Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride

Raghavachari, Nalini; Bao, Yijia; Li, Guangshan; Xie, Xinying; Müller, Ulrich

doi:10.1016/s0003-2697(02)00440-2

Cited by 45 publications

(26 citation statements)

References 6 publications

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“…The energy giving the highest signal strength was chosen for the batch treatment. Prior to hybridization, arrays were prehybridized with sodium borohydride to reduce background according to methods outlined by Raghavachari et al (25).…”

Section: Methodsmentioning

confidence: 99%

Transcriptional Profiling of Mycoplasma hyopneumoniae during Heat Shock Using Microarrays

Madsen¹,

Nettleton

Thacker³

et al. 2006

Infect Immun

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Bacterial pathogens undergo stress during host colonization and disease processes. These stresses result in changes in gene expression to compensate for potentially lethal environments developed in the host during disease. Mycoplasma hyopneumoniae colonizes the swine epithelium and causes a pneumonia that predisposes the host to enhanced disease from other pathogens. How M. hyopneumoniae responds to changing environments in the respiratory tract during disease progression is not known. In fact, little is known concerning the capabilities of mycoplasmas to respond to changing growth environments. With limited genes, mycoplasmas are thought to possess only a few mechanisms for gene regulation. A microarray consisting of 632 of the 698 open reading frames of M. hyopneumoniae was constructed and used to study gene expression differences during a temperature shift from 37°C to 42°C, a temperature swing that might be encountered during disease. To enhance sensitivity, a unique hexamer primer set was employed for generating cDNA from only mRNA species. Our analysis identified 91 genes that had significant transcriptional differences in response to heat shock conditions (P < 0.01) with an estimated false-discovery rate of 4 percent. Thirty-three genes had a change threshold of 1.5-fold or greater. Many of the heat shock proteins previously characterized in other bacteria were identified as significant in this study as well. A proportion of the identified genes (54 of 91) currently have no assigned function.

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Section: Methodsmentioning

confidence: 99%

Transcriptional Profiling of Mycoplasma hyopneumoniae during Heat Shock Using Microarrays

Madsen¹,

Nettleton

Thacker³

et al. 2006

Infect Immun

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“…28 Alternatively, the treatment of the surface with sodium borohydride to reduce unreacted glass aldehyde groups after the cross-linking reaction between glass aldehyde and dendrimer amine groups might contribute to the absence of the nonspecific binding affinity presumably by reduction of trace impurities of molecules, which otherwise would lead to nonspecific binding of oligonucleotides. 20 In summary, we have developed a three-dimensional support using silylated aldehyde slides and PAMAM dendrimers. An oligonucleotide array was prepared through a covalent crosslinking of oligonucleotides on the dendrimeric support.…”

Section: Resultsmentioning

confidence: 99%

“…In this study, we modified silylated aldehyde slides with PAMAM dendrimers because Schiff base formation between glass-aldehyde and dendrimer amine groups is followed by the treatment with sodium borate that reduces a background signal. 20 Here, we report, using the modified aldehyde slides with PAMAM dendrimers, that the dendrimeric surface improved both the immobilization of oligonucleotides and the hybridization yield. † Dedicated to Professor Yong Hae Kim for his distinguished achievements in organic chemistry.…”

Section: Introductionmentioning

confidence: 93%

Preparation of Oligonucleotide Arrays with High-Density DNA Deposition and High Hybridization Efficiency

2004

Bulletin of the Korean Chemical Society

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In DNA microarray produced by DNA-deposition technology, DNA-immobilization and -hybridization yields on a solid support are most important factors for its accuracy and sensitivity. We have developed a dendrimeric support using silylated aldehyde slides and polyamidoamine (PAMAM) dendrimers. An oligonucleotide array was prepared through a crosslinking between the dendrimeric support and an oligonucleotide. Both DNAimmobilization and -hybridization yields on the solid support increased by the modification with the dendrimers. The increase of the immobilization and hybridization efficiency seems to result from a threedimensional arrangement of the attached oligonucleotide. Therefore, our dendrimeric support may provide a simple and efficient solution to the preparation of DNA microarrays with high-density DNA-deposition and high hybridization efficiency.

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“…The slides were prehybridized at 42°in prehybridization buffer 53 SSC (Maniatis et al 1982), 0.1% sodium lauryl sulfate (SDS), and 0.1 mg/ml bovine serum albumin) for 1 hr and then washed three times in 0.13 SSC. To decrease autofluorescence, slides were incubated for 30 min at 42°in blocking buffer (23 SSC, 0.05% SDS, 0.25% sodium borohydride) and then washed three times in 0.13 SSC (Raghavachari et al 2003). Slides were dried by centrifugation for 5 min at 800 rpm in a Beckman Allegra 25R centrifuge and used within 24 hr.…”

Section: Methodsmentioning

confidence: 99%

High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora

et al. 2007

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The wealth of sequence information available for Neurospora crassa and other fungi has greatly facilitated evolutionary and molecular analyses of this group. Although ''reverse'' genetics, in which genes are first identified by their sequence rather than by their mutant phenotypes, serves as a valuable new approach for elucidating biological processes, classical ''forward'' genetic analysis is still extremely useful. Unfortunately, mapping mutations and identifying the corresponding genes has typically been slow and laborious. To facilitate forward genetics in Neurospora, we have adapted microarray-based restriction-site-associated DNA (RAD) mapping for use with N. crassa oligonucleotide microarrays. This technique was used to simultaneously detect an unprecedented number of genomewide restriction site polymorphisms from two N. crassa strains: Mauriceville and Oak Ridge. Furthermore, RAD mapping was used to quickly map a previously unknown gene, defective in methylation-7 (dim-7).

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Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride

Cited by 45 publications

References 6 publications

Transcriptional Profiling of Mycoplasma hyopneumoniae during Heat Shock Using Microarrays

Transcriptional Profiling of Mycoplasma hyopneumoniae during Heat Shock Using Microarrays

Preparation of Oligonucleotide Arrays with High-Density DNA Deposition and High Hybridization Efficiency

High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora

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