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Rapid method for the characterization of 3' and 5' UTRs of influenza viruses. 2003

Christopher Szymkowiak, and Wan-Sang Kwan, and Qin Su, and Timothy J Toner, and Alan R Shaw, and Rima Youil
Department of Virus and Cell Biology, Merck and Co Inc, 44L-206B West Point, PA 19486, USA.

A T4 RNA ligase based strategy is demonstrated that allows for the full characterization of 3' and 5' UTR regions of negative strand RNA viruses. Negative strand RNA viruses such as influenza have 3'OH and 5'P terminal ends that are capable of being ligated using T4 RNA ligase. Each segment can form a mixture of linear concatamers between like and different viral segments or can itself form a circular structure upon ligation. RT-PCR can then be performed on these circular RNA segments using gene specific primers subsequently allowing for the characterization of the true terminal sequence for each viral segment. The UTR regions of a number of influenza virus strains were defined accurately using this approach.

UI MeSH Term Description Entries
D008828 Microbiological Techniques Techniques used in microbiology. Microbiologic Technic,Microbiologic Technics,Microbiologic Technique,Microbiological Technics,Technic, Microbiologic,Technics, Microbiological,Technique, Microbiologic,Techniques, Microbiologic,Microbiologic Techniques,Microbiological Technic,Microbiological Technique,Technic, Microbiological,Technics, Microbiologic,Technique, Microbiological,Techniques, Microbiological
D009975 Orthomyxoviridae A family of RNA viruses causing INFLUENZA and other respiratory diseases. Orthomyxoviridae includes INFLUENZAVIRUS A; INFLUENZAVIRUS B; INFLUENZAVIRUS C; INFLUENZAVIRUS D; ISAVIRUS; and THOGOTOVIRUS. Influenza Viruses,Myxoviruses,Orthomyxoviruses,Influenza Virus,Myxovirus,Orthomyxovirus
D011118 Polynucleotide Ligases Catalyze the joining of preformed ribonucleotides or deoxyribonucleotides in phosphodiester linkage during genetic processes. EC 6.5.1. Polynucleotide Synthetases,Ligases, Polynucleotide,Synthetases, Polynucleotide
D011130 RNA Ligase (ATP) An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3. Polyribonucleotide Synthetase,tRNA Ligase,Ligase, tRNA,Synthetase, Polyribonucleotide
D012367 RNA, Viral Ribonucleic acid that makes up the genetic material of viruses. Viral RNA
D014764 Viral Proteins Proteins found in any species of virus. Gene Products, Viral,Viral Gene Products,Viral Gene Proteins,Viral Protein,Protein, Viral,Proteins, Viral
D020121 5' Untranslated Regions The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences. 5'UTR,Leader Sequences, mRNA,Leader mRNA Sequences,mRNA Leader Sequences,5' UTR,5' UTRs,5' Untranslated Region,5'UTRs,Leader Sequence, mRNA,Leader mRNA Sequence,Region, 5' Untranslated,Regions, 5' Untranslated,Sequence, Leader mRNA,Sequence, mRNA Leader,Sequences, Leader mRNA,Sequences, mRNA Leader,UTR, 5',UTRs, 5',Untranslated Region, 5',Untranslated Regions, 5',mRNA Leader Sequence,mRNA Sequence, Leader,mRNA Sequences, Leader
D020133 Reverse Transcriptase Polymerase Chain Reaction A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols. Polymerase Chain Reaction, Reverse Transcriptase,Reverse Transcriptase PCR,PCR, Reverse Transcriptase,Transcriptase PCR, Reverse
D020413 3' Untranslated Regions The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences. 3'UTR,3' UTR,3' Untranslated Region,3' UTRs,3'UTRs,Region, 3' Untranslated,Regions, 3' Untranslated,UTR, 3',UTRs, 3',Untranslated Region, 3',Untranslated Regions, 3'

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