A model for structure and thermodynamics of ssDNA and dsDNA near a surface: A coarse grained approach

Ambía, Joaquín; Vainrub, Arnold; Pettitt, B. Montgomery

doi:10.1016/j.cpc.2010.08.029

Cited by 71 publications

(65 citation statements)

References 41 publications

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“…Because ssDNA is very flexible, the contour length changes greatly at different conditions but the inter-base distance λ is relatively constant. 34,35 Here we adopt λ =0.42nm 34 since the ssDNA sequence is partially hybridized with the probe DNA. The effective charge of each nucleotide may vary slightly in different conditions 26 and for saline water we take q e = −0.25 e .…”

Section: Resultsmentioning

confidence: 99%

Sorting Short Fragments of Single-Stranded DNA with an Evolving Electric Double Layer

Zhao

Gao

et al. 2013

J. Phys. Chem. B

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We demonstrate a new procedure for separation of single-stranded DNA (ssDNA) fragments that are anchored to the surface of a gold electrode by end hybridization. The new separation procedure takes the advantage of the strong yet evolving non-uniform electric field near the gold surface in contact with a buffer solution gradually being diluted with deionized water. Separation of short ssDNA fragments is demonstrated by monitoring the DNA at the gold surface with in situ fluorescence measurement. The experimental results can be rationalized with a simple theoretical model of electric double layer that relates the strength of the surface pulling force to the ionic concentration of the changing buffer solution.

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Section: Resultsmentioning

confidence: 99%

Sorting Short Fragments of Single-Stranded DNA with an Evolving Electric Double Layer

Zhao

Gao

et al. 2013

J. Phys. Chem. B

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“…If we consider the spheres over the surface to be ion-penetrable, an analytic solution exists for our geometry [27, 28, 15]. The surface imposes an electrostatic boundary condition that can be taken into account simply by using the well known method of images [15, 14]. The free energy contribution including the solvation enthalpy and entropy changes will be different depending on the type of surface, conductor (C) or dielectric (D).…”

Section: Modelmentioning

confidence: 99%

Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach

Ambía¹,

Vainrub²,

Pettitt³

2011

J. Phys.: Condens. Matter

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A coarse grain model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider unpaired dangling end contributions. The parameters of the model differ when representing a double stranded DNA section, or a single stranded DNA section. The thermodynamic effects of the possibility of different dangling end combinations were considered in the presence of different types of surfaces. Configurational sampling was achieved by Metropolis Monte Carlo. To have a more complete picture of the free energy changes, an estimation of the conformational entropy was included. We find a strong thermodynamic effect for dangling mismatches due to sequence requirements when they are nearer the surface as opposed to being held away from the surface.

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“…The persistence length for DNA is 50 nm when double stranded and drops to 1.48 nm when single stranded. (13,23) The fragment length of the target DNA used in these experiments was 29 base pairs, which corresponds to a length of approximately 10 nm. Denaturation causes a conversion of dsDNA to ssDNA and, as such, explains the increase in heat transfer resistance around the melting temperature of the selected probe DNA sequence.…”

Section: 1: Target Concentration To Effect Size Ratiomentioning

confidence: 99%

“…The persistence length of dsDNA is 50 nm, which is why dsDNA fragments with less than 100 base pairs can be considered as "stiff rods". (13,23) For ssDNA the persistence length drops to 1.48 nm (23) causing them to curl up in irregular sphere-like shapes, and their typical Flory radius can be approximated using formula 1.1, where L is the total length of the DNA fragment and L p its persistence length. (13) (1.1).…”

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confidence: 99%

Heat transfer resistance as a tool to quantify hybridization efficiency of DNA on a nanocrystalline diamond surface

Cornelis

Vandenryt

Wackers

et al. 2014

Diamond and Related Materials

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Proefschrift ingediend tot het behalen van de graad van master in de biomedische wetenschappenDe transnationale Universiteit Limburg is een uniek samenwerkingsverband van twee universiteiten in twee landen: de Universiteit Hasselt en Maastricht University. 2013•2014 FACULTEIT GENEESKUNDE EN LEVENSWETENSCHAPPEN master in de biomedische wetenschappen MasterproefHeat transfer resistance as a tool to quantify hybridization efficiency of DNA on a nanocrystalline diamond surface These last two years studying at Hasselt University have been very memorable thanks to all my wonderful fellow students. Thanks for all those exiting times we spend together. And I would like to specially thank Gideon for being an exceptional colleague these past few months.And finally, of course, all my family and friends whose support has been instrumental in giving me the strength and persistence to get here.In God we trust. All others must bring data. W. Edwards DemingIn der Beschränkung Zeigt sich erst der Meister SummaryThis work reports on a label-free real-time method based on heat transfer resistivity for thermal monitoring of DNA denaturation and its potential to quantify DNA fragments with a specific sequence of interest. Determining the contamination level of water for example, is something that could be achieved using this technique. Probe DNA, consisting of a 36-mer fragment, was covalently immobilized on a nanocrystalline diamond surface, created by chemical vapor deposition on a silicon substrate. Various concentrations of full matched 29-mer target DNA fragments were hybridized with this probe DNA. The observation that the change in heat transfer resistance upon denaturation depends on the concentration of target DNA used during the hybridization allowed for the determination of a dose response curve. Therefore, these results illustrate the potential of this technique to quantify the concentration of a specific DNA fragment and to quantify the hybridization efficiency to its probe, which is the percentage of the target DNA exposed to the sensor that is effectively hybridized to the probes. The low hybridization efficiency of around 8 % calculated for the current sensor corresponds with literature. Improving the efficiency could lower the limit of detection of this technique as well as extend the range of concentrations that can be measured. Analysis of the measurement data generated by the setup is a multi-step process that is sensitive to human variability. In order to remove all human error and variability from the analysis process, a software program was developed to automate this task. It not only enhanced the heat transfer method (HTM) used in this study, but also allows for future development of a device that can automatically perform a measurement and generate the corresponding result.

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A model for structure and thermodynamics of ssDNA and dsDNA near a surface: A coarse grained approach

Cited by 71 publications

References 41 publications

Sorting Short Fragments of Single-Stranded DNA with an Evolving Electric Double Layer

Sorting Short Fragments of Single-Stranded DNA with an Evolving Electric Double Layer

Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach

Heat transfer resistance as a tool to quantify hybridization efficiency of DNA on a nanocrystalline diamond surface

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