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

BioTechniques ◽  
2005 ◽  
Vol 39 (1) ◽  
pp. 89-96 ◽  
Author(s):  
Régis Peytavi ◽  
Liu-ying Tang ◽  
Frédéric R. Raymond ◽  
Karel Boissinot ◽  
Luc Bissonnette ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Hybridization ◽  
Capture Probe ◽  
Target Nucleic Acid ◽  
Hybridization Efficiency ◽  
Microarray Dna

scholarly journals Improved In Situ Hybridization Efficiency with Locked-Nucleic-Acid-Incorporated DNA Probes

2006 ◽  
Vol 72 (8) ◽  
pp. 5311-5317 ◽  
Author(s):  
Kengo Kubota ◽  
Akiyoshi Ohashi ◽  
Hiroyuki Imachi ◽  
Hideki Harada
Keyword(s):  
In Situ Hybridization ◽  
Nucleic Acid ◽  
Fluorescence Intensity ◽  
Dna Probes ◽  
Locked Nucleic Acid ◽  
Factors Affecting ◽  
Hybridization Efficiency ◽  
Probe Hybridization ◽  
Major Factors

ABSTRACT Low signal intensity due to poor probe hybridization efficiency is one of the major drawbacks of rRNA-targeted in situ hybridization. There are two major factors affecting the hybridization efficiency: probe accessibility and affinity to the targeted rRNA molecules. In this study, we demonstrate remarkable improvement in in situ hybridization efficiency by applying locked-nucleic-acid (LNA)-incorporated oligodeoxynucleotide probes (LNA/DNA probes) without compromising specificity. Fluorescently labeled LNA/DNA probes with two to four LNA substitutions exhibited strong fluorescence intensities equal to or greater than that of probe Eub338, although these probes did not show bright signals when they were synthesized as DNA probes; for example, the fluorescence intensity of probe Eco468 increased by 22-fold after three LNA bases were substituted for DNA bases. Dissociation profiles of the probes revealed that the dissociation temperature was directly related to the number of LNA substitutions and the fluorescence intensity. These results suggest that the introduction of LNA residues in DNA probes will be a useful approach for effectively enhancing probe hybridization efficiency.

scholarly journals Scanning single-molecule counting system for Eprobe with highly simple and effective approach

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243319
Author(s):  
Takeshi Hanami ◽  
Tetsuya Tanabe ◽  
Takuya Hanashi ◽  
Mitsushiro Yamaguchi ◽  
Hidetaka Nakata ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Detection System ◽  
Signal To Noise Ratio ◽  
High Sensitivity ◽  
Nucleic Acid Detection ◽  
Digital Measurement ◽  
Excitation Light ◽  
Target Nucleic Acid ◽  
Fluorescent Molecules

Here, we report a rapid and ultra-sensitive detection technique for fluorescent molecules called scanning single molecular counting (SSMC). The method uses a fluorescence-based digital measurement system to count single molecules in a solution. In this technique, noise is reduced by conforming the signal shape to the intensity distribution of the excitation light via a circular scan of the confocal region. This simple technique allows the fluorescent molecules to freely diffuse into the solution through the confocal region and be counted one by one and does not require statistical analysis. Using this technique, 28 to 62 aM fluorescent dye was detected through measurement for 600 s. Furthermore, we achieved a good signal-to-noise ratio (S/N = 2326) under the condition of 100 pM target nucleic acid by only mixing a hybridization-sensitive fluorescent probe, called Eprobe, into the target oligonucleotide solution. Combination of SSMC and Eprobe provides a simple, rapid, amplification-free, and high-sensitive target nucleic acid detection system. This method is promising for future applications to detect particularly difficult to design primers for amplification as miRNAs and other short oligo nucleotide biomarkers by only hybridization with high sensitivity.

Distinguishing L from M photopigment coding sequences by hybridization to novel locked nucleic acid (LNA) oligonucleotide probes

2008 ◽  
Vol 25 (3) ◽  
pp. 283-287
Author(s):  
CHRISTINA PETTAN-BREWER ◽  
LI FU ◽  
SAMIR S. DEEB
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Macaca Nemestrina ◽  
Oligonucleotide Probes ◽  
Coding Sequences ◽  
Cone Mosaic ◽  
Target Nucleic Acid ◽  
High Degree

Many attempts have been made over the years to distinguish human and primate L (long-wavelength sensitive) from M (middle-wavelength sensitive) cone photoreceptors using either immunohistochemistry or in situ hybridization. These attempts have been unsuccessful due to the very high degree of identity between the sequences of the L and M proteins and encoding mRNAs. The recent development of chemically modified oligonucleotide probes, referred to as locked nucleic acid (LNA) probes, has shown that they hybridize with much greater affinity and specificity to the target nucleic acid. This has greatly increased the potential for differentiating L from M cones by in situ hybridization. We have designed LNA oligonucleotide probes that are complementary to either the L or M coding sequences located in exon 5 of the Macaca nemestrina L and M pigment genes. We have shown that the LNA-M and LNA-L probes hybridize specifically to their respective target nucleic acid sequences in vitro. This result strongly suggests that these probes would be instrumental in rapidly distinguishing L from M cone in the entire retina, and in defining the cone mosaic during development and in adults.

scholarly journals Detection of insulin synthesis in mammalian anterior pituitary cells by immunohistochemistry and demonstration of insulin-related transcripts by in situ RNA-DNA hybridization.

1986 ◽  
Vol 34 (5) ◽  
pp. 673-678 ◽  
Author(s):  
G C Budd ◽  
B Pansky ◽  
B Cordell
Keyword(s):  
Growth Hormone ◽  
Nucleic Acid ◽  
Dna Hybridization ◽  
Anterior Pituitary ◽  
Secretory Granules ◽  
Pituitary Cells ◽  
Insulin Synthesis ◽  
Anterior Pituitary Cells ◽  
Pancreatic B Cells

Insulin or highly homologous transcripts is shown to be synthesized in cultures of mammalian anterior pituitary cells using cloned insulin-specific cDNA probes and nucleic acid cytochemistry. The insulin-hybridizing cells are less abundant than the growth hormone-producing cells, occurring in the cultures at approximately one tenth the frequency. Immunocytochemistry demonstrates that insulin or insulin-like proteins is also synthesized by the cultured pituitary cells and that the insulin immunoreactivity is contained within secretory granules. It appears that many of these secretory granules are concentrated around the periphery of the cell, unlike the insulin-containing granules in pancreatic B-cells.

scholarly journals RNAblueprint: flexible multiple target nucleic acid sequence design

2017 ◽  
Vol 33 (18) ◽  
pp. 2850-2858 ◽  
Author(s):  
Stefan Hammer ◽  
Birgit Tschiatschek ◽  
Christoph Flamm ◽  
Ivo L Hofacker ◽  
Sven Findeiß
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Sequence ◽  
Multiple Target ◽  
Sequence Design ◽  
Target Nucleic Acid
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