Genomes and Genes
Summary: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.
- Chotteau Lelievre A, Dolle P, Gofflot F. Expression analysis of murine genes using in situ hybridization with radioactive and nonradioactively labeled RNA probes. Methods Mol Biol. 2006;326:61-87 pubmed
- Dirks R, Tanke H. Advances in fluorescent tracking of nucleic acids in living cells. Biotechniques. 2006;40:489-96 pubmed..Recent live-cell imaging studies have already provided important insights into the dynamic behaviors of chromatin and RNAs in the cell. ..
- Krigar D, Kaltschmitt J, Krieger J, Eickholz P. Two subgingival plaque-sampling strategies used with RNA probes. J Periodontol. 2007;78:72-8 pubmed..However, this observation only was statistically significant for the frequency of Td. ..
- Silverman A, Kool E. RNA probes of steric effects in active sites: high flexibility of HIV-1 reverse transcriptase. J Am Chem Soc. 2007;129:10626-7 pubmed
- Ramkissoon S, Mainwaring L, Sloand E, Young N, Kajigaya S. Nonisotopic detection of microRNA using digoxigenin labeled RNA probes. Mol Cell Probes. 2006;20:1-4 pubmed..A labeled probe for U6 small nuclear RNA served as an internal control. The use of DIG-labeled RNA probes was equally sensitive compared to 32P-labeled probes in detecting miRNA quantities as low as 50 ng...
- Cervantes S, Prudhomme J, Carter D, Gopi K, Li Q, Chang Y, et al. High-content live cell imaging with RNA probes: advancements in high-throughput antimalarial drug discovery. BMC Cell Biol. 2009;10:45 pubmed publisher..We have developed a new P. falciparum RNA high-content imaging growth inhibition assay that is robust with time and energy efficiency. ..
- Ji M, Lee Y, Do S, Nam S, Jung K, Kim H, et al. Developmental patterns of mST3GalV mRNA expression in the mouse: in situ hybridization using DIG-labeled RNA probes. Arch Pharm Res. 2000;23:525-30 pubmed..mouse embryogenesis [embryonic (E) days; E9, E11, E13, E15] by in situ hybridization with digoxigenin-labeled RNA probes. All tissues from E9 and E11 were positive for mST3GalV mRNA...
- Xi X, Roane D, Zhou J, Ryan D, Martin R. Double-color fluorescence in situ hybridization with RNA probes. Biotechniques. 2003;34:914-6, 918 pubmed
- Long S, Rebagliati M. Sensitive two-color whole-mount in situ hybridizations using digoxygenin- and dinitrophenol-labeled RNA probes. Biotechniques. 2002;32:494, 496, 498 passim pubmed
- Simard C, Lemieux R, Cote S. Urea substitutes toxic formamide as destabilizing agent in nucleic acid hybridizations with RNA probes. Electrophoresis. 2001;22:2679-83 pubmed..have compared the efficiency of urea to that of formamide as denaturing agent in nucleic acid hybridization with RNA probes. We show that urea at concentrations of 2-4 molar in solution performs as good as 50% formamide to reduce ..
- Molenaar C, Marras S, Slats J, Truffert J, Lemaitre M, Raap A, et al. Linear 2' O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res. 2001;29:E89-9 pubmed..Antisense 2' OMe RNA probes showed fast hybridization kinetics, whereas conventional oligodeoxyribonucleotide (DNA) probes did not...
- David R, Wedlich D. PCR-based RNA probes: a quick and sensitive method to improve whole mount embryo in situ hybridizations. Biotechniques. 2001;30:769-72, 74 pubmedWe have developed a PCR-based technique for the preparation of RNA probes that can be used for whole mount in situ hybridization on embryos...
- Rausch J, Sztuba Solińska J, Lusvarghi S, Le Grice S. Novel Biochemical Tools for Probing HIV RNA Structure. Methods Mol Biol. 2016;1354:91-117 pubmed publisher..Combinational application of these techniques provides a formidable arsenal for exploring the structures of HIV RNAs and associated nucleoprotein complexes. ..
- Mayer G, Famulok M. In vitro selection of conformational probes for riboswitches. Methods Mol Biol. 2009;540:291-300 pubmed publisher..By this means, and after determination of the binding region, domains which are necessary for proper function of a full-length riboswitch can be identified. ..
