On the ionic‐strength dependence of the intrinsic viscosity of DNA

Odijk, Theo

doi:10.1002/bip.1979.360181215

Cited by 93 publications

(52 citation statements)

References 12 publications

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“…Previously, Brochard and de Gennes (29) developed a scaling argument explaining polymer stretching under confinement within a channel, where a selfavoiding chain is considered as a series of blobs provided that channel dimensions are much larger than the persistence length (D Ͼ Ͼ P) and the polymer contour length is greater than D (L Ͼ Ͼ D). In their treatment, the stretch (X/L) of a polymer (persistence length P and molecule width w) in a channel (width (10,29,32,33); however, this argument is not valid for highly stretched polymers (e.g., X/L Ͼ 0.5). Instead, for highly stretched polymer chains under nanoconfinement, a different scaling argument (25) treats polymer stretching within a nanochannel as a long chain deflected by the walls of a nanochannel with the stretch given by…”

Section: Resultsmentioning

confidence: 99%

A single-molecule barcoding system using nanoslits for DNA analysis

Dhingra

Odijk

et al. 2007

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

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Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro-and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.

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Section: Resultsmentioning

confidence: 99%

A single-molecule barcoding system using nanoslits for DNA analysis

Dhingra

Odijk

et al. 2007

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

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292

392

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“…40,41 Theoretical work in support of the ionic strength influence is also available. 65,66 Analysis of available data shows, for example, that a 100% change (0.1 ? 0.2M) in salt concentration causes $6% change (reduction) in [g].…”

Section: Salt Effectmentioning

confidence: 98%

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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“…[73,74] For a charged polymer, it is necessary to introduce an electrostatic contribution L e (the total persistence length being L t ¼ L p þ L e at a given ionic concentration) following the Odijk development. [75] The local stiffness of the polysaccharides allows the high viscosity obtained to be interpreted for a given molecular weight compared to a flexible polymer. The L p value, obtained in a large excess of salt, is characteristic of the local structure of the polysaccharides and can be predicted from molecular modeling, as recently shown.…”

Section: Conformation and Stiffnessmentioning

confidence: 99%

Non‐Covalent Interactions in Polysaccharide Systems

Rinaudo

2006

Macromolecular Bioscience

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[Chemical structure: see text] This paper describes the behavior of some polysaccharides with well-known chemical structures and in which the influence of cooperative secondary interactions play an important role. The roles played by hydrophobic and ionic interactions (including ionic selectivity) on polysaccharide conformation and gelation are discussed. Electrostatic attractions are also important in the complexes formed between surfactants and polyelectrolytes of opposite charge. Finally, van der Waals dipolar interactions and particularly hydrogen-bond formation are examined. The role of hydrogen bonds in solubility, conformation, and especially the local stiffness of polysaccharides, but also in polymer-polymer complexes frequently obtained with polysaccharides, is developed. Repeat unit for a number polysaccharides.

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On the ionic‐strength dependence of the intrinsic viscosity of DNA

Cited by 93 publications

References 12 publications

A single-molecule barcoding system using nanoslits for DNA analysis

A single-molecule barcoding system using nanoslits for DNA analysis

The intrinsic viscosity of linear DNA

Non‐Covalent Interactions in Polysaccharide Systems

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