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

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 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 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.

Effects of a Supplemental Spanish Phonological Awareness Intervention on Latinx Preschoolers' Dual Language Emergent Literacy Skills

2020 ◽  
Vol 29 (3) ◽  
pp. 1283-1300
Author(s):  
Xigrid T. Soto ◽  
Andres Crucet-Choi ◽  
Howard Goldstein
Keyword(s):  
At Risk ◽  
Phonological Awareness ◽  
Emergent Literacy ◽  
Language Learners ◽  
Literacy Instruction ◽  
Dual Language ◽  
Literacy Skills ◽  
Dual Language Learners ◽  
Probe Design ◽  
Emergent Literacy Skills

Purpose Preschoolers' phonological awareness (PA) and alphabet knowledge (AK) skills are two of the strongest predictors of future reading. Despite evidence that providing at-risk preschoolers with timely emergent literacy interventions can prevent academic difficulties, there is a scarcity of research focusing on Latinx preschoolers who are dual language learners. Despite evidence of benefits of providing Latinxs with Spanish emergent literacy instruction, few studies include preschoolers. This study examined the effects of a supplemental Spanish PA and AK intervention on the dual emergent literacy skills of at-risk Latinx preschoolers. Method A multiple probe design across four units of instruction evaluated the effects of a Spanish supplemental emergent literacy intervention that explicitly facilitated generalizations to English. Four Latinx preschoolers with limited emergent literacy skills in Spanish and English participated in this study. Bilingual researchers delivered scripted lessons targeting PA and AK skills in individual or small groups for 12–17 weeks. Results Children made large gains as each PA skill was introduced into intervention and generalized the PA skills they learned from Spanish to English. They also improved their English initial sound identification skills, a phonemic awareness task, when instruction was delivered in Spanish but with English words. Children made small to moderate gains in their Spanish letter naming and letter–sound correspondence skills and in generalizing this knowledge to English. Conclusion These findings provide preliminary evidence Latinx preschoolers who are dual language learners benefit from emergent literacy instruction that promotes their bilingual and biliterate development.

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