Influence of Nanometric Holes on the Sensitivity of a Waveguide-Mode Sensor: Label-Free Nanosensor for the Analysis of RNA Aptamer−Ligand Interactions

2008 ◽  
Vol 80 (17) ◽  
pp. 6602-6609 ◽  
Author(s):  
Subash C. B. Gopinath ◽  
Koichi Awazu ◽  
Makoto Fujimaki ◽  
Katsuaki Sugimoto ◽  
Yoshimichi Ohki ◽  
...  
Keyword(s):  
Waveguide Mode ◽  
Rna Aptamer ◽  
Label Free ◽  
Ligand Interactions

Label-free RNA aptamer-based capacitive biosensor for the detection of C-reactive protein

2010 ◽  
Vol 12 (32) ◽  
pp. 9176 ◽  
Author(s):  
Anjum Qureshi ◽  
Yasar Gurbuz ◽  
Saravan Kallempudi ◽  
Javed H. Niazi
Keyword(s):  
Rna Aptamer ◽  
Label Free ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
Capacitive Biosensor

scholarly journals Fluorogenic RNA Aptamers: A Nano-platform for Fabrication of Simple and Combinatorial Logic Gates

Nanomaterials ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 984 ◽  
Author(s):  
Victoria Goldsworthy ◽  
Geneva LaForce ◽  
Seth Abels ◽  
Emil Khisamutdinov
Keyword(s):  
Rna Binding ◽  
Fluorescent Dyes ◽  
Free Ligand ◽  
Logic Gates ◽  
Boolean Logic ◽  
Rna Aptamers ◽  
Nucleic Acid Detection ◽  
Rna Aptamer ◽  
Label Free ◽  
Half Adder

RNA aptamers that bind non-fluorescent dyes and activate their fluorescence are highly sensitive, nonperturbing, and convenient probes in the field of synthetic biology. These RNA molecules, referred to as light-up aptamers, operate as molecular nanoswitches that alter folding and fluorescence function in response to ligand binding, which is important in biosensing and molecular computing. Herein, we demonstrate a conceptually new generation of smart RNA nano-devices based on malachite green (MG)-binding RNA aptamer, which fluorescence output controlled by addition of short DNA oligonucleotides inputs. Four types of RNA switches possessing AND, OR, NAND, and NOR Boolean logic functions were created in modular form, allowing MG dye binding affinity to be changed by altering 3D conformation of the RNA aptamer. It is essential to develop higher-level logic circuits for the production of multi-task nanodevices for data processing, typically requiring combinatorial logic gates. Therefore, we further designed and synthetized higher-level half adder logic circuit by “in parallel” integration of two logic gates XOR and AND within a single RNA nanoparticle. The design utilizes fluorescence emissions from two different RNA aptamers: MG-binding RNA aptamer (AND gate) and Broccoli RNA aptamer that binds DFHBI dye (XOR gate). All computationally designed RNA devices were synthesized and experimentally tested in vitro. The ability to design smart nanodevices based on RNA binding aptamers offers a new route to engineer “label-free” ligand-sensing regulatory circuits, nucleic acid detection systems, and gene control elements.

scholarly journals Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine

2019 ◽  
Vol 48 (2) ◽  
pp. 949-961 ◽  
Author(s):  
Elke Duchardt-Ferner ◽  
Michael Juen ◽  
Benjamin Bourgeois ◽  
Tobias Madl ◽  
Christoph Kreutz ◽  
...  
Keyword(s):  
Malachite Green ◽  
Rna Structure ◽  
Random Sequence ◽  
Structural Complexity ◽  
Binding Mode ◽  
Flavin Mononucleotide ◽  
Rna Aptamer ◽  
Wide Range ◽  
Ligand Interactions ◽  
Resolution Structure

