with urea denaturation was performed by CE with (i.e., RIalpha-cAMP) and without (i.e., cAMP-stripped RIalpha) excess cAMP in the buffer during electromigration. The presence of cAMP in the buffer confirmed greater stabilization of the protein, as reflected by a higher standard free energy change (DeltaG(U) degrees) of 10.1 +/- 0.5 kcal x mol(+1) and greater cooperativity in unfolding (m) of -2.30 +/- 0.11 kcal x mol(-1) M(-1). CE offers a rapid, yet versatile platform for probing the thermodynamics of cAPK and other types of receptor-ligand complexes in free solution.     

Activation of C-H / H-H bonds by rhodium(II) porphyrin bimetalloradicals

Reactivity, kinetic, and thermodynamic studies are reported for reactions of a rhodium(II) bimetalloradical with H(2), and with the methyl C-H bonds for a series of substrates CH(3)R (R = H, CH(3), OH, C(6)H(5)) using a m-xylyl diether tethered diporphyrin ligand. Bimolecular substrate reactions involving the intramolecular use of two metalloradical centers and preorganization of the four-centered transition state (M*...X...Y*...M) result in large rate enhancements as compared to termolecular reactions of monometalloradicals. Activation parameters and deuterium kinetic isotope effects for the substrate reactions are reported. The C-H bond reactions become less thermodynamically favorable as the substrate steric requirements increase, and the activation free energy (DeltaG++) decreases regularly as DeltaG degrees becomes more favorable. An absolute Rh-H bond dissociation enthalpy of 61.1 +/- 0.4 kcal mol(-1) is directly determined, and the derived Rh-CH(2)R BDE values increase regularly with the increase in the C-H BDE.     

Thermodynamic and kinetic characterization of nitrogen-containing polycyclic aromatic hydrocarbons in reversed-phase liquid chromatography

A series of five nitrogen-containing polycyclic aromatic hydrocarbons (NPAHs) was studied on polymeric octadecylsilica using methanol and acetonitrile as the mobile phase. The thermodynamic and kinetic behavior was examined as a function of ring number, annelation structure, and position of the nitrogen atom. The retention factors for the NPAHs are smaller than those for the parent PAHs in methanol, while the converse is true in acetonitrile. The changes in molar enthalpy are relatively comparable in both mobile phases with 1-aminopyrene having values of -5.0 +/- 0.2 kcal/mol in methanol and -6.3 +/- 0.7 kcal/mol in acetonitrile (1 cal = 4.184 J). However, the rate constants from mobile to stationary phase (k(sm)) and from stationary to mobile phase (k(ms)) demonstrate large differences as a function of mobile phase. For example, the rate constants k(ms) for 1-aminopyrene and 4-azapyrene are 675 and 62 s(-1), respectively, in methanol at 303 K. In contrast, the same solutes demonstrate rate constants of 3.47 and 3.9 x 10(-3) s(-1), respectively, in acetonitrile. The activation energies for transfer from mobile phase to transition state (deltaE(double dagger(m)) and from stationary phase to transition state (deltaE(double dagger(s)) also differ as a function of mobile phase. For example, the activation energies deltaE(double dagger(s)), for 1-aminopyrene are 21 and approximately 0 kcal/mol, whereas those for 4-azapyrene are 19 and 23 kcal/mol, in methanol and acetonitrile, respectively. Based on these thermodynamic and kinetic results, the relative contributions from the partition and adsorption mechanisms are discussed.     

Thermal stabilities of some benzaldehyde 2,4-dinitrophenylhydrazones

The thermal stability of some benzaldehyde 2,4-dinitrophenylhydrazones has been studied using DSC technique. The crystalline solids are thermally stable and start to decompose after melting. Non-isothermal DSC curves, recorded at several heating rates, were used to evaluate the melting properties and the kinetics of thermal decomposition. Both isoconversional and model fitting methods were used for the evaluation of the kinetic parameters. Based on the results of the model free method, a kinetic model was derived and the kinetic parameters were obtained by means of a multivariate non-linear regression. A good agreement between the experimental and fitted data was found.     

