The transcriptional coactivator CREB-binding protein cooperates with STAT1 and NF-kappa B for synergistic transcriptional activation of the CXC ligand 9/monokine induced by interferon-gamma gene.
AuthorsHiroi M, Ohmori Y
JournalJ Biol Chem
PubMed ID12403783
'Signal transducers and activators of transcription 1 (STAT1) and NF-kappaB cooperatively regulate the expression of many inflammatory genes. In the present study, we demonstrate that the transcriptional coactivator CREB-binding protein (CBP) mediated the STAT1/NF-kappaB synergy for transcription of the gene for CXC ligand 9 (CXCL9), an interferon-gamma (IFN-gamma)-inducible chemokine. Reporter ... More
Gel staining methods for detection of telomerase activity with the telomeric repeat amplification protocol (TRAP) assay.
AuthorsFujita M, Tomita S, Ueda Y, Fujimori T
JournalMol Pathol
PubMed ID10193516
DOTAP cationic liposomes prefer relaxed over supercoiled plasmids.
AuthorsEven-Chen S, Barenholz Y
JournalBiochim Biophys Acta
PubMed ID11118529
'Cationic liposomes and DNA interact electrostatically to form complexes called lipoplexes. The amounts of unbound (free) DNA in a mixture of cationic liposomes and DNA at different cationic lipid:DNA molar ratios can be used to describe DNA binding isotherms; these provide a measure of the binding efficiency of DNA to ... More
Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold.
AuthorsChen F, Lu JR, Binder BJ, Liu YC, Hodson RE
JournalAppl Environ Microbiol
PubMed ID11157214
'A novel nucleic acid stain, SYBR Gold, was used to stain marine viral particles in various types of samples. Viral particles stained with SYBR Gold yielded bright and stable fluorescent signals that could be detected by a cooled charge-coupled device camera or by flow cytometry. The fluorescent signal strength of ... More
pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response.
AuthorsYoshida H, Oku M, Suzuki M, Mori K
JournalJ Cell Biol
PubMed ID16461360
'Upon the accumulation of unfolded proteins in the mammalian endoplasmic reticulum (ER), X-box binding protein 1 (XBP1) premessenger RNA (premRNA) is converted to mature mRNA by unconventional splicing that is mediated by the endonuclease inositol-requiring enzyme 1. The transcription factor protein (p) XBP1 spliced (S), which is translated from mature ... More
Targeted quantum dot conjugates for siRNA delivery.
AuthorsDerfus AM, Chen AA, Min DH, Ruoslahti E, Bhatia SN
JournalBioconjug Chem
PubMed ID17630789
'Treatment of human diseases such as cancer generally involves the sequential use of diagnostic tools and therapeutic modalities. Multifunctional platforms combining therapeutic and diagnostic imaging functions in a single vehicle promise to change this paradigm. in particular, nanoparticle-based multifunctional platforms offer the potential to improve the pharmacokinetics of drug formulations, ... More
Protein kinase CK2 phosphorylates the high mobility group domain protein SSRP1, inducing the recognition of UV-damaged DNA.
'The structure-specific recognition protein SSRP1 plays a role in transcription and replication in the chromatin context. Mediated by its C-terminal high mobility group (HMG) box domain, SSRP1 binds DNA non-sequence specifically but recognizes certain DNA structures. Using acetic acid urea polyacrylamide gel electrophoresis and mass spectrometry, we have examined the ... More
Nuclease activities and cell death processes associated with the development of surface cultures of Streptomyces antibioticus ETH 7451.
AuthorsFernández M, Sánchez J
JournalMicrobiology
PubMed ID11832504
'The presence and significance of developmentally regulated nucleases in Streptomyces antibioticus ETH 7451 has been studied in relation to the lytic processes occurring during differentiation. The cell-death processes have been followed in surface cultures by a propidium iodide viability assay. This has allowed the visualization of dead (membrane-damaged, red fluorescent) ... More
Analysis of glomerulosclerosis and atherosclerosis in lecithin cholesterol acyltransferase-deficient mice.
