Orientational Fluctuations and Bimodality in Semiflexible Nunchucks

Semiflexible nunchucks are block copolymers consisting of two long blocks with high bending rigidity jointed by a short block of lower bending stiffness. Recently, the DNA nanotube nunchuck was introduced as a simple nanoinstrument that mechanically magnifies the bending angle of short double-stranded (ds) DNA and allows its measurement in a straightforward way [Fygenson et al., Nano Lett. 2020, 20, 2, 1388–1395]. It comprises two long DNA nanotubes linked by a dsDNA segment, which acts as a hinge. The semiflexible nunchuck geometry also appears in dsDNA with a hinge defect (e.g., a quenched denaturation bubble or a nick), and in end-linked stiff filaments. In this article, we theoretically investigate various aspects of the conformations and the tensile elasticity of semiflexible nunchucks. We analytically calculate the distribution of bending fluctuations of a wormlike chain (WLC) consisting of three blocks with different bending stiffness. For a system of two weakly bending WLCs end-jointed by a rigid kink, with one end grafted, we calculate the distribution of positional fluctuations of the free end. For a system of two weakly bending WLCs end-jointed by a hinge modeled as harmonic bending spring, with one end grafted, we calculate the positional fluctuations of the free end. We show that, under certain conditions, there is a pronounced bimodality in the transverse fluctuations of the free end. For a semiflexible nunchuck under tension, under certain conditions, there is bimodality in the extension as a function of the hinge position. We also show how steric repulsion affects the bending fluctuations of a rigid-rod nunchuck.

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Stimuli-responsive organization of block copolymers on DNA nanotubes

Chemical Science ◽

10.1039/c2sc01065h ◽

2012 ◽

Vol 3 (6) ◽

pp. 1980 ◽

Cited By ~ 40

Author(s):

Karina M. M. Carneiro ◽

Graham D. Hamblin ◽

Kevin D. Hänni ◽

Johans Fakhoury ◽

Manoj K. Nayak ◽

...

Keyword(s):

Block Copolymers ◽

Stimuli Responsive ◽

Dna Nanotubes

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Characterizing titin's I-band Ig domain region as an entropic spring

Journal of Cell Science ◽

10.1242/jcs.111.11.1567 ◽

1998 ◽

Vol 111 (11) ◽

pp. 1567-1574 ◽

Cited By ~ 9

Author(s):

W.A. Linke ◽

M.R. Stockmeier ◽

M. Ivemeyer ◽

H. Hosser ◽

P. Mundel

Keyword(s):

Muscle Protein ◽

Persistence Length ◽

Thick Filament ◽

Contour Length ◽

Chain Model ◽

Bending Rigidity ◽

Force Extension ◽

Average Force ◽

Wormlike Chain ◽

C Terminus

The poly-immunoglobulin domain region of titin, located within the elastic section of this giant muscle protein, determines the extensibility of relaxed myofibrils mainly at shorter physiological lengths. To elucidate this region's contribution to titin elasticity, we measured the elastic properties of the N-terminal I-band Ig region by using immunofluorescence/immunoelectron microscopy and myofibril mechanics and tried to simulate the results with a model of entropic polymer elasticity. Rat psoas myofibrils were stained with titin-specific antibodies flanking the Ig region at the N terminus and C terminus, respectively, to record the extension behaviour of that titin segment. The segment's end-to-end length increased mainly at small stretch, reaching approximately 90% of the native contour length of the Ig region at a sarcomere length of 2.8 microm. At this extension, the average force per single titin molecule, deduced from the steady-state passive length-tension relation of myofibrils, was approximately 5 or 2.5 pN, depending on whether we assumed a number of 3 or 6 titins per half thick filament. When the force-extension curve constructed for the Ig region was simulated by the wormlike chain model, best fits were obtained for a persistence length, a measure of the chain's bending rigidity, of 21 or 42 nm (for 3 or 6 titins/half thick filament), which correctly reproduced the curve for sarcomere lengths up to 3.4 microm. Systematic deviations between data and fits above that length indicated that forces of >30 pN per titin strand may induce unfolding of Ig modules. We conclude that stretches of at least 5–6 Ig domains, perhaps coinciding with known super repeat patterns of these titin modules in the I-band, may represent the unitary lengths of the wormlike chain. The poly-Ig regions might thus act as compliant entropic springs that determine the minute levels of passive tension at low extensions of a muscle fiber.

