Triple-helix DNA structural studies using a Love wave acoustic biosensor

Papadakis, George; Tsortos, Achilleas; Gizeli, Electra

doi:10.1016/j.bios.2009.08.015

Cited by 24 publications

(19 citation statements)

References 48 publications

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“…3 /g. This has been proven true for DNAs of various lengths and for a great variety of shapes [19][20][21][22] , but has never been shown for proteins. In order to confirm this we performed independent measurements of the intrinsic viscosity of s1ZipA by viscometry (see SI).…”

Section: Please Do Not Adjust Marginsmentioning

confidence: 99%

Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

et al. 2016

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Section: Please Do Not Adjust Marginsmentioning

confidence: 99%

Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

et al. 2016

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“…[11][12][13][14][15] Its importance in biotechnology is also noted; changes in the hydrodynamic properties of DNA chains are shown to reflect on and be very useful in the study of intercalating pharmaceutical molecules. 9,[16][17][18] Recently, attention is paid to novel applications in molecule detection with biosensors where structure-based hydrodynamics is important.…”

Section: Introductionmentioning

confidence: 99%

The intrinsic viscosity of linear DNA

2011

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We measured the intrinsic viscosity of very small synthetic DNA molecules, of 20-395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M approximately 2 × 10(6) . It is found that in the range of approximately 7 × 10(3) ≤ M ≤ 2 × 10(6) , the intrinsic viscosity scales as [η] approximately M(1.05) , suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2 × 10(6) ≤ M ≤ 8 × 10(10) is [η] approximately M(0.69) . A comparison of our results with existing equations, for much narrower data distributions, is made, and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns such as the effect of ionic strength, polydispersity, temperature, and shear rate are discussed in detail. Some issues concerning the Huggins coefficient, polymer chain stiffness, and the relationship between the Mark-Houwink constants K, α are also presented; it is found that log K = 1.156 - 6.19α.

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“…Firstly, it is characteristic of the size and shape, of the attached DNA molecule, and defines the biomolecule's acoustic signature. This has been well documented for double stranded DNA molecules varying in length and DNAs of the same length but with different degrees of curvature13 as well as the hybridization of double15 and triple16 DNAs and characterization of a Holliday nanoswitch junction17. Secondly, at equilibrium, the acoustic ratio is independent of the sample concentration loaded on the surface and thirdly, it is independent of the surface history, i.e., previous loading steps13.…”

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confidence: 84%

Acoustic detection of DNA conformation in genetic assays combined with PCR

Papadakis

Tsortos

Kordas

et al. 2013

Sci Rep

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Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.

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Triple-helix DNA structural studies using a Love wave acoustic biosensor

Cited by 24 publications

References 48 publications

Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

The intrinsic viscosity of linear DNA

Acoustic detection of DNA conformation in genetic assays combined with PCR

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