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Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region
2011
Nucleic Acids Research
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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
2001
Nucleic Acids Research
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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
1999
Nucleic Acids Research
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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
2005
Nucleic Acids Research
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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
2008
Langmuir
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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
2019
Computational and Structural Biotechnology Journal
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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
2003
Applied and Environmental Microbiology
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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
2011
Chemistry - A European Journal
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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
2010
Langmuir
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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
2006
Journal of the American Chemical Society
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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
2014
Nucleic Acids Research
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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
2010
PLoS ONE
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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
2005
BioTechniques
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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
2014
Open Biochemistry Journal
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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
1993
Nucleic Acids Research
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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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