AuthorsLambert G, Sakai N, Vaisman BL, Neufeld EB, Marteyn B, Chan CC, Paigen B, Lupia E, Thomas A, Striker LJ, Blanchette-Mackie J, Csako G, Brady JN, Costello R, Striker GE, Remaley AT, Brewer HB, Santamarina-Fojo S
JournalJ Biol Chem
PubMed ID11278414
'To evaluate the biochemical and molecular mechanisms leading to glomerulosclerosis and the variable development of atherosclerosis in patients with familial lecithin cholesterol acyl transferase (LCAT) deficiency, we generated LCAT knockout (KO) mice and cross-bred them with apolipoprotein (apo) E KO, low density lipoprotein receptor (LDLr) KO, and cholesteryl ester transfer ... More
Modulation of the viral ATPase activity by the portal protein correlates with DNA packaging efficiency.
AuthorsOliveira L, Henriques AO, Tavares P
JournalJ Biol Chem
PubMed ID16735502
'DNA packaging in tailed bacteriophages and herpesviruses requires assembly of a complex molecular machine at a specific vertex of a preformed procapsid. As in all these viruses, the DNA translocation motor of bacteriophage SPP1 is composed of the portal protein (gp6) that provides a tunnel for DNA entry into the ... More
Improvement of a recombinant anti-monkey anti-CD3 diphtheria toxin based immunotoxin by yeast display affinity maturation of the scFv.
AuthorsWang Z, Kim GB, Woo JH, Liu YY, Mathias A, Stavrou S, Neville DM
JournalBioconjug Chem
PubMed ID17352456
'Recently, a bivalent recombinant anti-human CD3 diphtheria toxin (DT) based immunotoxin derived from the scFv of UCHT1 antibody has been made that shows enhanced bioactivity and is free from the side effects of Fc receptor interaction. In this case, the diminution of CD3 binding due to the placement of the ... More
Label-Free Fluorescent Detection of Ions, Proteins, and Small Molecules Using Structure-Switching Aptamers, SYBR Gold, and Exonuclease I.
AuthorsZheng D, Zou R, Lou X,
JournalAnal Chem
PubMed ID22424113
'We have demonstrated a label-free sensing strategy employing structure-switching aptamers (SSAs), SYBR Gold, and exonuclease I to detect a broad range of targets including inorganic ions, proteins, and small molecules. This nearly universal biosensor approach is based on the observation that SSAs at binding state with their targets, which fold ... More
Protein-free parallel triple-stranded DNA complex formation.
'A 14 nt DNA sequence 5''-AGAATGTGGCAAAG-3'' from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar-phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) ... More
DNA polymerase V allows bypass of toxic guanine oxidation products in vivo.
'Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. ... More
One tube mutation detection using sensitive fluorescent dyeing of MutS protected DNA.
AuthorsSachadyn P, Stanislawska A, Kur J
JournalNucleic Acids Res
PubMed ID10734213
'A novel, universal method for mutation detection utilising the ability of MutS protein to recognise DNA incomplementarities is proposed. The examined and reference DNA fragments are PCR amplified. The PCR products are purified, mixed, heated and cooled to form heteroduplexes. In the case of mutation the heteroduplex DNA containing mismatch ... More
Comet assay: rapid processing of multiple samples.
'The present study describes modifications to the basic comet protocol that increase productivity and efficiency without sacrificing assay reliability. A simple technique is described for rapidly preparing up to 96 comet assay samples simultaneously. The sample preparation technique allows thin layers of agarose-embedded cells to be prepared in multiple wells ... More
Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus.
AuthorsKumar PP, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S
JournalNat Cell Biol
PubMed ID17173041
'The function of the subnuclear structure the promyelocytic leukaemia (PML) body is unclear largely because of the functional heterogeneity of its constituents. Here, we provide the evidence for a direct link between PML, higher-order chromatin organization and gene regulation. We show that PML physically and functionally interacts with the matrix ... More
A potent new class of reductively activated peptide gene delivery agents.
