scholarly journals Lab on a single microbead: an ultrasensitive detection strategy enabling microRNA analysis at the single-molecule level

2015 ◽  
Vol 6 (11) ◽  
pp. 6213-6218 ◽  
Author(s):  
Xiaobo Zhang ◽  
Chenghui Liu ◽  
Lingbo Sun ◽  
Xinrui Duan ◽  
Zhengping Li
Keyword(s):  
Single Molecule ◽  
Ultrasensitive Detection ◽  
Single Molecule Level ◽  
Detection Strategy ◽  
Sensing Platform

A single microbead-based sensing platform has been developed, which enables the detection of microRNA at the single-molecule level.

A plasmonic aptasensor for ultrasensitive detection of thrombin via arrested rolling circle amplification

2015 ◽  
Vol 51 (37) ◽  
pp. 7927-7930 ◽  
Author(s):  
Sai Wang ◽  
Sai Bi ◽  
Zonghua Wang ◽  
Jianfei Xia ◽  
Feifei Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Rolling Circle Amplification ◽  
Signal Generation ◽  
Ultrasensitive Detection ◽  
Eye Detection ◽  
Rolling Circle ◽  
Single Molecule Level ◽  
Nanoparticle Growth ◽  
Naked Eye ◽  
Naked Eye Detection

A sensitive signal generation mechanism for gold nanoparticle growth is applied in a plasmonic aptasensor, achieving naked-eye detection of thrombin at the single-molecule level.

scholarly journals Single-molecule calorimeter and free energy landscape

2021 ◽  
Vol 118 (23) ◽  
pp. e2104598118
Author(s):  
Yi Wang ◽  
Zhuodong Tang ◽  
Hong-Yuan Chen ◽  
Wei Wang ◽  
Nongjian Tao ◽  
...  
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Local Heating ◽  
Energy Landscape ◽  
Optical Tweezer ◽  
Free Energy Landscape ◽  
Complex Nature ◽  
Kinetic Properties ◽  
Single Molecule Level ◽  
Sensing Platform

The precise measurement of thermodynamic and kinetic properties for biomolecules provides the detailed information for a multitude of applications in biochemistry, biosensing, and health care. However, sensitivity in characterizing the thermodynamic binding affinity down to a single molecule, such as the Gibbs free energy (Gb), enthalpy (Hb), and entropy (Sb), has not materialized. Here, we develop a nanoparticle-based technique to probe the energetic contributions of single-molecule binding events, which introduces a focused laser of optical tweezer to an optical path of plasmonic imaging to accumulate and monitor the transient local heating. This single-molecule calorimeter uncovers the complex nature of molecular interactions and binding characterizations, which can be employed to identify the thermodynamic equilibrium state and determine the energetic components and complete thermodynamic profile of the free energy landscape. This sensing platform promises a breakthrough in measuring thermal effect at the single-molecule level and provides a thorough description of biomolecular specific interactions.

scholarly journals DNA breathing initiated strand displacement circuits for mimicking ant foraging with nanopore readout

2021 ◽  
Author(s):  
Jinbo Zhu ◽  
Jinglin Kong ◽  
Ulrich Keyser ◽  
Erkang Wang
Keyword(s):  
Single Molecule ◽  
Dna Nanotechnology ◽  
Path Selection ◽  
Strand Displacement ◽  
Initiation Mechanism ◽  
Single Molecule Level ◽  
Sensing Platform ◽  
Dna Strand Displacement ◽  
Dna Strand Exchange ◽  
Dna Strand

Abstract DNA strand displacement reaction is essential for the development of molecular computing based on DNA nanotechnology. Additional DNA strand exchange strategies with high selectivity for input will enable novel complex systems including biosensing applications. Most approaches use bulk readout methods based on fluorescent probes that complicate the monitoring of parallel computations. Herein we propose an autocatalytic strand displacement (ACSD) circuit, which is initiated by DNA breathing and accelerated by seesaw catalytic reaction. The special initiation mechanism of the ACSD circuit enables detection of single base mutations at multiple sites in the input strand with much higher sensitivity than classic toehold-mediated strand displacement. A swarm intelligence model is constructed using the ACSD circuit to mimic foraging behaviour of ants. We introduce a multiplexed nanopore sensing platform to report the output results of a parallel path selection system on the single-molecule level. The ACSD strategy and nanopore multiplexed readout method enhance the toolbox for the future development of DNA computing.

Atomic Force Microscopy (AFM) for Topography and Recognition Imaging at Single Molecule Level

2013 ◽  
pp. 102-112
Author(s):  
Memed Duman ◽  
Andreas Ebner ◽  
Christian Rankl ◽  
Jilin Tang ◽  
Lilia A. Chtcheglova ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Imaging

Curaxin-Induced DNA Topology Alterations Trigger the Distinct Binding Response of CTCF and FACT at the Single-Molecule Level

Biochemistry ◽  
2021 ◽  
Vol 60 (7) ◽  
pp. 494-499
Author(s):  
Ke Lu ◽  
Cuifang Liu ◽  
Yinuo Liu ◽  
Anfeng Luo ◽  
Jun Chen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Topology ◽  
Single Molecule Level

scholarly journals Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

2021 ◽  
Author(s):  
David A Garcia ◽  
Gregory Fettweis ◽  
Diego M Presman ◽  
Ville Paakinaho ◽  
Christopher Jarzynski ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Power Law ◽  
Dwell Time ◽  
Specific Binding ◽  
Power Law Distribution ◽  
Single Molecule Level ◽  
Binding Behavior ◽  
Chromatin Template ◽  
Nuclear Domains

Abstract Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs—one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.

Magnetic Nanoparticles as a Tool for Remote DNA Manipulations at a Single-Molecule Level

2021 ◽  
Vol 13 (12) ◽  
pp. 14458-14469
Author(s):  
Aleksey A. Nikitin ◽  
Anton Yu Yurenya ◽  
Timofei S. Zatsepin ◽  
Ilya O. Aparin ◽  
Vladimir P. Chekhonin ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Single Molecule ◽  
Single Molecule Level
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