Abstract RNA aptamers—artificially created RNAs with high affinity and selectivity for their target ligand generated from random sequence pools—are versatile tools in the fields of biotechnology and medicine. On a more fundamental level, they also further our general understanding of RNA-ligand interactions e. g. in regard to the relationship between structural complexity and ligand affinity and specificity, RNA structure and RNA folding. Detailed structural knowledge on a wide range of aptamer–ligand complexes is required to further our understanding of RNA–ligand interactions. Here, we present the atomic resolution structure of an RNA–aptamer binding to the fluorescent xanthene dye tetramethylrhodamine. The high resolution structure, solved by NMR-spectroscopy in solution, reveals binding features both common and different from the binding mode of other aptamers with affinity for ligands carrying planar aromatic ring systems such as the malachite green aptamer which binds to the tetramethylrhodamine related dye malachite green or the flavin mononucleotide aptamer.

scholarly journals Paper-based fluorogenic RNA aptamer sensors for label-free detection of small molecules

2020 ◽  
Vol 12 (21) ◽  
pp. 2674-2681
Author(s):  
Fatemeh Shafiei ◽  
Kathleen McAuliffe ◽  
Yousef Bagheri ◽  
Zhining Sun ◽  
Qikun Yu ◽  
...  
Keyword(s):  
Small Molecules ◽  
Rapid Detection ◽  
Rna Aptamer ◽  
Label Free ◽  
Target Analytes ◽  
Label Free Detection

A paper-based portable fluorogenic RNA sensor for the selective, sensitive, and rapid detection of target analytes.

Label-free detection of protein-ligand interactions in real time using micromachined bulk acoustic resonators

2010 ◽  
Vol 96 (12) ◽  
pp. 123702 ◽  
Author(s):  
Hao Zhang ◽  
Wei Pang ◽  
Mong S. Marma ◽  
Chuang-Yuan Lee ◽  
Sanat Kamal-Bahl ◽  
...  
Keyword(s):  
Real Time ◽  
Label Free ◽  
Acoustic Resonators ◽  
Protein Ligand Interactions ◽  
Label Free Detection ◽  
Ligand Interactions

RNA Aptamer-Based Electrochemical Biosensor for Selective and Label-Free Analysis of Dopamine

2012 ◽  
Vol 85 (1) ◽  
pp. 121-128 ◽  
Author(s):  
Elaheh Farjami ◽  
Rui Campos ◽  
Jesper S. Nielsen ◽  
Kurt V. Gothelf ◽  
Jørgen Kjems ◽  
...  
Keyword(s):  
Electrochemical Biosensor ◽  
Rna Aptamer ◽  
Label Free

scholarly journals Surface state of the dopamine RNA aptamer affects specific recognition and binding of dopamine by the aptamer-modified electrodes

The Analyst ◽  
2015 ◽  
Vol 140 (12) ◽  
pp. 4089-4096 ◽  
Author(s):  
Isabel Álvarez-Martos ◽  
Rui Campos ◽  
Elena E. Ferapontova
Keyword(s):  
Surface State ◽  
Surface Coverage ◽  
Modified Electrodes ◽  
Rna Aptamer ◽  
Label Free ◽  
Specific Recognition ◽  
Electrochemical Label

An electrochemical label-free aptasensor monitors physiological levels of dopamine with improved sensitivity when the aptamer surface coverage is optimized and with no interference from other catecholamines.

scholarly journals A ClyA nanopore tweezer for analysis of functional states of protein-ligand interactions

2019 ◽  
Author(s):  
Xin Li ◽  
Kuohao Lee ◽  
Jianhan Chen ◽  
Min Chen
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Bound States ◽  
Conformational Dynamics ◽  
Electrical Current ◽  
Label Free ◽  
Protein Motions ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Molecular Tweezer

AbstractConformational changes of proteins are essential to their functions. Yet it remains challenging to measure the amplitudes and timescales of protein motions. Here we show that the ClyA nanopore can be used as a molecular tweezer to trap a single maltose-binding protein (MBP) within its lumen, which allows conformation changes to be monitored as electrical current fluctuations in real time. The current measurements revealed three distinct ligand-bound states for MBP in the presence of reducing saccharides. Our biochemical and kinetic analysis reveal that these three states represented MBP bound to different isomers of reducing sugars. These findings shed light on the mechanism of substrate recognition by MBP and illustrate that the nanopore tweezer is a powerful, label-free, single-molecule approach for studying protein conformational dynamics under functional conditions.

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