Sequence-specific scission of DNA by the chemical nuclease activity of 1,10-phenanthroline-copper(I) targeted by RNA.
AuthorsChen CB, Gorin MB, Sigman DS
JournalProc Natl Acad Sci U S A
PubMed ID7683427
'RNAs modified with the chemical nuclease 1,10-phenanthroline-copper(I) can achieve the sequence-specific scission of single- and double-stranded DNA targets. The RNAs are prepared in vitro by using 5-(3-aminoallyl)-UTP as the sole source of UTP and can be readily modified with 1,10-phenanthroline by using N-succinimidyl 3-(2-pyridyl-dithio)propionate (SPDP) to cross-link the ligand to ... More
Fluorescent labelling of cRNA for microarray applications.
Authors't Hoen PA, de Kort F, van Ommen GJ, den Dunnen JT
JournalNucleic Acids Res
PubMed ID12595569
'Microarrays of oligonucleotide expression libraries can be hybridised with either cDNA, generated from mRNA during reverse transcription, or cRNA, generated in an Eberwine mRNA amplification procedure. While methods for fluorescent labelling of cDNA have been thoroughly investigated, methods for cRNA labelling have not. To this purpose, we developed an aminoallyl-UTP ... More
Aminomodified nucleobases: functionalized nucleoside triphosphates applicable for SELEX.
AuthorsSchoetzau T, Langner J, Moyroud E, Roehl I, Vonhoff S, Klussmann S
JournalBioconjug Chem
PubMed ID13129394
5-Aminoallyl-2'-fluoro-dUTP, 5-aminoallyl-UTP, and N(6)-([6-aminohexyl]carbamoylmethyl)-ATP were systematically tested for their suitability for the systematic evolution of ligands by exponential enrichment (SELEX) process with the aim of introducing additional functionalities to RNA libraries. All three aminomodified nucleoside triphosphates proved to be compatible with the enzymatic steps required for SELEX and maintained strict ... More
Comparison of fluorescent tag DNA labeling methods used for expression analysis by DNA microarrays.
AuthorsRichter A, Schwager C, Hentze S, Ansorge W, Hentze MW, Muckenthaler M
JournalBiotechniques
PubMed ID12238772
Gene expression profiling by DNA microarrays has found wide application in many fields of biomedical research. The protocols for this technique are not yet standardized, and for each given step in microarray analysis a number of different protocols are in use. As a consequence, results obtained in different laboratories can ... More
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer.
AuthorsHughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS
JournalNat Biotechnol
PubMed ID11283592
We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, ... More
Survey of four different photoreactive moieties for DNA photoaffinity labeling of yeast RNA polymerase III transcription complexes.
AuthorsTate JJ, Persinger J, Bartholomew B
JournalNucleic Acids Res
PubMed ID9490787
In order to optimize the detection of protein-DNA contacts by DNA photoaffinity labeling, we attached four different photoreactive groups to DNA and examined their ability to crosslink yeast RNA polymerase III (Pol III) transcription complexes. Photoreactive nucleotides containing an aryl azide (AB-dUMP), benzophenone (BP-dUMP), perfluorinated aryl azide (FAB-dUMP) or diazirine ... More
Non-isotopic RNA probes. Comparison between different labels and detection systems.
AuthorsGiaid A, Hamid Q, Adams C, Springall DR, Terenghi G, Polak JM
JournalHistochemistry
PubMed ID2613556
Several studies have shown the use of non-radioactive labelled DNA probes for in situ hybridisation, mainly to identify cellular DNA. In this study mRNA in situ hybridisation was performed on rat pituitary with biotinylated complementary (c) RNA probes for rat prolactin and growth hormone (GH), and compared with radioactive 35S-radiolabelled ... More
Comparison of biotinylated DNA and RNA probes for rapid detection of varicella-zoster virus genome by in situ hybridization.
AuthorsForghani B, Yu GJ, Hurst JW
JournalJ Clin Microbiol
PubMed ID1645371
We describe a general method for the production of nonisotopic DNA and RNA probes for the detection of the varicella-zoster virus (VZV) genome by in situ hybridization. VZV DNA was extracted from purified viral nucleocapsids, cleaved with restriction enzyme (RE) BamHI, and cloned into plasmid pBR322 by the standard vector ... More