What's new for 'Trypanosomatids' in PubMed

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Sent on Thursday, 2011 Jun 09
Search kinetoplastids OR kinetoplastid OR Kinetoplastida OR "trypanosoma brucei" OR leishmania OR brucei OR leishmaniasis OR "African trypanosomiasis"
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PubMed Results

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1.	Methods Mol Biol. 2011;718:245-57. Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target. Wachtel C, Michaeli S. Source The Mina and Everard Goodman Faculty of Life Sciences and the Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel. Abstract The recent discovery of thousands of small noncoding RNAs (ncRNAs), in many different organisms, has led to the need for methods to study their function. One way to help understand their function is to determine what other RNAs interact with the ncRNAs. We have developed a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed "RNA walk." The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR. Domains carrying the cross-linked adducts are less efficiently amplified than domains that are not cross-linked. Real-time PCR is used to quantify the results. Further mapping of the interactions is performed by primer extension to determine the exact cross-linked adduct.
	PMID: 21370053 [PubMed - indexed for MEDLINE]
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2.	Methods Mol Biol. 2011;718:209-26. Analysis of tRNA editing in native and synthetic substrates. Spears JL, Gaston KW, Alfonzo JD. Source Department of Microbiology, The Ohio State Center for RNA Biology, The Ohio State University, Columbus, OH, USA. Abstract The primary sequence of all nucleic acids in a cell contain 4 canonical nucleotides (G, A, T, and C for DNA and G, A, U, and C for RNA). However, post-transcriptionally, nucleic acids can undergo a number of chemical modifications, which may change their structure and function. tRNAs contain the most diverse array of post-transcriptionally added chemical groups that involve both editing and modification. Because editing and modification events can serve vital roles in cell function, it is important to develop techniques that allow for fast and accurate analysis of these events. This chapter describes the methods used to purify tRNAs from total native RNA pools and for subsequent analysis of their edited and modified states using reverse transcriptase-based approaches. These techniques, in combination with 2D-TLC, allow for the routine analysis and quantitation of edited and modified nucleotides in a fast, cost effective manner and without the need for special equipment such as HPLC or a mass spectrometer. Admittedly, the techniques described here are only applicable to a subset of post-transcriptional changes occurring in a tRNA such as C to U and A to I editing as well as modifications that prevent reverse transcriptase elongation; these have been highlighted throughout the chapter.
	PMID: 21370051 [PubMed - indexed for MEDLINE]
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