Mapping of RNA–protein interactions

Gopinath, Subash C.B.

doi:10.1016/j.aca.2009.01.052

Cited by 22 publications

(17 citation statements)

References 133 publications

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“…5b). These RNA molecules play functional roles by forming complexes characterized as ligand-induced RNAs, RNA-induced ligands, or coinduced conformational changes (Gopinath 2009). In this regard, several shortened aptamers have been proposed with different analytes (Gopinath et al 2006a), as smaller aptamers perform better as chimeras because longer aptamers may undergo degradation.…”

Section: Aptamer-based Chimerasmentioning

confidence: 99%

Cell-targeting aptamers act as intracellular delivery vehicles

Gopinath

Lakshmipriya

Chen

et al. 2016

Appl Microbiol Biotechnol

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Aptamers are single-stranded nucleic acids or peptides identified from a randomized combinatorial library through specific interaction with the target of interest. Targets can be of any size, from small molecules to whole cells, attesting to the versatility of aptamers for binding a wide range of targets. Aptamers show drug properties that are analogous to antibodies, with high specificity and affinity to their target molecules. Aptamers can penetrate disease-causing microbial and mammalian cells. Generated aptamers that target surface biomarkers act as cell-targeting agents and intracellular delivery vehicles. Within this context, the "cell-internalizing aptamers" are widely investigated via the process of cell uptake with selective binding during in vivo systematic evolution of ligands by exponential enrichment (SELEX) or by cell-internalization SELEX, which targets cell surface antigens to be receptors. These internalizing aptamers are highly preferable for the localization and functional analyses of multiple targets. In this overview, we discuss the ways by which internalizing aptamers are generated and their successful applications. Furthermore, theranostic approaches featuring cell-internalized aptamers are discussed with the purpose of analyzing and diagnosing disease-causing pathogens.

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Section: Aptamer-based Chimerasmentioning

confidence: 99%

Cell-targeting aptamers act as intracellular delivery vehicles

Gopinath

Lakshmipriya

Chen

et al. 2016

Appl Microbiol Biotechnol

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“…These omnipotent roles displayed by RNA are attributable to the presence of the hydroxyl group at the 2' position, which adds to the flexibility of these molecules (Wiegand et al 1996). Hence, remarkable features manifested by RNA have made these molecules the subject of intense study and analysis in a wide variety of applications, including RNA-protein mapping with nuclease protection assay, toe-printing analyses, RNAse protection assay, boundary analysis, SELEX (Gopinath 2009), RNomics (Tang et al 2009) and others.…”

Section: Introductionmentioning

confidence: 99%

A rapid and cost effective method in purifying small RNA

Citartan

Tan

Tang

2011

World J Microbiol Biotechnol

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Purification of RNA fragments from a complex mixture is a very common technique, and requires consideration of the time, cost, purity and yield of the purified RNA fragments. This study describes the fastest method of purifying small RNA with the lowest cost possible, without compromizing the yield and purity. The technique describes the purification of small RNA from polyacrylamide gel, resulting in a good yield of small RNA with minimum experimental steps in avoiding degradation of the RNA, obviating the use of ethidium bromide and phenol-chloroform extraction, as well as siliconized glass wools to remove the polyacrylamide gel particles. The purified small RNA is suitable for a wide variety of applications such as ligation, end labelling with radio isotope, RT-PCR (Reverse Transcriptase-PCR), Northern blotting, experimental RNomics study and also Systematic Evolution of Ligands by Exponential Enrichment (SELEX).

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“…In particular, kethoxal compound, which selectively reacts with guanine, is useful for structural probing studies of the single-stranded RNA aptamers [2]. Another glyoxal derivative, 3′,4′,5′-trimethoxyphenylglyoxal (TMPG), has been recently reported to react with the deoxyguanosine in the single-stranded oligodeoxynucleotide selectively [3].…”

Section: Introductionmentioning

confidence: 99%

Biotinylation of Deoxyguanosine at the Abasic Site in Double-Stranded Oligodeoxynucleotides

2016

Journal of Analytical Methods in Chemistry

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Biotinylation of deoxyguanosine at an abasic site in double-stranded oligodeoxynucleotides was studied. The biotinylation of deoxyguanosine is achieved by copper-catalyzed click reaction after the conjugation of the oligodeoxynucleotide with 2-oxohex-5-ynal. The biotinylation enables visualization of the biotinylated oligodeoxynucleotides by chemiluminescence on a nylon membrane. In order to investigate the biotinylated site, the biotinylated oligodeoxynucleotides were amplified by the DNA polymerase chain reaction. Replacement of guanine opposing the abasic site with adenine generated by the activity of the terminal deoxynucleotidyl transferase of DNA polymerase was detected by DNA sequencing analysis and restriction endonuclease digestion. This study suggests that 2-oxohex-5-ynal may be useful for the detection of the unpaired deoxyguanosine endogenously generated at abasic sites in genomic DNA.

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Mapping of RNA–protein interactions

Cited by 22 publications

References 133 publications

Cell-targeting aptamers act as intracellular delivery vehicles

Cell-targeting aptamers act as intracellular delivery vehicles

A rapid and cost effective method in purifying small RNA

Biotinylation of Deoxyguanosine at the Abasic Site in Double-Stranded Oligodeoxynucleotides

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