AuthorsMcKenzie DL, Kwok KY, Rice KG
JournalJ Biol Chem
PubMed ID10744672
'A new class of peptide gene delivery agents were developed by inserting multiple cysteine residues into short (dp 20) synthetic peptides. Substitution of one to four cysteine residues for lysine residues in Cys-Trp-Lys(18) resulted in low molecular weight DNA condensing peptides that spontaneously oxidize after binding to plasmid DNA to ... More
Dual role of the Cdc7-regulatory protein Dbf4 during yeast meiosis.
AuthorsValentin G, Schwob E, Della Seta F
JournalJ Biol Chem
PubMed ID16319063
'The Dbf4-dependent Cdc7 kinase (DDK) is essential for chromosome duplication in all eukaryotes, but was proposed to be dispensable for yeast pre-meiotic DNA replication. This discrepancy led us to investigate the role of the unstable Cdc7-regulatory protein Dbf4 in meiosis. We show that, when Dbf4 is depleted at the time ... More
Flow cytometric analysis of bacteria- and virus-like particles in lake sediments.
AuthorsDuhamel S, Jacquet S
JournalJ Microbiol Methods
PubMed ID16081175
'Flow cytometry (FCM) was successfully used to analyze freshwater bacteria and viruses in lake sediments after relatively simple sample treatment and optimization of dilution/fixation/staining procedures. Biological particles from Lakes Geneva and Bourget were first separated from the sediments by using both Sodium Pyrophosphate (0.01 M final concentration) and Polyoxyethylene-Sorbitan Monooleate ... More
A real-time DNase assay (ReDA) based on PicoGreen fluorescence.
AuthorsTolun G, Myers RS
JournalNucleic Acids Res
PubMed ID12954787
'DNA nucleases (DNases) perform a wide variety of important cellular functions and are also very useful for research and in biotechnological applications. Due to the biological and technological importance of DNases and their use in a wide range of applications, DNase activity assays are essential. Traditional DNase assays employ radiolabeled ... More
Fluorescence resonance energy transfer (FRET) using ssDNA binding fluorescent dye.
AuthorsOrpana AK
JournalBiomol Eng
PubMed ID15113557
'There is a need for simple and inexpensive methods for genotyping single nucleotide polymorphisms (SNPs) and short insertion/deletion variations (InDels). In this work, I demonstrate that a single-stranded DNA (ssDNA) binding dye can be used as a donor fluorophore for fluorescence resonance energy transfer (FRET). The method presented is a ... More
The phage-driven microbial loop in petroleum bioremediation.
AuthorsRosenberg E, Bittan-Banin G, Sharon G, Shon A, Hershko G, Levy I, Ron EZ,
JournalMicrob Biotechnol
PubMed ID21255344
'During the drilling process and transport of crude oil, water mixes with the petroleum. At oil terminals, the water settles to the bottom of storage tanks. This drainage water is contaminated with emulsified oil and water-soluble hydrocarbons and must be treated before it can be released into the environment. In ... More
Nucleic acid stain-dependent single strand conformation polymorphisms.
AuthorsMcKee DR, Thomson MS
JournalBiotechniques
PubMed ID15283199
Localization and imaging of nucleic acids on nanoporous aluminum oxide membranes.
AuthorsErali M, Durtschi JD, Voelkerding KV, Smith RE
JournalClin Chem
PubMed ID15308594
Generation of a complete thymic microenvironment by MTS24(+) thymic epithelial cells.
AuthorsGill J, Malin M, Holländer GA, Boyd R
JournalNat Immunol
PubMed ID12068292
The epithelial component of the thymic microenvironment is indispensable for the generation of T lymphocytes. Although the heterogeneity of this epithelium is well documented, little is known about precursor-progeny relationships between distinct thymic epithelial lineages. Here we characterized a thymic epithelial cell subpopulation identified by the cell surface glycoprotein MTS24. ... More
Rapid quantitation and monitoring of plasmid DNA using an ultrasensitive DNA-binding dye.
