Evaluation of Rationally Designed Label-free Stem-loop DNA Probe Opening in the Presence of miR-21 by Circular Dichroism and Fluorescence Techniques.

Scientific Reports
Nasrin FarahaniBijan Ranjbar

Abstract

The characteristic features of stem-loop structured probes make them robust tools to detect targets with high sensitivity and selectivity. The basis of the hairpin based sensors operation is a conformational change that occurs upon hybridization of target with stem-loop probe. The design of the stem-loop probe has an important role in target recognition. Therefore, we designed a label-free stem loop probe for targeting miR-21 as a cancer biomarker investigated by web-based tools; its thermodynamic parameters obtained by thermal UV spectroscopy. The efficiency of stem-loop structure opening in the presence of target and non-target sequences was evaluated by fluorescence spectroscopy and circular dichroism spectro-polarimetry. The results showed that the target sequence opens the structure of hairpin efficiently in comparison to non-target sequences. To optimize the stem-loop hybridization to its target, the buffer ionic strength was changed by adding different concentrations of NaCl, KCl and MgCl2. It was shown that buffering conditions have a significant role in loop structure opening and its optimization, led to an increase in sensitivity detection and have improved LOD from 60 pM to 45 pM.

References

Apr 1, 1979·Biopolymers·C A SprecherW C Johnson
Jan 1, 1992·Methods in Enzymology·D M GrayM R Vaughan
Feb 3, 1998·Nature Biotechnology·S TyagiF R Kramer
Mar 1, 1996·Nature Biotechnology·S Tyagi, F R Kramer
May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·G BonnetF R Kramer
Jun 14, 2000·Current Opinion in Structural Biology·M Zuker
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·M M Mhlanga, L Malmberg
May 15, 2002·Trends in Biotechnology·Natalia E Broude
Feb 13, 2003·Nucleic Acids Research·Andrew TsourkasGang Bao
Jul 22, 2004·Analytical Biochemistry·Gang Yao, Weihong Tan
May 10, 2005·Nucleic Acids Research·Caroline Crey-DesbiollesChristian J Leumann
Jul 11, 2006·Nucleic Acids Research·Yang GaoRosina M Georgiadis
Sep 1, 2006·Analytical Biochemistry·Christos D Georgiou, Ioannis Papapostolou
Feb 5, 2009·Nucleic Acids Research·Jaroslav KyprMichaela Vorlícková
Jul 2, 2009·Chemical Biology & Drug Design·Bijan Ranjbar, Pooria Gill
Aug 13, 2010·The Journal of Physical Chemistry. B·Marie Z Markarian, Joseph B Schlenoff
Sep 13, 2011·Nucleic Acids Research·Julian P VenablesFrançois Juge
Sep 13, 2011·Chemical Communications : Chem Comm·Evanthia Papadopoulou, Steven E J Bell
Jun 15, 2012·Chirality·Michaela VorlíčkováJaroslav Kypr
May 15, 2013·Sensors·Anette Thyssen JonstrupAnni Hangaard Andersen
May 25, 2013·Journal of the National Cancer Institute·Yuji ToiyamaAjay Goel
Apr 3, 2014·Biosensors & Bioelectronics·Xiangmin MiaoLiansheng Ling
Oct 8, 2014·Analytical Chemistry·Xiaohong TanMarcel P Bruchez
Mar 18, 2015·Chemical Society Reviews·Jing ZhengWeihong Tan
Apr 29, 2015·Sensors·Ambra GiannettiFrancesco Baldini

❮ Previous
Next ❯

Citations

Jun 3, 2021·International Journal of Molecular Sciences·Maria DedeEmmanuele Crespan
Sep 15, 2021·BioTechniques·Menachem AilenbergOri D Rotstein

❮ Previous
Next ❯

Methods Mentioned

BETA
biosensors
circular dichroism
fluorescence assay

Software Mentioned

Jasco analyzer
Mfold
715
OligoAnalyzer
Beacon Designer

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.