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Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region

M. I. Onyshchenko, T. I. Gaynutdinov, E. A. Englund, D. H. Appella, R. D. Neumann, I. G. Panyutin
2011 Nucleic Acids Research  
Using the gel shift assay, chemical probing and dimethyl sulfate (DMS) protection studies, we determined that uncharged zwitterionic PNA has the highest binding specificity while preserving efficient duplex  ...  In addition, we examined DNA-duplex invasion potential of PNAs of various charges.  ...  There are several studies performed where formation of secondary structures in DNA is related with the increased ability to bind complementary oligonucleotide probes.  ... 
doi:10.1093/nar/gkr259 pmid:21593130 pmcid:PMC3167611 fatcat:xhrrvsvfkrejtarignflw45na4

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA

F. Dong
2001 Nucleic Acids Research  
DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA.  ...  The differences in the secondary structure of DNA molecules revealed by 5′-nuclease probing were used to design structurespecific probes for mutation discrimination that target the regions of structural  ...  samples and Natasha Lyamicheva for katG DNA clones.  ... 
doi:10.1093/nar/29.15.3248 pmid:11470883 pmcid:PMC55824 fatcat:42pkbryrkvfb7gfyrepwoz2y7m

Design of modified oligodeoxyribonucleotide probes to detect telomere repeat sequences in FISH assays

J. Hacia
1999 Nucleic Acids Research  
Several dye-labeled oligonucleotide probes were found that could effectively stain the telomeric repeat sequences of either cytidine-or guanosine-rich strands in a specific manner.  ...  structures (7-deazaguanosine and 6thioguanosine residues), which might interfere with binding to the target.  ...  Design of probes to bind to (C 3 TA 2 ) n repeats Unlike the case of cytosine-rich oligonucleotide probes designed to bind to (T 2 AG 3 ) n repeats, there has been limited reported success in binding guanine-rich  ... 
doi:10.1093/nar/27.20.4034 pmid:10497268 pmcid:PMC148671 fatcat:7skykp3so5bgzjtsax65uzzerm

Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations

L. Zhang
2005 Nucleic Acids Research  
We have evaluated the effect of the position of the fluorescent label [position of label (POL)] relative to the probe-target duplex on the signal output of oligonucleotide microarrays.  ...  POL as a critical factor affecting signal intensity rather than binding efficiency.  ...  An application for a patent on the POL effect has been filed by the University Bremen. Funding to pay the Open Access publication charges for this article was provided by BMBF.  ... 
doi:10.1093/nar/gni156 pmid:16257977 pmcid:PMC1275592 fatcat:qsf6cfrx25abdafrp3ero7xdnu

Molecular Beacon−Metal Nanowire Interface: Effect of Probe Sequence and Surface Coverage on Sensor Performance

Kristin B. Cederquist, Rebecca Stoermer Golightly, Christine D. Keating
2008 Langmuir  
We report the effect of surface coverage and sequence on the performance of 5′ thiolated, 3′ fluorophore-labeled DNA hairpin probes bound to Au/Ag striped ("barcoded") metal nanowires.  ...  Because we are interested in multiplexed assays, we also compared several beacon probe sequences having different stabilities for secondary structure formation in solution; we found that both probe surface  ...  Philip Bevilacqua and Nate Siegfried for their help with DNA hairpin melting and T m determinations.  ... 
doi:10.1021/la703854x pmid:18624416 pmcid:PMC2677025 fatcat:rlp3fq7jirggva4c4v6kec5bs4

In-silico design of DNA oligonucleotides: Challenges and approaches

Michaela Hendling, Ivan Barišić
2019 Computational and Structural Biotechnology Journal  
The key event of each oligonucleotide-based assay is the specific binding between oligonucleotides and their target DNA.  ...  However, single-stranded DNA molecules also tend to bind to unintended targets or themselves. The probability of such unspecific binding increases with the complexity of an assay.  ...  Secondary Structure Formation As oligonucleotides are single-stranded DNA molecules, they can form secondary structures and limit the hybridization of oligonucleotides to the target DNA [72] [73] [74]  ... 
doi:10.1016/j.csbj.2019.07.008 pmid:31452858 pmcid:PMC6700205 fatcat:fg64f46sg5a3rl6dpgpxpzz4wq

Optimization Strategies for DNA Microarray-Based Detection of Bacteria with 16S rRNA-Targeting Oligonucleotide Probes

J. Peplies, F. O. Glockner, R. Amann
2003 Applied and Environmental Microbiology  
Subsequent parameter analysis revealed that this was mainly an effect of reduced accessibility of probe binding sites caused by the secondary structures of the target molecules.  ...  20 oligonucleotide probes.  ...  This work was done in the framework of the Centre of Applied Gensensorik (CAG) at the University of Bremen and supported by the German Ministry of Education and Research (BMBF, contract 0311833A) and by  ... 
doi:10.1128/aem.69.3.1397-1407.2003 pmid:12620822 pmcid:PMC150098 fatcat:lvuyv2ow2bgc7pelcyzdsu2nzq

Molecular-Beacon-Based Tricomponent Probe for SNP Analysis in Folded Nucleic Acids

Camha Nguyen, Jeffrey Grimes, Yulia V. Gerasimova, Dmitry M. Kolpashchikov
2011 Chemistry - A European Journal  
Here we demonstrate that MB probe is not efficient in direct analysis of secondary structure-folded analytes, while MB-based tricomponent probe is suitable for these purposes.  ...  Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures.  ...  Acknowledgments This study was supported by NHGRI R21 HG004060 and by UCF College of Science and Chemistry Department.  ... 
doi:10.1002/chem.201101987 pmid:21956816 pmcid:PMC3221966 fatcat:we57ypufijffrf6xd5qo4ydogq