AuthorsNoites IS, O'Kennedy RD, Levy MS, Abidi N, Keshavarz-Moore E
JournalBiotechnol Bioeng
PubMed ID10577474
A sensitive fluorescence-based method for monitoring plasmid DNA during production was investigated. This simple method of assaying for plasmid DNA allows rapid monitoring of plasmid yields from a recombinant Escherichia coli fed-batch fermentation. The assay has several advantages over traditional methods of plasmid DNA measurement. The fluorescent dye is highly ... More
Assessment of fluorochromes for two-photon laser scanning microscopy of biofilms.
AuthorsNeu TR, Kuhlicke U, Lawrence JR
JournalAppl Environ Microbiol
PubMed ID11823234
A major limitation for the use of two-proton laser scanning microscopy (2P-LSM) in biofilm and other studies is the lack of a thorough understanding of the excitation-emission responses of potential fluorochromes. In order to use 2P-LSM, the utility of various fluorochromes and probes specific for a range of biofilm constituents ... More
Yeast tRNA as carrier in the isolation of microscale RNA for global amplification and expression profiling.
AuthorsWang QT, Xiao W, Mindrinos M, Davis RW
JournalBiotechniques
PubMed ID12398187
The characterization of global gene expression patterns of microscale samples is important in many areas of biological and clinical research. The choice of carrier is critical for the efficient isolation and successful amplification of RNA at the nanogram level. Here we show that recovery of nanograms of RNA is significantly ... More
Isolating and engineering human antibodies using yeast surface display.
This protocol describes the process of isolating and engineering antibodies or proteins for increased affinity and stability using yeast surface display. Single-chain antibody fragments (scFvs) are first isolated from an existing nonimmune human library displayed on the yeast surface using magnetic-activated cell sorting selection followed by selection using flow cytometry. ... More
High-throughput conformation-sensitive gel electrophoresis for discovery of SNPs.
AuthorsLeung YF, Tam PO, Tong WC, Baum L, Choy KW, Lam DS, Pang CP
JournalBiotechniques
PubMed ID11233602
High-throughput screening for single nucleotide polymorphisms (SNPs) or mutations can be achieved by inexpensive technologies. We modified the original protocols of conformation-sensitive gel electrophoresis (CSGE) to increase throughput several fold to 1.3 samples/min, which is about five times faster than denaturing high-performance liquid chromatography (DHPLC). The modifications include decreasing the ... More
Induction of pluripotent stem cells from adult human fibroblasts by defined factors.
AuthorsTakahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S,
JournalCell
PubMed ID18035408
Successful reprogramming of differentiated human somatic cells into a pluripotent state would allow creation of patient- and disease-specific stem cells. We previously reported generation of induced pluripotent stem (iPS) cells, capable of germline transmission, from mouse somatic cells by transduction of four defined transcription factors. Here, we demonstrate the generation ... More
Fluorescence instrument for in situ monitoring of viral abundance in water, wastewater and recycled water.
AuthorsPollard PC,
JournalJ Virol Methods
PubMed ID22326275
In a world of advanced molecular methods quantifying viruses in water remains one of the most inefficient and costly. Using a general molecular DNA/RNA probe - SYBR Gold combined with differential filtration a fast, cost effective and sensitive method is presented to determine the concentration of viruses in water in ... More
Use of chromophoric ligands to visually screen co-crystals of putative protein-nucleic acid complexes.
AuthorsJiang X, Egli M,
JournalCurr Protoc Nucleic Acid Chem
PubMed ID21901673
Distinguishing between crystals of protein-nucleic acid complexes and those containing protein alone is a common problem in structural studies of protein-nucleic acid interactions. Currently, there are several methods available for detecting nucleic acid in crystals, including gel electrophoresis, SYBR Gold fluorescence dye staining, and methyl violet staining. However, they require ... More
A rapid in situ procedure for determination of bacterial susceptibility or resistance to antibiotics that inhibit peptidoglycan biosynthesis.
Antibiotics which inhibit bacterial peptidoglycan biosynthesis are the most widely used in current clinical practice. Nevertheless, resistant strains increase dramatically, with serious economic impact and effects on public health, and are responsible for thousands of deaths each year. Critical clinical situations should benefit from a rapid procedure to evaluate the ... More
TLR2 and TLR4 gene promoter methylation status during chronic periodontitis.
