Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

Leroy, J. L.; Kochoyan, Michel; Huynh‐Dinh, Tam; Guéron, Maurice

doi:10.1016/0022-2836(88)90236-7

Cited by 208 publications

(230 citation statements)

References 47 publications

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“…The inequality takes into account the additional enthalpy (still unknown) necessary for the formation of an open region inside of a duplex as well as the fact that the activation enthalpy is normally larger than the enthalpy changes. The EЈ a value was also estimated from the NMR studies of dsDNA opening dynamics as EЈ a Х 40-100 kJ⅐mol Ϫ1 (44)(45)(46). Thus, it is reasonable to expect for the high-temperature pcPNA invasion the E a # value to be around or lower than 100 kJ⅐mol Ϫ1 , which is indeed the case for PNA I (see Fig.…”

Section: Is Approximately Valid Even Atmentioning

confidence: 81%

Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids

Demidov

Protozanova

Izvolsky

et al. 2002

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

102

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If adenines and thymines in two mutually complementary mixedbase peptide nucleic acid (PNA) oligomers are substituted with diaminopurines and thiouracils, respectively, so-called pseudocomplementary PNAs (pcPNAs) are created. Pairs of pcPNAs have recently demonstrated an ability to highly selectively target essentially any designated site on double-stranded DNA (dsDNA) by forming very stable PNA-DNA strand-displacement complexes via double duplex invasion (helix invasion). These properties of pcPNAs make them unique and very promising ligands capable of denying the access of DNA-binding proteins to dsDNA. To elucidate the sequence-unrestricted mechanism of sequence-specific dsDNA recognition by pcPNAs, we have studied the kinetics of formation of corresponding PNA-DNA complexes at various temperatures by the gel-shift assay. In parallel, the conditions for possible selfhybridization of pcPNA oligomers have been assayed by mixing curve (Job plot) and thermal melting experiments. The data indicate that, at physiological temperatures (Ϸ37°C), the equilibrium is shifted toward the pairing of corresponding pcPNAs with each other. This finding explains a linear concentration dependence, within the submicromolar range, of the pcPNA invasion rate into dsDNA at 37°C. At elevated temperatures (>50°C), the rather unstable pcPNA duplexes dissociate, yielding the expected quadratic dependence for the rate of pcPNA invasion on the PNA concentration. The polycationic character of pcPNA pairs, carrying the duplicated number of protonated terminal PNA residues commonly used to increase the PNA solubility and binding affinity, also explains the self-inhibition of pcPNA invasion observed at higher PNA concentrations. Melting of pcPNA duplexes occurs with the integral transition enthalpies ranged from ؊235 to ؊280 kJ⅐mol ؊1 , contributing to an anomalously high activation energy of Ϸ150 kJ⅐mol ؊1 found for the helix invasion of pcPNAs carrying four different nucleobases. A simplified kinetic model for pcPNAs helix invasion is proposed that interprets all unusual features of pcPNAs binding to dsDNA. Our findings have important implications for rational use of pcPNAs.double-stranded DNA ͉ pseudocomplementary PNA ͉ sequence-selective recognition P eptide nucleic acids (PNAs) and their derivatives are of significant biomedical and biotechnological interest as prospective biomolecular tools for highly selective manipulation of nucleic acids (1-8). Recently, a new modification of PNAs has been introduced for sequence-unrestricted targeting of doublestranded DNA (dsDNA). Along with ordinary guanines and cytosines, these PNAs, dubbed pseudocomplementary PNAs (pcPNAs; refs. 9 and 10), carry 2,6-diaminopurines (D) and 2-thiouracils ( s U) instead of adenines and thymines, respectively.Model building revealed a steric clash between the bulky thio group of s U (or similarly modified thymine) and one of the two amino groups of D within the s U-D pair (9, 11). This clashing effect must severely destabilize the pcPNA-pcPNA duplexes whereas bindin...

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Section: Is Approximately Valid Even Atmentioning

confidence: 81%

Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids

Demidov

Protozanova

Izvolsky

et al. 2002

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

102

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“…Microscopically, experiments based on protondeuterium exchange methods [28] have shown that the base pair lifetimes are of order of milliseconds at T ∼ 305K with AT-pairs lifetimes being three times shorter than those of GC-pairs. Fluorescence correlation spectroscopy [29] has further revealed that the breathing modes have a time scale in the 20 − 100 microseconds range and bubbles of 2 to 10 base pairs open at T ∼ 310K under low salt conditions.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamics of twisted DNA with solvent interaction

Zoli

2011

The Journal of Chemical Physics

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The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over ∼ 10 7 − 10 8 base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.

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“…From the dynamical point of view, there are studies about localized energy modes [14] that were identified as precursors of the denaturation and transcription process. These modes could also prescribe the dynamic of DNA in room temperature, in which large amplitude and highly localized motions had been experimentally verified [15,16]. From the thermodynamical point of view, the original model describes quantitatively the expected results for the DNA denaturation temperature.…”

Section: Introductionmentioning

confidence: 88%

Analysis of Lattice Size, Energy Density and Denaturation for a One-Dimensional DNA Model

Slade¹,

Ribeiro²,

Filho³

et al. 2012

WJM

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There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is studied under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The thermodynamics analysis using the transfer integral operator method is briefly reviewed. In particular, the lattice size is discussed and a conjecture about the minimum energy to denaturation is proposed. In terms of the dynamical aspects of the model, the equations of motion for the system are integrated and the results determine the energy density where the denaturation occurs. The behavior of the lattice near the phase transition is analyzed. The relation between the thermodynamical and dynamical results is discussed.

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Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

Cited by 208 publications

References 47 publications

Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids

Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids

Thermodynamics of twisted DNA with solvent interaction

Analysis of Lattice Size, Energy Density and Denaturation for a One-Dimensional DNA Model

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