- Semino Mora C, Liu H, McAvoy T, Nieroda C, Studeman K, Sardi A, et al. Pseudomyxoma peritonei: is disease progression related to microbial agents? A study of bacteria, MUC2 AND MUC5AC expression in disseminated peritoneal adenomucinosis and peritoneal mucinous carcinomatosis. Ann Surg Oncol. 2008;15:1414-23 pubmed publisher..Because Gram-negative organisms can upregulate MUC2 mucin gene expression, we determined whether bacteria were detectable in PMP tissues...
- Lecuyer E. High resolution fluorescent in situ hybridization in Drosophila. Methods Mol Biol. 2011;714:31-47 pubmed publisher..Furthermore, the protocol outlines details for conducting FISH in microtiter plates, which greatly enhances the throughput, practicality, and economy of the procedure. ..
- Zijlmans H, Fleuren G, Baelde H, Eilers P, Kenter G, Gorter A. Role of tumor-derived proinflammatory cytokines GM-CSF, TNF-alpha, and IL-12 in the migration and differentiation of antigen-presenting cells in cervical carcinoma. Cancer. 2007;109:556-65 pubmed..The results suggest that GM-CSF as well as TNF-alpha, produced by cervical carcinoma cells, may play a role in the differentiation of monocytes into mature DC. Furthermore, TNF-alpha may influence the migration of LHC from the tumor. ..
- Tsuruga E, Yajima T, Irie K. Induction of fibulin-5 gene is regulated by tropoelastin gene, and correlated with tropoelastin accumulation in vitro. Int J Biochem Cell Biol. 2004;36:395-400 pubmed..These results may suggest that the fibulin-5 gene induction is directly or indirectly regulated by tropoelastin gene expression and plays a role in the accumulation of elastic fibers within matrices. ..
- Kawakami M, Kawakami K, Takahashi S, Abe M, Puri R. Analysis of interleukin-13 receptor alpha2 expression in human pediatric brain tumors. Cancer. 2004;101:1036-42 pubmed..Because the IL-13Ralpha2 chain is a major binding component of the IL-13R complex, these results suggest that the targeting of IL-13R may represent a useful approach for the treatment of pediatric brain tumors. ..
- Stoilov I, Rezaie T, Jansson I, Schenkman J, Sarfarazi M. Expression of cytochrome P4501b1 (Cyp1b1) during early murine development. Mol Vis. 2004;10:629-36 pubmed..5, 10.5, and 11.5 dpc were obtained by timed breeding experiments. Antisense and sense RNA probes labeled with digoxigenin UTP were generated by in vitro transcription of an 848 bp Cyp1b1 cDNA fragment that was ..
- Zuccarello D, Morini E, Douzgou S, Ferlin A, Pizzuti A, Salpietro D, et al. Preliminary data suggest that mutations in the CgRP pathway are not involved in human sporadic cryptorchidism. J Endocrinol Invest. 2004;27:760-4 pubmed..These preliminary data suggest that these genes are not major factors for cryptorchidism in humans. ..
- Taxman D, Livingstone L, Zhang J, Conti B, Iocca H, Williams K, et al. Criteria for effective design, construction, and gene knockdown by shRNA vectors. BMC Biotechnol. 2006;6:7 pubmed..However, application of a modification based on the central shRNA stability should provide a useful improvement to the design of effective shRNA vectors. ..
- Ohlin A, Backman A, Björkqvist M, Mölling P, Jurstrand M, Schollin J. Real-time PCR of the 16S-rRNA gene in the diagnosis of neonatal bacteraemia. Acta Paediatr. 2008;97:1376-80 pubmed publisher..The method managed to detect bacteraemia with high specificity even though the sensitivity was low. Factors causing the low sensitivity are identified and further strategies to develop the method are described. ..
- Hajduk P, Murphy P, Puri P. Fgf10 gene expression is delayed in the embryonic lung mesenchyme in the adriamycin mouse model. Pediatr Surg Int. 2010;26:23-7 pubmed publisher..Embryos were harvested on days 10-13, stained after whole mount in situ hybridization with labeled RNA probes to detect Fgf10 transcripts (n = 5 for each treatment/day of gestation)...
- Kominek P, Bryxiová M. Comparison of three techniques for detection of grapevine leafroll-associated virus 1. Acta Virol. 2005;49:37-43 pubmed..tested using double-antibody sandwich ELISA (DAS-ELISA), RT-PCR and molecular hybridization with non-radioactive RNA probes. Both molecular methods were based on a detection of the GLRaV-1 heat-shock protein 70 (HSP70) gene and showed a ..