AuthorsDe Oliveira NF, Andia DC, Planello AC, Pasetto S, Marques MR, Nociti FH, Line SR, De Souza AP,
JournalJ Clin Periodontol
PubMed ID21899586
The objective of this study was to analyse the status of DNA methylation in the promoter region of the toll-like receptor (TLR)2 and TLR4 genes in gingival tissue samples from healthy subjects, smokers and non-smokers affected by chronic periodontitis. Genomic DNA and total RNA were purified from gingival tissue using ... More
Molecular modeling and in vivo imaging can identify successful flexible triazine dendrimer-based siRNA delivery systems.
AuthorsMerkel OM, Zheng M, Mintzer MA, Pavan GM, Librizzi D, Maly M, Höffken H, Danani A, Simanek EE, Kissel T,
JournalJ Control Release
PubMed ID21342661
This study aimed to identify suitable siRNA delivery systems based on flexible generation 2-4 triazine dendrimers by correlating physico-chemical and biological in vitro and in vivo properties of the complexes with thermodynamic parameters calculated using molecular modeling. The siRNA binding properties of the dendrimers and PEI 25 kDa were simulated, ... More
SYBR Gold and SYBR Green II are not mutagenic in the Ames test.
AuthorsKirsanov KI, Lesovaya EA, Yakubovskaya MG, Belitsky GA,
JournalMutat Res
PubMed ID20403457
Favorable photo-physical properties and high affinity to nucleic acids make new fluorescent cyanine dyes of the SYBR-type particularly useful for DNA and RNA visualization. The growing popularity of SYBR-type dyes is also explained by the fact that removal of the dye from the nucleic acids by ethanol precipitation is more ... More
Targeted generation of DNA strand breaks using pyrene-conjugated triplex-forming oligonucleotides.
AuthorsBenfield AP, Macleod MC, Liu Y, Wu Q, Wensel TG, Vasquez KM,
JournalBiochemistry
PubMed ID18473480
Gene targeting by triplex-forming oligonucleotides (TFOs) has proven useful for gene modulation in vivo. Photoreactive molecules have been conjugated to TFOs to direct sequence-specific damage in double-stranded DNA. However, the photoproducts are often repaired efficiently in cells. This limitation has led to the search for sequence-specific photoreactive reagents that can ... More
Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis.
AuthorsHuang Q, Fu WL,
JournalClin Chem Lab Med
PubMed ID16201894
Ethidium bromide (EB) is a mutagen and toxin that is widely used in the laboratory for visualization of nucleic acids. Safer nucleic acid stains, such as SYBR Gold, SYBR Green, GoldView, GeneFinder, and GoldStar, have been developed. However, there has been no systematic comparative analysis of the staining efficiencies of ... More
Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures.
AuthorsKorlach J, Marks PJ, Cicero RL, Gray JJ, Murphy DL, Roitman DB, Pham TT, Otto GA, Foquet M, Turner SW,
JournalProc Natl Acad Sci U S A
PubMed ID18216253
Optical nanostructures have enabled the creation of subdiffraction detection volumes for single-molecule fluorescence microscopy. Their applicability is extended by the ability to place molecules in the confined observation volume without interfering with their biological function. Here, we demonstrate that processive DNA synthesis thousands of bases in length was carried out ... More
Improvements in siRNA properties mediated by 2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (FANA).
AuthorsDowler T, Bergeron D, Tedeschi AL, Paquet L, Ferrari N, Damha MJ,
JournalNucleic Acids Res
PubMed ID16554553
RNA interference (RNAi) has emerged recently as an efficient mechanism for specific gene silencing. Short double-stranded small interfering RNAs (siRNAs) are now widely used for cellular or drug target validation; however, their use for silencing clinically relevant genes in a therapeutic setting remains problematic because of their unfavourable metabolic stability ... More
Programmable in situ amplification for multiplexed imaging of mRNA expression.