Bimetallo-radical carbon-hydrogen bond activation of methanol and methane

Carbon-hydrogen bond cleavage reactions of CH3OH and CH4 by a dirhodium(II) diporphyrin complex with a m-xylyl tether (.Rh(m-xylyl)Rh.(1)) are reported. Kinetic-mechanistic studies show that the substrate reactions are bimolecular and occur through the use of two Rh(II) centers in the molecular unit of 1. Second-order rate constants (T = 296 K) for the reactions of 1 with methanol (k(CH3OH) = 1.45 x 10-2 M-1 s-1) and methane (k(CH4) = 0.105 M-1 s-1) show a clear kinetic preference for the methane activation process. The methanol and methane reactions with 1 have large kinetic isotope effects (k(CH3OH)/k(CD3OD) = 9.7 +/- 0.8, k(CH4)/k(CD4) = 10.8 +/- 1.0, T = 296 K), consistent with a rate-limiting step of C-H bond homolysis through a linear transition state. Activation parameters for reaction of 1 with methanol (DeltaH = 15.6 +/- 1.0 kcal mol-1; DeltaS = -14 +/- 5 cal K-1 mol-1) and methane (DeltaH = 9.8 +/- 0.5 kcal mol-1; DeltaS = -30 +/- 3 cal K-1 mol-1) are reported.     

Synthesis, characterization, and sorption properties of silica gel-immobilized pyrimidine derivative

5-Benzylidene-2-thiobarbituric acid (BzTBA), a pyrimidine derivative, was used to modify the surface of silica gel-chloropropyltrimethoxysilane (Si-Cl) via chemical immobilization to produce a new pyrimidine silica phase (Si-BzTBA). Identification of the surface modification was characterized and performed on the basis of infrared as well as elemental analysis. Thermal desorption method was found to give 0.129-0.143 mmol g(-1) as surface coverage values. Metal sorption properties of Si-BzTBA were also studied and the evaluated results refer to the high metal sorption of Si-BzTBA for copper(II), mercury(II), cadmium(II), and lead(II) with the same order. These four Si-BzTBA-metal complexes were also synthesized and the stoichiometric ratios were identified as 1:1 except lead complex was found to give a 1:2 ratio. Electron impact-mass spectrometric analysis (EI-MS) with 70 eV ionization energy was used as a potential thermal method for the confirmation of surface modification of Si-BzTBA and its metal complexes based on fragmentation elucidation of thermally desorbed ion peaks. The EI-MS of Si-BzTBA was found to show several characteristic fragment ion peaks that are directly related to the chemical binding of BzTBA to SiCl phase. Differential scanning calorimetry study (DSC) was also performed to evaluate the various kinetic and thermodynamic parameters of thermal degradation processes and have been enumerated. The results of EI-MS and DSC are very similar in many respects.     

Kinetics of thermal unfolding of phenylalanine hydroxylase variants containing different metal cofactors (FeII, CoII, and ZnII) and their isokinetic relationship

The kinetics of thermal unfolding of apo- and holo-Chromobacterium violaceum phenylalanine hydroxylase (cPAH) was investigated using circular dichroism (CD) over the temperature range 44-76 degrees C. In addition to the native cofactor (FeII), the unfolding kinetics of holo-cPAH was characterized using ZnII and CoII as cofactors. Kinetic profiles for apo- and holo-cPAH showed a single-phase exponential rise in the CD signal at lambda=222 nm and a first-order dependence on protein concentration. The extrapolated unfolding rate constants (ku) at ambient temperature followed the order apo>Fe>Zn>Co. Transition-state analysis of the activation parameters revealed an isokinetic correlation, which suggests a common mechanism for the enzyme variants. The values of the entropy of activation (DeltaS++) for apo- and Fe-cPAH were negative but small: -34+/-24 and -32+/-18 J mol(-1) K(-1), respectively. On the other hand, DeltaS++ values for Zn- and Co-cPAH were large and positive: 54+/-9 and 175+/-27 J mol(-1) K(-1), respectively. Therefore, at higher temperatures the unfolding rates of Zn- and Co-cPAH are affected significantly by entropy, while the unfolding rates of apo- and Fe-cPAH are dominated by enthalpy even at higher temperatures. The rate of unfolding of holo-cPAH did not depend on excess metal concentrations and maintained single-phase kinetic profiles, refuting the occurrence of adventitious metal binding and the notion that unfolding occurs via apo-cPAH exclusively. Isothermal titration calorimetry (ITC) was employed to measure cPAH binding affinities for Fe, Zn, and Co as well as the enthalpy of metal coordination. Dissociation constants (Kd) decreased in the order Fe>Zn>Co. The non-native metals, Zn and Co, were bound more tightly than Fe. The activation enthalpy for unfolding (DeltaH++) displayed a linear correlation with the enthalpy of metal binding obtained from ITC measurements (DeltaHITC). On this basis, a common mechanism (transition state) is suggested for this family of metal cofactors, and the varying enthalpy of activation arises from the differing stabilities of enzyme variants having different metal cofactors.     