Hybridization Efficiency of Molecular Beacons Bound to Gold Nanowires: Effect of Surface Coverage and Target Length

Kristin B. Cederquist, Christine D. Keating
2010 Langmuir  
We report the hybridization efficiency for surfaceimmobilized hairpin DNA probes.  ...  single-stranded probes, which are typically designed to avoid secondary structure.  ...  This work was funded by the National Institutes of Health (R01 EB000268 and R21 CA137595).  ... 
doi:10.1021/la1031703 pmid:21038880 pmcid:PMC2994276 fatcat:bgb37plcmzdvloz3qebodzhhhi

Distance-Dependent Emission from Dye-Labeled Oligonucleotides on Striped Au/Ag Nanowires: Effect of Secondary Structure and Hybridization Efficiency

Rebecca L. Stoermer, Christine D. Keating
2006 Journal of the American Chemical Society  
We present experiments exploring the effect of label position and secondary structure in oligonucleotide probes as a function of hybridization buffer, which impacts the percentage of double-stranded probes  ...  In contrast, fluorophore labeled oligonucleotides designed to form hairpin secondary structures analogous to solution-phase molecular beacon probes are relatively insensitive to hybridization efficiency  ...  Acknowledgments This work was funded by the National Institutes of Health (R01 EB000268), the National Science Foundation (NIRT CCR-0303976), and Pennsylvania State University.  ... 
doi:10.1021/ja0637200 pmid:17017805 pmcid:PMC2837913 fatcat:jwyjq7qpcre3xchyzrh33eiwti

Microarrays for identifying binding sites and probing structure of RNAs

Ryszard Kierzek, Douglas H. Turner, Elzbieta Kierzek
2014 Nucleic Acids Research  
In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence.  ...  High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides.  ...  Often hybridization yield of the same DNA probes was more efficient for shorter transcripts than for longer ones.  ... 
doi:10.1093/nar/gku1303 pmid:25505162 pmcid:PMC4288193 fatcat:aevvb7un4zhtfmp3s6ex55ltu4

DNA Suspension Arrays: Silencing Discrete Artifacts for High-Sensitivity Applications

Matthew S. Lalonde, Eric J. Arts, Jean-Pierre Vartanian
2010 PLoS ONE  
Specifically: 1) tethering of unligated probes on the template DNA elicited false signal and 2) unpredictable probe secondary structures impaired probe capture and suppressed legitimate signal from the  ...  Two sets of oligonucleotides were used to disrupt these structures; one to displace unligated reporter labels from the bead-bound species and another to occupy sequences which interfered with array hybridization  ...  Acknowledgments We would like to thank Rick Gibson and Denis Tebit for helpful discussions of the manuscript as well as Kenneth Nelson for useful discussions about the competimer oligonucleotides.  ... 
doi:10.1371/journal.pone.0015476 pmid:21079742 pmcid:PMC2975679 fatcat:zssqxvzprjfkfh3feracdlnyuq

Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid

Régis Peytavi, Liu-ying Tang, Frédéric R. Raymond, Karel Boissinot, Luc Bissonnette, Maurice Boissinot, François J. Picard, Ann Huletsky, Marc Ouellette, Michel G. Bergeron
2005 BioTechniques  
In order to examine the hybridization efficiency of capture probes along target nucleic acid, 20-mer oligonucleotide probes were designed to hybridize at different distances from the 5′ end of two overlapping  ...  This study delineates key predictable parameters that govern the hybridization efficiency of short capture probes arrayed on glass slides.  ...  These parameters include steric hindrance, secondary structure of the target DNA, and binding capacity of the surfacebound probe.  ... 
doi:10.2144/05391rr01 pmid:16060373 fatcat:cjob3xlqozcuvoqdo5r3fvno2a

Effect of Target Length on Specificity and Sensitivity of Oligonucleotide Microarrays: A Comparison between Dendrimer and Modified PCR based Labelling Methods

Abdullah Gibriel
2014 Open Biochemistry Journal  
DNA microarrays are widely used as end point detectors for gene expression analysis.  ...  This report also shows the advantages of using the modified PCR method over other labelling methods in generating labelled amplicons of the desired lengths to maximize hybridization efficiency.  ...  Effect of probe length on hybridization efficiency.  ... 
doi:10.2174/1874091x01408010011 pmid:24551024 pmcid:PMC3927376 fatcat:uqvabvxh3nap3mnnzcbmgxdzeu

A single amino-acid substitution in the Ets domain alters core DNA binding specificity of Ets1 to that of the related transcription factors Elf1 and E74

Rémy Bosselut, Jonathan Levin, Elisabeth Adjadj, Jacques Ghysdael
1993 Nucleic Acids Research  
Ets proteins form a family of sequence specific DNA binding proteins which bind DNA through a 85 aminoacids conserved domain, the Ets domain, whose sequence is unrelated to any other characterized DNA  ...  This, together with the fact that mutation of two invariant arginine residues in CRIII abolishes DNA binding, Indicates that CRIII plays a key role in Ets domain recognition of the GGAA/T core motif and  ...  During the earlier part of this work, R.B. was supported by a fellowship from the Agence Nationale de Recherches sur le SIDA.  ... 
doi:10.1093/nar/21.22.5184 pmid:8255775 pmcid:PMC310635 fatcat:anifwidhzvev5damm4g33itg5a
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