AuthorsChoi HM, Chang JY, Trinh le A, Padilla JE, Fraser SE, Pierce NA,
JournalNat Biotechnol
PubMed ID21037591
In situ hybridization methods enable the mapping of mRNA expression within intact biological samples. With current approaches, it is challenging to simultaneously map multiple target mRNAs within whole-mount vertebrate embryos, representing a significant limitation in attempting to study interacting regulatory elements in systems most relevant to human development and disease. ... More
Cyclooxygenase (COX)-2 and granulosa cell apoptosis in vitro.
AuthorsCaffrey AS, Patton WC, Corselli JU, Swensen RE, King A, Chan PJ
JournalJ Assist Reprod Genet
PubMed ID12503890
PURPOSE: C-myc was studied in cyclooxygenase (COX)-2 associated granulosa cell apoptosis, METHODS: Granulosa cells (N = 5 cases) were incubated for 24 h in either 1 or 50 microM COX-2 inhibitor, 1 or 50 microM COX-1/COX-2 inhibitor, negative or positive controls Single primer polymerase chain reaction of c-myc exon 1 ... More
UV- and visible-excited fluorescence of nucleic acids separated by capillary electrophoresis.
AuthorsZabzdyr JL, Lillard SJ
JournalJ Chromatogr A
PubMed ID11293588
UV- and visible-excited fluorescence detection strategies were compared for nucleic acids separated by capillary electrophoresis (CE). A dual-polymer sieving matrix consisting of hydroxypropylmethylcellulose and poly(vinylpyrrolidone) was used to separate DNA fragments from a 100-base pair ladder and RNA from individual cells. Two nucleic acid dyes, SYBR Gold and SYBR Green ... More
L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs).
AuthorsQi X, Bakht S, Devos KM, Gale MD, Osbourn A
JournalNucleic Acids Res
PubMed ID11713336
A flexible, non-gel-based single nucleotide polymorphism (SNP) detection method is described. The method adopts thermostable ligation for allele discrimination and rolling circle amplification (RCA) for signal enhancement. Clear allelic discrimination was achieved after staining of the final reaction mixtures with Cybr-Gold and visualisation by UV illumination. The use of a ... More
A new method of competitive reverse transcription polymerase chain reaction with SYBR Gold staining for quantitative analysis of mRNA.
AuthorsOba R, Kudo Y, Sato N, Noda R, Otsuka Y
JournalElectrophoresis
PubMed ID16688698
There are several methods available to analyze the mRNA concentration quantitatively. Among them, the competitive reverse transcription (RT-)PCR method is very useful. For this method, Cy5-labeled primers were used, and after gel electrophoresis in 7 M urea, the Cy5-labeled single-strand DNA was measured by a fluorescence detector. However, as the ... More
Methylation-sensitive, single-strand conformation analysis (MS-SSCA): A rapid method to screen for and analyze methylation.
AuthorsBianco T, Hussey D, Dobrovic A
JournalHum Mutat
PubMed ID10502775
We have developed methylation-sensitive, single-strand conformation analysis (MS-SSCA) as a method of screening for methylation changes. Bisulfite modification converts cytosines to thymines, but methylated cytosines remain unchanged. This modification creates sequence differences between methylated and unmethylated samples, which can be resolved by SSCA. SSCA is 70-95% efficient at detecting single ... More
Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators.
AuthorsTuma RS, Beaudet MP, Jin X, Jones LJ, Cheung CY, Yue S, Singer VL
JournalAnal Biochem
PubMed ID10075818
The highest sensitivity nucleic acid gel stains developed to date are optimally excited using short-wavelength ultraviolet or visible light. This is a disadvantage for laboratories equipped only with 306- or 312-nm UV transilluminators. We have developed a new unsymmetrical cyanine dye that overcomes this problem. This new dye, SYBR Gold ... More
A whole new way of looking at things: the use of Dark Reader technology to detect fluorophors.
AuthorsSeville M
JournalElectrophoresis
PubMed ID11332748
The Dark Reader optical system (Clare Chemical Research, Denver, CO, USA) uses relatively low intensity broad-band visible blue light in combination with broad-band optical filters to detect fluorescence with a level of sensitivity that often surpasses that of UV transilluminators and can rival that of laser-based scanners. Applications of DR ... More
DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels.