- Tompsett A, Park J, Zhang X, Jones P, Newsted J, Au D, et al. In situ hybridization to detect spatial gene expression in medaka. Ecotoxicol Environ Saf. 2009;72:1257-64 pubmed publisher..The ISH method developed in this study allowed tissue-specific resolution of gene expression in a whole animal model, as well as the ability to analyze cellular morphological detail in the same organism. ..
- Kahala M, Maki M, Lehtovaara A, Tapanainen J, Katiska R, Juuruskorpi M, et al. Characterization of starter lactic acid bacteria from the Finnish fermented milk product viili. J Appl Microbiol. 2008;105:1929-38 pubmed publisher..lactis subsp. lactis. The results obtained give an overview of the microbial population of viili starters and can be exploited in the development of optimized starter cultures for industrial-scale manufacture of viili. ..
- ..The major steps involved in in situ hybridization are as follows: probe preparation and labeling, tissue fixation, permeabilization, hybridization, and signal detection and these are described in detail in this chapter. ..
- Harvey J, Brant S, Knutson J, Han M. SNP analysis using CataCleave probes. J Clin Lab Anal. 2008;22:192-203 pubmed publisher..Cleavage rates were proportional to target concentration. Probe length and position of fluorescent labels may also be modified for use in multiplexing high-throughput SNP assays. This represents a novel method for the detection of SNPs. ..
- Parfett C, Zhou G, Silverman F. End-linked amino-modified 50-mer oligonucleotides as RNA profiling probes on nylon arrays: comparison to UV cross-linked DNA probes. Biotechniques. 2005;38:690, 692, 694 pubmed
- Brown D, Joy E, Greatorex J, Gait M, Lever A. Steric block high affinity oligonucleotide analogues: a new tool for mapping RNA-protein binding sites. Nucleosides Nucleotides Nucleic Acids. 2008;27:196-212 pubmed publisher..We also demonstrate direct binding of oligonucleotide to their binding sites and confirm this interaction does not alter global RNA conformation, making them highly specific, nondisruptive probes of RNA protein interactions. ..
- Depboylu C, Eiden L, Weihe E. Increased APOBEC3G expression is associated with extensive G-to-A hypermutation in viral DNA in rhesus macaque brain during lentiviral infection. J Neuropathol Exp Neurol. 2007;66:901-12 pubmed..Upregulation of APOBEC3G may restrict spread of SIV in the brain and thus limit brain damage during lentiviral infection. ..
- Kim N, Shin J, Elmetwaly S, Gan H, Schlick T. RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics. 2007;23:2959-60 pubmed..The web server is accessible on the web at http://rubin2.biomath.nyu.edu ..
- Xu L, Sun C, Petrovics G, Makarem M, Furusato B, Zhang W, et al. Quantitative expression profile of PSGR in prostate cancer. Prostate Cancer Prostatic Dis. 2006;9:56-61 pubmed..Strikingly high-percentage CaP cells overexpress PSGR warrants further studies of PSGR expression alterations to define subsets of CaPs. ..
- Shimakage M, Kawahara K, Harada S, Sasagawa T, Shinka T, Oka T. Expression of Epstein-Barr virus in renal cell carcinoma. Oncol Rep. 2007;18:41-6 pubmed..These results suggest that the expression of EBV may be involved in the pathogenesis of RCC and nephroblastoma. ..
- Hammond S. microRNA detection comes of age. Nat Methods. 2006;3:12-3 pubmed
- Budhraja V, Spitznagel E, Schaiff W, Sadovsky Y. Incorporation of gene-specific variability improves expression analysis using high-density DNA microarrays. BMC Biol. 2003;1:1 pubmed..We recommend its incorporation to any computation of gene expression changes using high-density DNA microarrays. A Java application implementing our T-score is available at http://www.sadovsky.wustl.edu/tscore.html. ..
- Lea R, Bonev B, Dubaissi E, Vize P, Papalopulu N. Multicolor fluorescent in situ mRNA hybridization (FISH) on whole mounts and sections. Methods Mol Biol. 2012;917:431-44 pubmed publisher..Here, we describe a protocol for performing multicolor FISH in Xenopus embryos in whole mounts and sections that can be further combined with antibody staining. ..