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The effect of steric repulsion between highly branched hydrophilic blocks on inverse cubic mesophase formation in block copolymers

RSC Advances ◽

10.1039/c9ra04966e ◽

2019 ◽

Vol 9 (44) ◽

pp. 25423-25428 ◽

Cited By ~ 1

Author(s):

Yulin Sun ◽

Jiwon Kim ◽

Kyoung Taek Kim

Keyword(s):

Block Copolymers ◽

Self Assembly ◽

Steric Repulsion ◽

Mesophase Formation

The solution-based self-assembly of block copolymers (BCPs) into nanoparticulate or microparticulate inverse cubic mesophases, or polymer cubosomes, is of growing interest.

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EFFECT OF MEMBRANE BENDING STIFFNESS ON THE DEFORMATION OF ELASTIC CAPSULES IN EXTENSIONAL FLOW: A LATTICE BOLTZMANN STUDY

International Journal of Modern Physics C ◽

10.1142/s0129183107011315 ◽

2007 ◽

Vol 18 (08) ◽

pp. 1277-1291 ◽

Cited By ~ 4

Author(s):

Y. SUI ◽

Y. T. CHEW ◽

P. ROY ◽

H. T. LOW

Keyword(s):

Lattice Boltzmann ◽

Present Model ◽

Extensional Flow ◽

Bending Stiffness ◽

Immersed Boundary ◽

Two Dimensional ◽

Bending Rigidity ◽

Elastic Membranes ◽

Membrane Bending ◽

Boltzmann Method

The transient deformation of liquid capsules enclosed by elastic membranes in two-dimensional extensional flow is studied numerically, using an improved immersed boundary-lattice Boltzmann method. The purpose of the present study is to investigate the effect of interfacial bending stiffness on the deformation of such capsules, under the subcritical elasticity capillary number conditions. The present model can simulate flow-induced deformation of capsules with arbitrary resting shapes (concerning the in-plane tension) and bending-free configurations. The deformation of capsules with initially circular, elliptical, and biconcave resting shapes was investigated in the present study; the capsules' bending-free configurations were considered as either circular shapes or their initially resting shapes. The results show that for capsules with bending-free configuration as circles, membrane bending rigidity has significant rounding effect on the steady deformed profiles. For elliptical and biconcave capsules with resting shapes as the bending-free configurations, it is found that with the bending stiffness increasing, the capsules' steady shapes are more akin to their initial shapes.

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Self-assembly and phase transformations of π-conjugated block copolymers that bend and twist: from rigid-rod nanowires to highly curvaceous gyroids

Soft Matter ◽

10.1039/c1sm05724c ◽

2011 ◽

Vol 7 (21) ◽

pp. 10429 ◽

Cited By ~ 44

Author(s):

Yi-Huan Lee ◽

Wei-Che Yen ◽

Wei-Fang Su ◽

Chi-An Dai

Keyword(s):

Block Copolymers ◽

Phase Transformations ◽

Self Assembly ◽

Rigid Rod

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Engineering DNA nanotubes for resilience in an E. coli TXTL system

Synthetic Biology ◽

10.1093/synbio/ysy001 ◽

2018 ◽

Vol 3 (1) ◽

Cited By ~ 5

Author(s):

Melissa A Klocke ◽

Jonathan Garamella ◽

Hari K K Subramanian ◽

Vincent Noireaux ◽

Elisa Franco

Keyword(s):

Deoxyribonucleic Acid ◽

Dna Nanotechnology ◽

Dna Degradation ◽

Dna Nanostructures ◽

E Coli ◽

Physiological Conditions ◽

Double Stranded Dna ◽

Dna Nanotubes ◽

Sticky End ◽

Dna Nanotube

Abstract Deoxyribonucleic acid (DNA) nanotechnology is a growing field with potential intracellular applications. In this work, we use an Escherichia coli cell-free transcription–translation (TXTL) system to assay the robustness of DNA nanotubes in a cytoplasmic environment. TXTL recapitulates physiological conditions as well as strong linear DNA degradation through the RecBCD complex, the major exonuclease in E. coli. We demonstrate that chemical modifications of the tiles making up DNA nanotubes extend their viability in TXTL for more than 24 h, with phosphorothioation of the sticky end backbone being the most effective. Furthermore, we show that a Chi-site double-stranded DNA, an inhibitor of the RecBCD complex, extends DNA nanotube lifetime significantly. These complementary approaches are a first step toward a systematic prototyping of DNA nanostructures in active cell-free cytoplasmic environments and expand the scope of TXTL utilization for bioengineering.

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