A “four-ferrocene” modified stem-loop structure as a probe for sensitive detection and single-base mismatch discrimination of DNA

2012 ◽  
Vol 59 ◽  
pp. 57-63 ◽  
Author(s):  
Grégory Chatelain ◽  
Micaël Ripert ◽  
Carole Farre ◽  
Salomé Ansanay-Alex ◽  
Carole Chaix
Keyword(s):  
Sensitive Detection ◽  
Loop Structure ◽  
Stem Loop ◽  
Single Base ◽  
Stem Loop Structure ◽  
Single Base Mismatch ◽  
Base Mismatch ◽  
Mismatch Discrimination

A stem–loop structure in the 5′ untranslated region of bean pod mottle virus RNA2 is specifically required for RNA2 accumulation

2013 ◽  
Vol 94 (6) ◽  
pp. 1415-1420 ◽  
Author(s):  
Junyan Lin ◽  
Ahmed Khamis Ali ◽  
Ping Chen ◽  
Said Ghabrial ◽  
John Finer ◽  
...  
Keyword(s):  
Mottle Virus ◽  
Genome Replication ◽  
Loop Structure ◽  
Stem Loop ◽  
Bean Pod Mottle Virus ◽  
Specific Element ◽  
Stem Loop Structure ◽  
The Family ◽  
Base Mismatch ◽  
Nucleotide Region

Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus of the family Secoviridae. Its RNA1 encodes all proteins needed for genome replication and is capable of autonomous replication. By contrast, BPMV RNA2 must utilize RNA1-encoded proteins for replication. Here, we sought to identify RNA elements in RNA2 required for its replication. The exchange of 5′ untranslated regions (UTRs) between genome segments revealed an RNA2-specific element in its 5′ UTR. Further mapping localized a 66 nucleotide region that was predicted to fold into an RNA stem–loop structure, designated SLC. Additional functional analysis indicated the importance of the middle portion of the stem and an adjacent two-base mismatch. This is the first report of a cis-acting RNA element in RNA2 of a bipartite secovirus.

Single-base mismatch discrimination by T7 exonuclease with target cyclic amplification detection

2015 ◽  
Vol 51 (14) ◽  
pp. 2954-2956 ◽  
Author(s):  
Zhen-Kun Wu ◽  
Dian-Ming Zhou ◽  
Zhan Wu ◽  
Xia Chu ◽  
Ru-Qin Yu ◽  
...  
Keyword(s):  
High Specificity ◽  
Single Base ◽  
Single Base Mismatch ◽  
Base Mismatch ◽  
Mismatch Discrimination ◽  
First Time ◽  
T7 Exonuclease

T7 exonuclease is reported for the first time to have high specificity in discriminating single-base mismatch.

scholarly journals Single-Step FRET-Based Detection of Femtomoles DNA

Sensors ◽  
2019 ◽  
Vol 19 (16) ◽  
pp. 3495 ◽  
Author(s):  
Sapkota ◽  
Kaur ◽  
Megalathan ◽  
Donkoh-Moore ◽  
Dhakal
Keyword(s):  
Sample Size ◽  
Single Molecule ◽  
Single Step ◽  
Small Sample ◽  
Sensitive Detection ◽  
Quantitative Detection ◽  
Single Base ◽  
Single Base Mismatch ◽  
Mechanical Methods ◽  
Base Mismatch

Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), we show that these sensors can be regenerated in situ, and they allow detection of femtomoles DNA without the need for target amplification while still using a dramatically small sample size (fewer than three orders of magnitude compared to the typical sample size of bulk fluorescence). In addition, these single-molecule sensors exhibit a dynamic range of approximately two orders of magnitude. Using one of the sensors, we demonstrate that the single-base mismatch sequence can be discriminated from a fully matched DNA target, showing a high specificity of the method. These sensors with simple and recyclable design, sensitive detection of DNA, and the ability to discriminate single-base mismatch sequences may find applications in quantitative analysis of nucleic acid biomarkers.

Stem–loop clutch probes for sequence-specific dsDNA analysis with improved single-mismatch selectivity

2019 ◽  
Vol 55 (52) ◽  
pp. 7514-7517
Author(s):  
Xing Lu ◽  
Guobao Zhou ◽  
Yixia Lu ◽  
Lei Li
Keyword(s):  
Stem Loop ◽  
Single Base ◽  
Single Base Mismatch ◽  
Base Mismatch ◽  
Guide Sequence ◽  
Single Mismatch

A stem–loop clutch probe based strategy has been proposed to guide sequence-specific dsDNA analysis with enhanced single-base mismatch selectivity.

968: Gelsolin Gene Silencing Involving Unusual Chromatin Structures and a Novel Stem Loop Structure of the Promoter Region in Human Bladder Cancer

2004 ◽  
Vol 171 (4S) ◽  
pp. 256-257
Author(s):  
Kazunori Haga ◽  
Ataru Sazawa ◽  
Toru Harabayashi ◽  
Nobuo Shinohara ◽  
Minoru Nomoto ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Gene Silencing ◽  
Promoter Region ◽  
Loop Structure ◽  
Human Bladder Cancer ◽  
Human Bladder ◽  
Stem Loop ◽  
Stem Loop Structure

Detection and sequence analysis of an imperfect stem-loop structure in cis activating gene element from SV40PolyA

2011 ◽  
Vol 33 (4) ◽  
pp. 337-346
Author(s):  
Hong-Gang WANG ◽  
Huan MA ◽  
Zhu LI ◽  
Bin ZHANG ◽  
Xiang-Yang JING ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
In Cis ◽  
Gene Element

scholarly journals Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

2021 ◽  
Vol 14 (2) ◽  
pp. 121
Author(s):  
André Miranda ◽  
Tiago Santos ◽  
Eric Largy ◽  
Carla Cruz
Keyword(s):  
Loop Structure ◽  
Binding Properties ◽  
Stem Loop ◽  
Affinity Ligand ◽  
Stem Loop Structure ◽  
Topology Maintenance ◽  
G Quadruplex ◽  
Dimeric Form ◽  
Biophysical Techniques ◽  
Melting Experiments

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.

Sign in / Sign up

Export Citation Format

Share Document