Temperature Effects on DNA Chip Experiments from Surface Plasmon Resonance Imaging: Isotherms and Melting Curves

Fiche, Jean-Bernard; Buhot, Arnaud; Calemczuk, R.; Livache, Thierry

doi:10.1529/biophysj.106.097790

Cited by 87 publications

(122 citation statements)

References 70 publications

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“…First of all, we propose formulae for chain free-boundary conditions, this information being encoded in the end vector |V given in Eq. (11). However, any other boundary condition can be treated following the same route, even though we shall not detail the calculations here.…”

Section: Discussionmentioning

confidence: 99%

Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation

2008

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Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of freedom in a more general mesoscopic model is needed. In this paper we do so by presenting a 1D Ising model, which describes the internal base pair states, coupled to a discrete worm like chain model describing the chain configurations [J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007)]. This coupled model is exactly solved using a transfer matrix technique that presents an analogy with the path integral treatment of a quantum two-state diatomic molecule. When the chain fluctuations are integrated out, the denaturation transition temperature and width emerge naturally as an explicit function of the model parameters of a well defined Hamiltonian, revealing that the transition is driven by the difference in bending (entropy dominated) free energy between bubble and double-stranded segments. The calculated melting curve (fraction of open base pairs) is in good agreement with the experimental melting profile of polydA-polydT and, by inserting the experimentally known bending rigidities, leads to physically reasonable values for the bare Ising model parameters. Among the thermodynamical quantities explicitly calculated within this model are the internal, structural, and mechanical features of the DNA molecule, such as bubble correlation length and two distinct chain persistence lengths. The predicted variation of the mean-square-radius as a function of temperature leads to a coherent novel explanation for the experimentally observed thermal viscosity transition. Finally, the influence of the DNA strand length is studied in detail, underlining the importance of finite size effects, even for DNA made of several thousand base pairs. Simple limiting formulae, useful for analyzing experiments, are given for the fraction of broken base pairs, Ising and chain correlation functions, effective persistence lengths, and chain mean-square-radius, all as a function of temperature and DNA length.

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Section: Discussionmentioning

confidence: 99%

Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation

2008

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“…A variety of aids to enhance hybridization performance is used, including surfactants and blocking agents to control nonspecific adsorption, washing procedures to develop contrast between fully and partially complementary sequences, and variation of assay parameters such as ionic strength or temperature. Physical studies (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) aim to distill down this complexity into scenarios where specific features of surface hybridization are brought out; for example, the impact of probe surface coverage on target hybridization (17,20,22,23,28).…”

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confidence: 99%

DNA surface hybridization regimes

Gong

Levicky²

2008

Proc. Natl. Acad. Sci. U.S.A.

224

282

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Surface hybridization reactions, in which sequence-specific recognition occurs between immobilized and solution nucleic acids, are routinely carried out to quantify and interpret genomic information. Although hybridization is fairly well understood in bulk solution, the greater complexity of an interfacial environment presents new challenges to a fundamental understanding, and hence application, of these assays. At a surface, molecular interactions are amplified by the two-dimensional nature of the immobilized layer, which focuses the nucleic acid charge and concentration to levels not encountered in solution, and which impacts the hybridization behavior in unique ways. This study finds that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes that compete with hybridization to analyte strands. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites. These results are interpreted and summarized in a diagram of hybridization regimes that maps specific behaviors to experimental ranges of ionic strength and probe coverage.biosensor ͉ ferrocene ͉ ionic strength ͉ microarray ͉ probe coverage S olid-phase or ''surface'' hybridization is the foundation of modern microarray and biosensing technologies widely used in applied genomics for genotyping, drug discovery, gene expression profiling, and related applications based on measurement of genomic information (1, 2). These tools function through detection of interactions between nucleic acids immobilized on a solid support, or ''probes,'' with analyte ''target'' nucleic acids present in solution. Binding, or hybridization, between probes and targets to form an immobilized duplex takes place based on the degree of complementarity between the probe and target base sequences. The tremendous growth in applications of surface hybridization has been mirrorred by increased emphasis on experimental and fundamental aspects of the assays that directly impact measurement and interpretation of data (3, 4).As summarized in several recent reviews (5-8), physical studies under simplified experimental conditions have begun to unravel the rich phenomenology that occurs in diagnostic assays. Applications typically operate away from equilibrium and are faced with a highly diverse pool of target sequences competing for the probe sites. A variety of aids to enhance hybridization performance is used, including surfactants and blocking agents to control nonspecific adsorp...

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“…This process occurs via the interplay of association of single-stranded DNAs, consisting of complementary base pairs, and dissociation of duplexes formed of these strands. The corresponding experiments were performed at room temperature, well below the DNA melting temperature, T (depending on the conditions, T is usually in the range from 70 to 110°C [15]), and the results obtained clearly indicate that the kinetics of dissociation of duplexes is non-exponential [30][31][32][33]. In particular, the experiments exhibit the fast initial phase followed by much slower late phase.…”

Section: Introductionmentioning

confidence: 98%

“…With the development and potential applications of nanoscience, many other aspects of the behaviour of complex biological molecules become of interest. One of the relevant examples, related to the development of ultrasensitive bioanalytical sensors, is DNA hybridization on nanoscale probes [26][27][28][29] and/or on DNA-modified surfaces [30][31][32][33][34]. This process occurs via the interplay of association of single-stranded DNAs, consisting of complementary base pairs, and dissociation of duplexes formed of these strands.…”

Section: Introductionmentioning

confidence: 99%

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Simulation of dissociation of DNA duplexes attached to the surface

Zhdanov¹,

Gunnarsson

Höök

2010

Open Physics

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Abstract:We present Monte Carlo simulations of dissociation of duplexes formed of complementary single-stranded DNAs with one of the strands attached to the surface. To describe the transition from the bound state to the unbound state of two strands located nearby, we use a lattice model taking DNA base-pair interactions and comformational changes into account. The results obtained are employed as a basis for a more coarse-grained model including strand backward association and diffusion resulting in complete dissociation. The distribution of the dissociation time is found to be exponential. This finding indicates that the non-exponential kinetic features observed in the corresponding experiments seem to be related to extrinsic factors, e.g., to the surface heterogeneity.

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Temperature Effects on DNA Chip Experiments from Surface Plasmon Resonance Imaging: Isotherms and Melting Curves

Cited by 87 publications

References 70 publications

Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation

Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation

DNA surface hybridization regimes

Simulation of dissociation of DNA duplexes attached to the surface

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