The Nature of the Force-Induced Conformation Transition of dsDNA Studied by Using Single Molecule Force Spectroscopy

Survivin, as an apoptosis suppressor, exists as a homodimer interfacing at the N-terminal portion (residues 6-13) of its baculovirus IAP repeat (BIR) domain and a linker segment (residues 89-102). Here we expressed full-length human Survivin (SurF) and a series of its mutants, SurΔN7, SurΔN13, and SurΔN18 with significant truncations of the N-terminus, all of which could still dimerize in solution. Single-molecule force spectroscopy (SMFS) was used to quantitate the unbinding forces of full-length and the mutant homodimers and revealed that the N-terminal residues up to Arg18 were not essential for dimerization. Meanwhile, the binding of SurΔN7 to Smac/DIABLO determined by ELISA was as efficient as the wild-type, but that of SurΔN13 was significantly reduced, and that of SurΔN18 was completely lost. Together, these findings provide direct evidence that the N-terminal sequence of Survivin is not critical for dimer formation but may contribute to correct folding and function of BIR.

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“…[27][28][29] The measured values ranged from 6 to 10 pN/ nm. Force curves were obtained at a constant stretching velocity of 0.5 µm/s.…”

Section: Methodsmentioning

confidence: 99%

N-Terminal Deletion Effects of Human Survivin on Dimerization and Binding to Smac/DIABLO in Vitro

Gao

Zhang

et al. 2010

J. Phys. Chem. B

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“…The extension against force shows a jump by a factor of ∼1·5−1·7 (depending on sequence, pulling geometry and solution) at ∼65-70 pN (Bosaeus et al 2012;Liu et al 2010;Vlassakis et al 2008;Williams et al 2002). Several models have been proposed to explain the sudden increase in length, which is widely agreed to be the signal of a collective structural transition.…”

Section: Introductionmentioning

confidence: 99%

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

Taghavi

Schoot

Berryman

2017

Quart. Rev. Biophys.

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Abstract. Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure-function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for 'phase 1' amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the 'GADV world' hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code.

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“…With AFM, we can directly observe the morphological changes of single DNAs after the treatment with drugs in aqueous environment [9]. Besides morphology imaging, AFM can also measure the mechanics of single DNA by stretching the molecule [10,11]. Especially the development of high-speed AFM brings new opportunities for studying the structure and dynamics of single biomolecules in action [12].…”

Section: Introductionmentioning

confidence: 99%

The dynamic interactions between chemotherapy drugs and plasmid DNA investigated by atomic force microscopy

Liu

Xiao

et al. 2017

Sci. China Mater.

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The advent of atomic force microscopy (AFM) provides a powerful tool for imaging individual DNA molecules. Chemotherapy drugs are often related to DNAs. Though many specific drug-DNA interactions have been observed by AFM, knowledge about the dynamic interactions between chemotherapy drugs and plasmid DNAs is still scarce. In this work, AFM was applied to investigate the nanoscale interactions between plasmid DNAs and two commercial chemotherapy drugs (methotrexate and cisplatin). Plasmid DNAs were immobilized on mica which was coated by silanes in advance. AFM imaging distinctly revealed the dynamic changes of single plasmid DNAs after the stimulation of methotrexate and cisplatin. Geometric features of plasmid DNAs were extracted from AFM images and the statistical results showed that the geometric features of plasmid DNAs changed significantly after the stimulation of drugs. This research provides a novel idea to study the actions of chemotherapy drugs against plasmid DNAs at the single-molecule level.

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The Nature of the Force-Induced Conformation Transition of dsDNA Studied by Using Single Molecule Force Spectroscopy

Cited by 25 publications

References 49 publications

N-Terminal Deletion Effects of Human Survivin on Dimerization and Binding to Smac/DIABLO in Vitro

N-Terminal Deletion Effects of Human Survivin on Dimerization and Binding to Smac/DIABLO in Vitro

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

The dynamic interactions between chemotherapy drugs and plasmid DNA investigated by atomic force microscopy

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