Abstract:
BACKGROUND:Secondary structure in the target is a property not usually considered in software applications for design of optimal custom oligonucleotide probes. It is frequently assumed that eliminating self-complementarity, or screening for secondary structure in the probe, is sufficient to avoid interference with hybridization by stable secondary structures in the probe binding site. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrates that the properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and tethered oligonucleotide probe in a microarray experiment. RESULTS:Despite the relatively high hybridization temperatures and 1M monovalent salt imposed in the modeling process to approximate hybridization conditions used in the laboratory, we find that parts of the target molecules are likely to be inaccessible to intermolecular hybridization due to the formation of stable intramolecular secondary structure. For example, at 65 degrees C, 28 +/- 7% of the average cDNA target sequence is predicted to be inaccessible to hybridization. We also analyzed the specific binding sites of a set of 70mer probes previously designed for Brucella using a freely available oligo design software package. 21 +/- 13% of the nucleotides in each probe binding site are within a double-stranded structure in over half of the folds predicted for the cDNA target at 65 degrees C. The intramolecular structures formed are more stable and extensive when an RNA target is modeled rather than cDNA. When random shearing of the target is modeled for fragments of 200, 100 and 50 nt, an overall destabilization of secondary structure is predicted, but shearing does not eliminate secondary structure. CONCLUSION:Secondary structure in the target is pervasive, and a significant fraction of the target is found in double stranded conformations even at high temperature. Stable structure in the target has the potential to interfere with hybridization and should be a factor in interpretation of microarray results, as well as an explicit criterion in array design. Inclusion of this property in an oligonucleotide design procedure would change the definition of an optimal oligonucleotide significantly.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Ratushna VG,Weller JW,Gibas CJdoi
10.1186/1471-2164-6-31keywords:
subject
Has Abstractpub_date
2005-03-08 00:00:00pages
31issn
1471-2164pii
1471-2164-6-31journal_volume
6pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3395-6
更新日期:2017-01-31 00:00:00
abstract:BACKGROUND:Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of endobiotics is also modulated, resulting in potentially harmful effects. We therefore used 1,4-Bis ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-384
更新日期:2009-08-19 00:00:00
abstract:BACKGROUND:Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-777
更新日期:2013-11-11 00:00:00
abstract:BACKGROUND:The superior temporal gyrus (STG), which encompasses the primary auditory cortex, is believed to be a major anatomical substrate for speech, language and communication. The STG connects to the limbic system (hippocampus and amygdala), the thalamus and neocortical association areas in the prefrontal cortex, a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-199
更新日期:2008-04-29 00:00:00
abstract:BACKGROUND:Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in its genome promote rearrangements that impact its phenotype. One of the main virulence factors of this bacterium, its type thr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3921-1
更新日期:2017-07-12 00:00:00
abstract:BACKGROUND:Drug resistance has become a severe challenge for treatment of HIV infections. Mutations accumulate in the HIV genome and make certain drugs ineffective. Prediction of resistance from genotype data is a valuable guide in choice of drugs for effective therapy. RESULTS:In order to improve the computational pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S5-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Litchi (Litchi chinensis Sonn.) is an economically important evergreen fruit tree widely cultivated in subtropical areas. Low temperature is absolutely required for floral induction of litchi, but its molecular mechanism is not fully understood. Leaves of litchi played a key role during floral induction and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3747-x
更新日期:2017-05-10 00:00:00
abstract:BACKGROUND:Aluminium (Al) toxicity is the main factor limiting the crop production in acid soils and barley (Hordeum vulgare L.) is one of the most Al-sensitive of the small-grained cereals. The major gene for Al tolerance in barley is HvAACT1 (HvMATE) on chromosome 4H which encodes a multidrug and toxic compound extru...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2551-3
更新日期:2016-03-05 00:00:00
abstract:BACKGROUND:Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects un...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-9-630
更新日期:2008-12-23 00:00:00
abstract:BACKGROUND:Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transcriptome (RNA-Seq) and metabolome analysis (UPLC-MS/MS) to identify structural and regulatory genes a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07133-5
更新日期:2020-10-22 00:00:00
abstract:BACKGROUND:DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biological significance of DNA methylation in lung cancer. RESULTS:We integrated the gene expression pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1079
更新日期:2014-12-08 00:00:00
abstract:BACKGROUND:Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. RESULTS:To enable functional analysis of human transposase-derived genes, we comb...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2877-x
更新日期:2016-08-04 00:00:00
abstract:BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-10
更新日期:2014-01-05 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1020
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:Two strains of the silver fox (Vulpes vulpes), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-482
更新日期:2011-10-03 00:00:00
abstract:BACKGROUND:While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. Here, we performed a comparative analysis of the predicted (proved in part) orc/cdc6-associated replication origins in 15 completely sequenced haloarchaeal genomes to investigate t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-478
更新日期:2012-09-14 00:00:00
abstract:BACKGROUND:The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-368
更新日期:2013-06-01 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are an abundant class of small single-stranded non-coding RNA molecules ranging from 18 to 24 nucleotides. They negatively regulate gene expression at the post-transcriptional level and play key roles in many biological processes, including skeletal development and cartilage maturation. In...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-798
更新日期:2014-09-17 00:00:00
abstract:BACKGROUND:Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morphological and metabolic responses from seven Triticeae species including wild types with different droug...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4321-2
更新日期:2017-12-15 00:00:00
abstract:BACKGROUND:Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large per...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-156
更新日期:2014-02-24 00:00:00
abstract:BACKGROUND:The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular path...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-627
更新日期:2012-11-15 00:00:00
abstract:BACKGROUND:Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S11
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Psoriasis is a chronic autoimmune disease in which T cells have a predominant role in initiating and perpetuating the chronic inflammation in skin. However, the mechanisms that regulate T cell activation in psoriasis are still incompletely understood. The objective of the present study was to characterize th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-825
更新日期:2013-11-23 00:00:00
abstract:BACKGROUND:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5131-x
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that host sequence variants have a strong influence on the severity of influenza A disease progression. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-411
更新日期:2012-08-20 00:00:00
abstract:BACKGROUND:Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-326
更新日期:2011-06-23 00:00:00
abstract:BACKGROUND:Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06917-z
更新日期:2020-07-22 00:00:00
abstract:BACKGROUND:Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07027-6
更新日期:2020-10-15 00:00:00
abstract:BACKGROUND:Incilaria (= Meghimatium) fruhstorferi is an air-breathing land slug found in restricted habitats of Japan, Taiwan and selected provinces of South Korea (Jeju, Chuncheon, Busan, and Deokjeokdo). The species is on a decline due to depletion of forest cover, predation by natural enemies, and collection. To fac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5526-3
更新日期:2019-02-26 00:00:00
abstract:BACKGROUND:Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. RESULTS:In this study, we identified a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3502-3
更新日期:2017-03-14 00:00:00