- Vyboh K, Ajamian L, Mouland A. Detection of viral RNA by fluorescence in situ hybridization (FISH). J Vis Exp. 2012;:e4002 pubmed publisher..Once the probe has hybridized to the target mRNA in cells, subsequent antibody labelling steps (Figure 1) will reveal the localization of the mRNA as well as proteins of interest when performing FISH/IF. ..
- Wan K, Ebert B, Voigt J, Wang Q, Dai Y, Haag R, et al. In vivo tumor imaging using a novel RNAi-based detection mechanism. Nanomedicine. 2012;8:393-8 pubmed publisher..A new concept of tumor imaging is presented in this paper using a siRNA-based probe detecting protoporphyrin IX (PpIX), a fluorescent metabolite of the heme synthesis previously demonstrated to accumulate in cancer tissue. ..
- Bardea A, Burshtein N, Rudich Y, Salame T, Ziv C, Yarden O, et al. Sensitive detection and identification of DNA and RNA using a patterned capillary tube. Anal Chem. 2011;83:9418-23 pubmed publisher..The sample-analyte hybrids are detected by their fluorescence signal. We show that the new method is sensitive, is specific, can detect simultaneously both DNA and RNA from the same sample, and allows detection of analytes in serum. ..
- Merendino L, Falciatore A, Rochaix J. Expression and RNA binding properties of the chloroplast ribosomal protein S1 from Chlamydomonas reinhardtii. Plant Mol Biol. 2003;53:371-82 pubmed..The possible implications of these findings are discussed. ..
- Sarkar K, Bhattacharya S, Bhattacharyya S, Chatterjee S, Mallick A, Chakraborti S, et al. Oncogenic human papilloma virus and cervical pre-cancerous lesions in brothel-based sex workers in India. J Infect Public Health. 2008;1:121-8 pubmed publisher..Vaccination against HPV for newly entrant sex workers may be an important component for a successful intervention programme. ..
- Masse K, Bhamra S, Allsop G, Dale N, Jones E. Ectophosphodiesterase/nucleotide phosphohydrolase (Enpp) nucleotidases: cloning, conservation and developmental restriction. Int J Dev Biol. 2010;54:181-93 pubmed publisher..This is the first complete developmental analysis of gene expression of this gene family in vertebrates. ..
- Scumpia P, Kelly K, Reeves W, Stevens B. Double-stranded RNA signals antiviral and inflammatory programs and dysfunctional glutamate transport in TLR3-expressing astrocytes. Glia. 2005;52:153-62 pubmed
- Young W, Mezey E. Hybridization histochemistry of neural transcripts. Curr Protoc Neurosci. 2004;Chapter 1:Unit 1.3 pubmed publisher..This unit describes hybridization histochemical techniques using either oligonucleotide probes or RNA probes (riboprobes)...
- Dillman J, Phillips C. Comparison of non-human primate and human whole blood tissue gene expression profiles. Toxicol Sci. 2005;87:306-14 pubmed..These results show that human genechips can be used for expression profiling of NHP samples and provide a foundation for the development of tools for comparing human and NHP gene expression profiles. ..
- Suzuki I, Motokawa T. In situ hybridization: an informative technique for pigment cell researchers. Pigment Cell Res. 2004;17:10-4 pubmed..Although this technique has been utilized mainly in developmental biology, it will be fully advantageous when combined with high-throughput comprehensive transcriptome/proteome analyses. ..
- Ren J, Meng X. A relative quantitative method to detect OCT4A gene expression by exon-junction primer and locked nucleic acid-modified probe. J Zhejiang Univ Sci B. 2011;12:149-55 pubmed publisher..Additionally, the relative quantity of OCT4A mRNA was calculated by cycle threshold (C(t)) method and house keeping gene normalization. This technique proved to be effective for relative quantitation of OCT4A mRNA with high specificity. ..
- Wang L, Chen D, Yang L, Huang S, Zhang Y, Zhang H. Expression patterns of the creatine metabolism-related molecules AGAT, GAMT and CT1 in adult zebrafish Danio rerio. J Fish Biol. 2010;76:1212-9 pubmed publisher..rerio were investigated. The results reveal that AGAT, GAMT and CT1 are expressed widely in diverse tissues of D. rerio where the homologous genes in mammals are also expressed. ..
- Catrina I, Marras S, Bratu D. Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells. ACS Chem Biol. 2012;7:1586-95 pubmed..The results demonstrate that tiny molecular beacons hybridize to target mRNA at faster rates than classically designed molecular beacons and are able to access previously inaccessible target regions. ..