The influence of size on the thermal stability of oligonucleotides: the case of AT sequences

Luchi, Daniela De; Gouyette, Catherine; Subirana, Juan A.

doi:10.1016/j.ab.2003.08.008

Cited by 8 publications

(9 citation statements)

References 16 publications

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“…Figure 2 indeed indicates a 77 . 0 / 540 N dependence, which is still larger than the decrease predicted by statistical models but is in qualitative agreement with both the N / 500 dependence that is plugged in most online oligonucleotide property calculators and the experimental results reported in [35].…”

Section: -Taking Sequence Length Effects Into Accountsupporting

confidence: 88%

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Dynamical versus statistical mesoscopic models for DNA denaturation

Joyeux¹,

Florescu²

2008

J. Phys.: Condens. Matter

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We recently proposed a dynamical mesoscopic model for DNA, which is based, like the statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present paper, we first describe how the parameters of this model are varied to get predictions in better agreement with experimental results that were not addressed up to now, like mechanical unzipping, the evolution of the critical temperature with sequence length and temperature resolution. We show that the model with the new parameters provides results that are in quantitative agreement with those obtained from statistical models. Investigation of the critical properties of the dynamical model suggests that DNA denaturation looks like a first-order phase transition in a broad temperature interval, but that there necessarily exists, very close to the critical temperature, a crossover to another regime. The exact nature of the melting dynamics in this second regime still has to be elucidated. We finally point out that the descriptions of the physics of the melting transition inferred from statistical and dynamical models are not completely identical and discuss the relevance of our model from the biological point of view.

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Section: -Taking Sequence Length Effects Into Accountsupporting

confidence: 88%

“…dependence that is plugged in most online oligonucleotide property calculators and the experimental results reported in [35].…”

Section: -New Parametersmentioning

confidence: 99%

Dynamical versus statistical mesoscopic models for DNA denaturation

Joyeux¹,

Florescu²

2008

J. Phys.: Condens. Matter

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“…Most probably, they are associated with an enhanced fraying effect in the terminal adenines. It should be noticed that this short duplex is not very stable, as confirmed by melting studies (38). The imino resonances are not observed at 5 °C, indicating that the duplex is mainly denatured at this temperature.…”

Section: Structure Of D(atatat) In Solutionmentioning

confidence: 60%

“…However, in all cases the NMR data show that these oligonucleotides mainly form standard Watson-Crick duplexes in solution. The UV spectra and melting curves did not show either any feature that might indicate the presence of Hoogsteen DNA (38).…”

Section: Structure Of D(atatat) In Solutionmentioning

confidence: 80%

X-ray and NMR Studies of the DNA Oligomer d(ATATAT): Hoogsteen Base Pairing in Duplex DNA

et al. 2004

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We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA.

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“…[58] although our model cannot distinguish, for instance, a AT-followed by ATalong the backbone from AT-followed by TA-pair. Such differences may shift considerably the melting temperature in short fragments [59,60] with effects which are quantitatively not fully understood. Coherently with the notation used in Ref.…”

Section: Thermodynamical Resultsmentioning

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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The influence of size on the thermal stability of oligonucleotides: the case of AT sequences

Cited by 8 publications

References 16 publications

Dynamical versus statistical mesoscopic models for DNA denaturation

Dynamical versus statistical mesoscopic models for DNA denaturation

X-ray and NMR Studies of the DNA Oligomer d(ATATAT): Hoogsteen Base Pairing in Duplex DNA

Thermodynamics of twisted DNA with solvent interaction

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