Modeling single chain elasticity of single-stranded DNA: A comparison of three models

Cui, Shuxun; Yu, You; Lin, Zhangbi

doi:10.1016/j.polymer.2008.12.012

Cited by 52 publications

(72 citation statements)

References 28 publications

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“…Because (7)-(9) incorporate quantum mechanical (QM) results, the respective models are called QM-FJC, QM-FRC, and QM-WLC, each with only one free-fit parameter (l k , l b , and l p , respectively) [48].…”

Section: Three Polymer Models That Combine Elasticity From Quantum Mementioning

confidence: 99%

“…4). To obtain the inherent elasticity of NC, they measured the single-chain force curve of an NC sample prepared from an IL (1-allyl-3-methylimidazolium chloride, AMIMCl) [54] solution [42] and fitted it to the QM-FJC model [47,48], using the following three parameters derived by QM calculations on a glucose dimer: …”

Section: Natural Cellulosementioning

confidence: 99%

“…In order to find the most appropriate model to describe the single-chain elasticity of dsDNA in poor solvents, the force curves were fitted to three QM models [48]. Fitting results suggested that l k ¼ 0.59 nm for QM-FJC model and l b ¼ 0.295 nm for QM-FRC model (Fig.…”

Section: Dnamentioning

confidence: 99%

“…At the free state (F ¼ 0), there is more bound water around ssDNA. Upon elongation, the distances between the H-bond donors and acceptors of ssDNA are increased, which caused a [48] water rearrangement. Thus, an addition energy (0.58 k B T/unit) is needed for the water rearrangement, which is reflected by the deviation between the force curves obtained in water and organic solvent.…”

Section: Dnamentioning

confidence: 99%

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Supramolecular Chemistry and Mechanochemistry of Macromolecules: Recent Advances by Single-Molecule Force Spectroscopy

Cheng

Cui

2015

Topics in Current Chemistry

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Atomic force spectroscopy (AFM)-based single-molecule force spectroscopy (SMFS) was invented in the 1990s. Since then, SMFS has been developed into a powerful tool to study the inter- and intra-molecular interactions of macromolecules. Using SMFS, a number of problems in the field of supramolecular chemistry and mechanochemistry have been studied at the single-molecule level, which are not accessible by traditional ensemble characterization methods. In this review, the principles of SMFS are introduced, followed by the discussion of several problems of contemporary interest at the interface of supramolecular chemistry and mechanochemistry of macromolecules, including single-chain elasticity of macromolecules, interactions between water and macromolecules, interactions between macromolecules and solid surface, and the interactions in supramolecular polymers.

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Section: Three Polymer Models That Combine Elasticity From Quantum Mementioning

confidence: 99%

Section: Natural Cellulosementioning

confidence: 99%

Section: Dnamentioning

confidence: 99%

Section: Dnamentioning

confidence: 99%

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Supramolecular Chemistry and Mechanochemistry of Macromolecules: Recent Advances by Single-Molecule Force Spectroscopy

Cheng

Cui

2015

Topics in Current Chemistry

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“…According to eq 2, the maximum value of L[F]/L 0 is ∼1.06. In the range from 1 to 1.06, any value of L[F]/L 0 is practical and corresponds to a mapping value of F in the fitting curve, which can be derived with eq 2 17,45. Because L[F]/L 0 can be any value in the reasonable range (1−1.06 in this study), the model now has only one free parameter (l k ) left.…”

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Effects of Water on the Single-Chain Elasticity of Poly(U) RNA

2015

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Water, the dominant component under the physiological condition, is a complicated solvent which greatly affects the properties of solute molecules. Here, we utilize atomic force microscope-based single-molecule force spectroscopy to study the influence of water on the single-molecule elasticity of an unstructured single-stranded RNA (poly(U)). In nonpolar solvents, RNA presents its inherent elasticity, which is consistent with the theoretical single-chain elasticity calculated by quantum mechanics calculations. In aqueous buffers, however, an additional energy of 1.88 kJ/mol·base is needed for the stretching of the ssRNA chain. This energy is consumed by the bound water rearrangement (Ew) during chain elongation. Further experimental results indicate that the Ew value is uncorrelated to the salt concentrations and stretching velocity. The results obtained in an 8 M guanidine·HCl solution provide more evidence that the bound water molecules around RNA give rise to the observed deviation between aqueous and nonaqueous environments. Compared to synthetic water-soluble polymers, the value of Ew of RNA is much lower. The weak interference of water is supposed to be the precondition for the RNA secondary structure to exist in aqueous solution.

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