Oligonucleotide probe design — a new approach

Nature ◽  
1994 ◽  
Vol 367 (6465) ◽  
pp. 759-761 ◽  
Author(s):  
Masato Mitsuhashi ◽  
Allan Cooper ◽  
Mieko Ogura ◽  
Tatsuo Shinagawa ◽  
Katsusuke Yano ◽  
...  
Keyword(s):  
Oligonucleotide Probe ◽  
Probe Design ◽  
New Approach

scholarly journals mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization

2010 ◽  
Vol 77 (3) ◽  
pp. 1118-1122 ◽  
Author(s):  
L. Safak Yilmaz ◽  
Shreyas Parnerkar ◽  
Daniel R. Noguera
Keyword(s):  
Mathematical Models ◽  
Oligonucleotide Probe ◽  
Theoretical Framework ◽  
Probe Design ◽  
Oligonucleotide Probes ◽  
Web Tool ◽  
Web Based ◽  
Probe Target ◽  
Probability Of Success

ABSTRACTMathematical models of RNA-targeted fluorescencein situhybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.

scholarly journals Comprehensive viral oligonucleotide probe design using conserved protein regions

2007 ◽  
Vol 36 (1) ◽  
pp. e3-e3 ◽  
Author(s):  
Omar J. Jabado ◽  
Yang Liu ◽  
Sean Conlan ◽  
P. Lan Quan ◽  
Hédi Hegyi ◽  
...  
Keyword(s):  
Oligonucleotide Probe ◽  
Probe Design

scholarly journals Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications

2006 ◽  
Vol 72 (2) ◽  
pp. 1688-1691 ◽  
Author(s):  
Jost Liebich ◽  
Christopher W. Schadt ◽  
Song C. Chong ◽  
Zhili He ◽  
Sung-Keun Rhee ◽  
...  
Keyword(s):  
Free Energy ◽  
Oligonucleotide Probe ◽  
Binding Free Energy ◽  
Functional Gene ◽  
Design Criteria ◽  
Probe Design ◽  
Gene Microarray ◽  
Homologous Genes ◽  
Pcr Products ◽  
Percent Similarity

ABSTRACT To optimize oligonucleotide probe design criteria, PCR products with different similarities to probes were hybridized to a functional gene microarray designed to detect homologous genes from different organisms. In contrast to more restrictive probe designs based on a single criterion, simultaneous consideration of the percent similarity (≤90%), the length of identical sequence stretches (≤20 bases), and the binding free energy (≥−35 kcal mol−1) was found to be predictive of probe specificity.

scholarly journals Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes

2020 ◽  
Author(s):  
David Roe ◽  
Jonathan Williams ◽  
Keyton Ivery ◽  
Jenny Brouckaert ◽  
Nick Downey ◽  
...  
Keyword(s):  
Killer Cell ◽  
Ground Truth ◽  
Probe Design ◽  
Hybridization Probe ◽  
Physical Separation ◽  
New Approach ◽  
Long Read ◽  
Dna Interpretation ◽  
Full Length Gene ◽  
Kir Haplotypes

AbstractThe homology, recombination, variation, and repetitive elements in the natural killer-cell immunoglobulin-like receptor (KIR) region has made full haplotype DNA interpretation impossible without physical separation of chromosomes. Here, we present a new approach using long-read sequencing to efficiently capture, sequence, and assemble diploid human KIR haplotypes. Sequences for capture probe design were derived from public full-length gene and haplotype sequences. IDT xGen® Lockdown probes were used to capture 2-8 kb of sheared DNA fragments followed by sequencing on a PacBio Sequel. The sequences were error corrected, binned, and then assembled using the Canu assembler. The assembly was evaluated on 16 individuals (8 African American and 8 Europeans) from whom ground truth was known via long-range sequencing on fosmid-isolated chromosomes. Using only 18 capture probes, the results show that the assemblies cover 97% of the GenBank reference, are 99.97% concordant, and it takes only 1.8 contigs to cover 75% of the reference. We also report the first assembly of diploid KIR haplotypes from long-read WGS, including the first sequencing of cB05∼tB01, which pairs a KIR2DS2/KIR2DS3 fusion with the tB01 region. Our targeted hybridization probe capture and sequencing approach is the first of its kind to fully sequence and phase all diploid human KIR haplotypes, and it is efficient enough for population-scale studies and clinical use.

scholarly journals Empirical Establishment of Oligonucleotide Probe Design Criteria†

2005 ◽  
Vol 71 (7) ◽  
pp. 3753-3760 ◽  
Author(s):  
Zhili He ◽  
Liyou Wu ◽  
Xingyuan Li ◽  
Matthew W. Fields ◽  
Jizhong Zhou
Keyword(s):  
Free Energy ◽  
Oligonucleotide Probe ◽  
Binding Free Energy ◽  
Perfect Match ◽  
Oligonucleotide Array ◽  
Probe Design ◽  
Oligonucleotide Probes ◽  
Cross Hybridization ◽  
Probe Target ◽  
Sequence Identity

ABSTRACT Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide array that contained perfect match (PM) and mismatch probes (50-mers and 70-mers) based upon four genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were tested. Little hybridization was observed at a probe-target identity of ≤85% for both 50-mer and 70-mer probes. PM signal intensities (33 to 48%) were detected at a probe-target identity of 94% for 50-mer oligonucleotides and 43 to 55% for 70-mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a nonstretch probe (≤15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50-mer probes or a 50-base stretch for 70-mer probes had approximately 55% of the PM signal. Little cross-hybridization was observed for probes with a minimal binding free energy greater than −30 kcal/mol for 50-mer probes or −40 kcal/mol for 70-mer probes. Based on the experimental results, a set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and the experimentally established criteria should provide valuable information for new software and algorithms for microarray-based studies.

Boradipyrromethenecyanines on the base of a BODIPY nucleus annelated with a pyridone ring: a new approach to long-wavelength dual fluorescent probe design

RSC Advances ◽  
2013 ◽  
Vol 3 (46) ◽  
pp. 24193 ◽  
Author(s):  
Yuriy V. Zatsikha ◽  
Viktor P. Yakubovskyi ◽  
Mykola P. Shandura ◽  
Yuriy P. Kovtun
Keyword(s):  
Fluorescent Probe ◽  
Probe Design ◽  
New Approach ◽  
Long Wavelength
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