Set of Novel Tools for PCR Primer Design

Gorelenkov, V; Antipov, A.N.; Lejnine, Serguei; Daraselia, Nikolai; Yuryev, Anton

doi:10.2144/01316bc04

Cited by 19 publications

(12 citation statements)

References 18 publications

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“…Analysis was performed on a Perkin Elmer 3100 Automated Fluorescent Sequencer. Sequences were compiled and analyzed with the computer software package VectorNTI [36]. …”

Section: Methodsmentioning

confidence: 99%

Rrp1b, a New Candidate Susceptibility Gene for Breast Cancer Progression and Metastasis

et al. 2007

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A novel candidate metastasis modifier, ribosomal RNA processing 1 homolog B (Rrp1b), was identified through two independent approaches. First, yeast two-hybrid, immunoprecipitation, and functional assays demonstrated a physical and functional interaction between Rrp1b and the previous identified metastasis modifier Sipa1. In parallel, using mouse and human metastasis gene expression data it was observed that extracellular matrix (ECM) genes are common components of metastasis predictive signatures, suggesting that ECM genes are either important markers or causal factors in metastasis. To investigate the relationship between ECM genes and poor prognosis in breast cancer, expression quantitative trait locus analysis of polyoma middle-T transgene-induced mammary tumor was performed. ECM gene expression was found to be consistently associated with Rrp1b expression. In vitro expression of Rrp1b significantly altered ECM gene expression, tumor growth, and dissemination in metastasis assays. Furthermore, a gene signature induced by ectopic expression of Rrp1b in tumor cells predicted survival in a human breast cancer gene expression dataset. Finally, constitutional polymorphism within RRP1B was found to be significantly associated with tumor progression in two independent breast cancer cohorts. These data suggest that RRP1B may be a novel susceptibility gene for breast cancer progression and metastasis.

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“…Analysis was performed on a Perkin Elmer 3100 Automated Fluorescent Sequencer. Sequences were compiled and analyzed with the computer software package VectorNTI [36]. …”

Section: Methodsmentioning

confidence: 99%

Rrp1b, a New Candidate Susceptibility Gene for Breast Cancer Progression and Metastasis

et al. 2007

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show abstract

“…Purified PCR products were sequenced using PCR primers or internal sequencing primers, and the Big Dye s Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, Foster City, CA) according to the manufacturer's recommendations. Labeled products were separated on an Applied Biosystems 3730xl DNA Analyzer (Applied Biosystems) and analyzed using the Seqman Program and the Vector-NTI program [Gorelenkov et al, 2001] by two independent individuals.…”

Section: Dna Sequencing Of 3 0 Utrs and Mirnasmentioning

confidence: 99%

APPandBACE1miRNA genetic variability has no major role in risk for Alzheimer disease

et al. 2009

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Expression levels of the amyloid precursor protein (APP) and beta-site amyloid (Abeta) cleaving enzyme 1 (BACE1) have been implicated in Alzheimer disease (AD) progression. In a well-characterized Belgian group of 358 AD patients and 462 controls, we examined whether genetic variability in microRNA (miRNA) binding sites of APP and BACE1 or in associated miRNAs influenced risk for AD. Direct sequencing identified six variants in the 3' untranslated region (UTR) of APP and 29 variants in the 3' UTR of BACE1, of which few variants were restricted to patients: in APP; 4 variants in 6 patients ( approximately 2%) and in BACE1; 7 variants in 11 patients ( approximately 3.5%). Further genetic screening of the miR-29 cluster encoding the miR-29a/b-1 genes showed 10 variants in close proximity of this cluster. Association studies using all common variants detected in the 3' UTR of BACE1 and the miR-29 gene cluster did not identify an association with AD risk. However, we did observe statistical interaction between rs535860 (BACE1 3' UTR) and rs34772568 (near miR29a; odds ratio [OR](interaction), 0.4; 95% confidence interval [CI], 0.17-0.96; P=0.033). While the exact role of the patient-specific miRNA variants within the 3' UTR region of APP and BACE1 demands further analyses, this study does not support a major contribution of miRNA genetic variability to AD pathogenesis.

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“…Companies engaged in biosoftware development include: Alkami Biosystems, Molecular Biology Insights, PREMIER Biosoft International, IntelliGenetics Inc., Hitachi Inc., DNA Star, Advanced American Biotechnology and Imaging. Some scientists have also developed algorithms and computer programs for various purposes of primer design (Rychlik and Rhoades, 1989;Lowe et al, 1990;Lucas et al, 1991; O'Hara and Venezia, 1991; Tamura et Makarova et al, 1992;Osborne, 1992;Li et al,1997;Plasterer, 1997;Sze et al, 1998;Gorelenkov et al, 2001). Many programs aiding in the design of primers exist (Table 3).…”

Section: Software In Primer Designmentioning

confidence: 99%

Bioinformatic tools and guideline for PCR primer design

Abd‐Elsalam¹

2003

Afr. J. Biotechnol.

117

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Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no product due to non-specific amplification and/or primer-dimer formation, which can become competitive enough to suppress product formation. There are several online tools devoted to serving molecular biologist design effective PCR primers. This review intends to provide a guide to choosing the most efficient way to design a new specific-primer by applying current publicly available links and Web services. Also, the purpose here is to provide general recommendations for the design and use of PCR primers.

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Set of Novel Tools for PCR Primer Design

Cited by 19 publications

References 18 publications

Rrp1b, a New Candidate Susceptibility Gene for Breast Cancer Progression and Metastasis

Rrp1b, a New Candidate Susceptibility Gene for Breast Cancer Progression and Metastasis

APPandBACE1miRNA genetic variability has no major role in risk for Alzheimer disease

Bioinformatic tools and guideline for PCR primer design

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