scholarly journals Theory of force-extension curves for modular proteins and DNA hairpins

2015 ◽  
Vol 91 (5) ◽  
Author(s):  
L. L. Bonilla ◽  
A. Carpio ◽  
A. Prados
2005 ◽  
Vol 873 ◽  
Author(s):  
Jason T. Roland ◽  
Dora Guzman ◽  
Jane Bai ◽  
Zhibin Guan

AbstractNative load-bearing proteins, such as the muscle protein titin, exhibit a remarkable degree of combined toughness, strength, and elasticity which have yet to be matched by synthetic materials.Single molecule nanomechanical studies on titin and other modular proteins suggest that these exceptional properties arise from a modular elongation mechanism. The sequential unfolding allows modular biopolymers to sustain a large force over the whole extension of the chain, which makes the polymer strong, along with a large area under the force-extension curve, making it tough as well. In addition, when the external force is removed, the unfolded domains of modular proteins will refold automatically, making them elastic. Inspired by nature, one research effort in my group is aimed at designing synthetic macromolecules that form high order structures by programming non-covalent interactions into polymer chain. The goal is to achieve synthetic biomaterials with combined strength, toughness and elasticity. Three classes of well-defined modular polymers have been synthesized in our laboratory: (1) using quadruple hydrogen-bonding motif 2-ureidon-4-pyrimidone (Upy) to direct the formation loops along a polymer chain (J. Am. Chem. Soc.2004, 126, 2058); (2) using a peptidomimetic beta-sheet based double-closed loop (DCL) as module (J. Am. Chem. Soc.2004, 126, 14328); and (3) an engineered protein G domain III as module. Single molecule force-extension experiments revealed the sequential unfolding of the loops or domains as these modular polymers are stretched, resulting in sawtooth-patterned curves similar to those seen in titin and other biopolymers. In this paper, we will discuss our designs, syntheses and single-molecule studies of polymers having modular domain structures.


2019 ◽  
Vol 5 (6) ◽  
pp. eaav1697 ◽  
Author(s):  
Min Ju Shon ◽  
Sang-Hyun Rah ◽  
Tae-Young Yoon

Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity.


2021 ◽  
Vol 103 (6) ◽  
Author(s):  
Anurag Upadhyaya ◽  
Sanjay Kumar
Keyword(s):  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Li ◽  
Wenting Yu ◽  
Jiaojiao Zhang ◽  
Yuhang Dong ◽  
Xiaohui Ding ◽  
...  

AbstractDNA nanostructures have been demonstrated as promising carriers for gene delivery. In the carrier design, spatiotemporally programmable assembly of DNA under nanoconfinement is important but has proven highly challenging due to the complexity–scalability–error of DNA. Herein, a DNA nanotechnology-based strategy via the cascade hybridization chain reaction (HCR) of DNA hairpins in polymeric nanoframework has been developed to achieve spatiotemporally programmable assembly of DNA under nanoconfinement for precise siRNA delivery. The nanoframework is prepared via precipitation polymerization with Acrydite-DNA as cross-linker. The potential energy stored in the loops of DNA hairpins can overcome the steric effect in the nanoframework, which can help initiate cascade HCR of DNA hairpins and achieve efficient siRNA loading. The designer tethering sequence between DNA and RNA guarantees a triphosadenine triggered siRNA release specifically in cellular cytoplasm. Nanoframework provides stability and ease of functionalization, which helps address the complexity–scalability–error of DNA. It is exemplified that the phenylboronate installation on nanoframework enhanced cellular uptake and smoothed the lysosomal escape. Cellular results show that the siRNA loaded nanoframework down-regulated the levels of relevant mRNA and protein. In vivo experiments show significant therapeutic efficacy of using siPLK1 loaded nanoframework to suppress tumor growth.


2014 ◽  
Vol 51 ◽  
pp. 151-158 ◽  
Author(s):  
Sara Iliafar ◽  
Dmitri Vezenov ◽  
Anand Jagota
Keyword(s):  

2015 ◽  
Vol 13 (13) ◽  
pp. 4031-4040 ◽  
Author(s):  
David E. Thurston ◽  
Higia Vassoler ◽  
Paul J. M. Jackson ◽  
Colin H. James ◽  
Khondaker M. Rahman

Pyrrolobenzodiazepine (PBD) monomer GWL-78 reacts faster with DNA hairpins containing a hexaethylene glycol (HEG) loop compared to hairpins containing a TTT loop due to the greater structural flexibility of the HEG.


2013 ◽  
Vol 117 (50) ◽  
pp. 16105-16109 ◽  
Author(s):  
Roman Tsukanov ◽  
Toma E. Tomov ◽  
Yaron Berger ◽  
Miran Liber ◽  
Eyal Nir

2015 ◽  
Vol 16 (12) ◽  
pp. 3836-3844 ◽  
Author(s):  
Pierre Couleaud ◽  
Sergio Adan-Bermudez ◽  
Antonio Aires ◽  
Sara H. Mejías ◽  
Begoña Sot ◽  
...  
Keyword(s):  

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