A biosensor for the detection of single base mismatches in microRNA

A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH2, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl2 or MgSO4 cations. At 10 mM MgCl2 or MgSO4, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH2. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH2, MgCl2 and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.

Download Full-text

Graphene Oxide-based Amplified Fluorescence Sensor for Nucleic Acid Detection through Target-catalyzed Hairpin Assembly

Chemistry Letters ◽

10.1246/cl.150564 ◽

2015 ◽

Vol 44 (10) ◽

pp. 1353-1355 ◽

Cited By ~ 2

Author(s):

Yusuke Kitamura ◽

Takaaki Miyahata ◽

Hirotaka Matsuura ◽

Kazuto Hatakeyama ◽

Takaaki Taniguchi ◽

...

Keyword(s):

Graphene Oxide ◽

Nucleic Acid ◽

Fluorescence Sensor ◽

Nucleic Acid Detection ◽

Catalyzed Hairpin Assembly

Download Full-text

DNA-only, microwell-based bioassay for multiplex nucleic acid detection with single base-pair resolution using MNAzymes

Biosensors and Bioelectronics ◽

10.1016/j.bios.2020.112017 ◽

2020 ◽

Vol 152 ◽

pp. 112017 ◽

Cited By ~ 1

Author(s):

Saba Safdar ◽

Karen Ven ◽

Julie van Lent ◽

Benjamin Pavie ◽

Iene Rutten ◽

...

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Nucleic Acid Detection ◽

Single Base ◽

Single Base Pair

Download Full-text

Graphene oxide and self-avoiding molecular recognition systems-assisted recombinase polymerase amplification coupled with lateral flow bioassay for nucleic acid detection

Microchimica Acta ◽

10.1007/s00604-020-04637-5 ◽

2020 ◽

Vol 187 (12) ◽

Author(s):

Yi Wang ◽

Wei-wei Jiao ◽

Yu Wang ◽

Ya-cui Wang ◽

Chen Shen ◽

...

Keyword(s):

Graphene Oxide ◽

Nucleic Acid ◽

Molecular Recognition ◽

Lateral Flow ◽

Recombinase Polymerase Amplification ◽

Nucleic Acid Detection ◽

Recognition Systems

Download Full-text

Ultrasensitive nucleic acid detection based on phosphorothioated hairpin-assisted isothermal amplification

Scientific Reports ◽

10.1038/s41598-021-87948-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yujin Jung ◽

Jayeon Song ◽

Hyun Gyu Park

Keyword(s):

Nucleic Acid ◽

Design Principle ◽

Dynamic Range ◽

Isothermal Amplification ◽

Nucleic Acid Detection ◽

Strand Displacement ◽

Wide Dynamic Range ◽

Single Base ◽

Hairpin Probe ◽

Target Nucleic Acid

AbstractHerein, we describe a phosphorothioated hairpin-assisted isothermal amplification (PHAmp) method for detection of a target nucleic acid. The hairpin probe (HP) is designed to contain a 5′ phosphorothioate (PS)-modified overhang, a target recognition site, and a 3′ self-priming (SP) region. Upon binding to the target nucleic acid, the HP opens and the SP region is rearranged to serve as a primer. The subsequent process of strand displacement DNA synthesis recycles the bound target to open another HP and produces an extended HP (EP) with a PS-DNA/DNA duplex at the end, which would be readily denatured due to its reduced thermal stability. The trigger then binds to the denatured 3′ end of the EP and is extended, producing an intermediate double-stranded (ds) DNA product (IP). The trigger also binds to the denatured 3′ end of the IP, and its extension produces the final dsDNA product along with concomitant displacement and recycling of EP. By monitoring the dsDNA products, the target nucleic acid can be identified down to 0.29 fM with a wide dynamic range from 1 nM to 1 fM yielding an excellent specificity to discriminate even a single base-mismatched target. The unique design principle could provide new insights into the development of novel isothermal amplification methods for nucleic acid detection.

Download Full-text