AuthorsFoquet M, Korlach J, Zipfel W, Webb WW, Craighead HG
JournalAnal Chem
PubMed ID11922312
The fabrication of fluidic channels with dimensions smaller than 1 microm is described and characterized in respect to their use for detection of individual DNA molecules. The sacrificial layer technique is used to fabricate these devices as it provides CMOS-compatible materials exhibiting low fluorescence background. It also allows creating microfluidics ... More
Control of DNA hybridization with photocleavable adducts.
AuthorsGhosn B, Haselton FR, Gee KR, Monroe WT
JournalPhotochem Photobiol
PubMed ID15869326
Previous reports have shown that 1-(4,5-dimethoxy-2-nitrophenyl)ethyl ester (DMNPE) adducts coupled to DNA plasmids block transcription in vitro and in vivo until removed with light. In this report, we explore the use of DMNPE to control DNA hybridization. We found that DMNPE-caged oligonucleotides have changed spectrophotometric and electrophoretic properties that can ... More
Catalyzed relaxation of a metastable DNA fuel.
AuthorsSeelig G, Yurke B, Winfree E
JournalJ Am Chem Soc
PubMed ID16967972
Practically all of life's molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalytic transformation of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in nucleic-acid-based engineering as it is in biology. Here ... More
Sensitive determination of microbial growth by nucleic acid staining in aqueous suspension.
AuthorsMartens-Habbena W, Sass H
JournalAppl Environ Microbiol
PubMed ID16391029
The determination of cell numbers or biomass in laboratory cultures or environmental samples is usually based on turbidity measurements, viable counts, biochemical determinations (e.g., protein and lipid measurements), microscopic counting, or recently, flow cytometric analysis. In the present study, we developed a novel procedure for the sensitive quantification of microbial ... More
Novel splice variants of ING4 and their possible roles in the regulation of cell growth and motility.
AuthorsUnoki M, Shen JC, Zheng ZM, Harris CC
JournalJ Biol Chem
PubMed ID16973615
The ING4 gene is a candidate tumor suppressor gene that functions in cell proliferation, contact inhibition, and angiogenesis. We identified three novel splice variants of ING4 with differing activities in controlling cell proliferation, cell spreading, and cell migration. ING4_v1 (the longest splice variant), originally identified as ING4, encodes an intact ... More
ATM is activated in response to N-methyl-N'-nitro-N-nitrosoguanidine-induced DNA alkylation.
AuthorsAdamson AW, Kim WJ, Shangary S, Baskaran R, Brown KD
JournalJ Biol Chem
PubMed ID12151394
p53 plays an important role in response to ionizing radiation by regulating cell cycle progression and triggering apoptosis. These activities are controlled, in part, by the phosphorylation of p53 by the protein kinase ATM. Recent evidence indicates that the monofunctional DNA alkylating agent N-methyl-N'-nitro-N- nitrosoguanidine (MNNG) also triggers up-regulation and ... More
Versatile method employing basic techniques of genetic engineering to study the ability of low-molecular-weight compounds to bind covalently with DNA in cell-free systems.
AuthorsBartoszek A, Sielenko A, Wesiora M
JournalAnal Biochem
PubMed ID12576058
Numerous antitumor and carcinogenic compounds and free radicals are able to modify DNA by forming covalent bonds, mainly with nucleophilic centers in nucleobases. Such a binding is usually of utmost importance for the biological outcome. The level of DNA adducts formed by a given agent is in most cases extremely ... More
High-resolution genotyping by amplicon melting analysis using LCGreen.
BACKGROUND: High-resolution amplicon melting analysis was recently introduced as a closed-tube method for genotyping and mutation scanning (Gundry et al. Clin Chem 2003;49:396-406). The technique required a fluorescently labeled primer and was limited to the detection of mutations residing in the melting domain of the labeled primer. Our aim was ... More
Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution.
The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result ... More