The temperature dependence of the heat capacity change for micellization of nonionic surfactants

The thermodynamic parameters that govern micelle formation by four different nonionic surfactants were investigated by ITC and DSC. These included n-dodecyldimethylphosphine oxide (APO12), Triton X-100 (TX-100), n-octyltetraoxyethylene (C8E4), and N,N-dimethyloctylamine-N-oxide (DAO8). All of these surfactants had been previously investigated by solution calorimetry over smaller temperature ranges with conflicting conclusions as to the temperature dependence of the heat capacity change, DeltaCp, for the process. The temperature coefficient of the heat capacity change, B (cal/mol K2), was derived from the enthalpy data that were obtained at small intervals over a broad temperature range. The values obtained for each of the surfactants at 298.2 K for DeltaCp and B were -155+/-2 and 0.50+/-0.36 (APO12), -97+/-3 and -0.24+/-0.18 (TX-100), -105+/-2 and 1.0+/-0.3 (C8E4), and -82+/-1 and 0.36+/-0.04 (DAO8), cal/mol K and cal/mol K2, respectively. The resulting B-values did not correlate with the cmc, aggregation number, or structure of the monomer in an obvious way, but they were found to reflect the relative changes in hydration of the polar and nonpolar portions of the surfactant molecule as the micelles are formed. An analysis of the data obtained from DSC scans was used to describe the temperature dependence of the critical micelle concentration, cmc. An abrupt increase in heat capacity was observed for TX-100 and C8E4 solutions of 36.5+/-0.5 and 21+/-5 cal/mol K, respectively, as the temperature of the scan passed through the cloud point. This change in heat capacity may reflect the increased monomer concentration of the solutions that accompanies phase separation, although other interpretations of this jump are possible.     

Spectroscopic, and thermal studies of some new binuclear transition metal(II) complexes with hydrazone ligands containing acetoacetanilide and isoxazole

A new chelating ligand, 2-(2-(5-tert-butylisoxazol-3-yl)hydrazono)-N-(2,4-dimethylphenyl)-3-oxobutanamide (HL), and its four binuclear transition metal complexes, M(2)(L)(2) (micro-OCH(3))(2) [M=Ni(II), Co(II), Cu(II), Zn(II)], were synthesized using the procedure of diazotization, coupling and metallization. Their structures were postulated based on elemental analysis, (1)H NMR, MALDI-MS, FT-IR spectra and UV-vis electronic absorption spectra. Smooth films of these complexes on K9 glass substrates were prepared using the spin-coating method and their absorption properties were evaluated. The thermal properties of the metal(II) complexes were investigated by thermogravimetry (TG) and differential scanning calorimetry (DSC). Different thermodynamic and kinetic parameters namely activation energy (E*), enthalpy of activation (DeltaH*), entropy of activation (DeltaS*) and free energy change of activation (DeltaG*) are calculated using Coats-Redfern (CR) equation.     

Direct Measurement of Single‐Molecule DNA Hybridization Dynamics with Single‐Base Resolution

Herein, we report label‐free detection of single‐molecule DNA hybridization dynamics with single‐base resolution. By using an electronic circuit based on point‐decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal‐to‐noise ratio and bandwidth. These measurements reveal two‐level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base‐by‐base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base‐pair level. This measurement capability promises a label‐free single‐molecule approach to probe biomolecular interactions with fast dynamics.