Rapid method for the characterization of 3' and 5' UTRs of influenza viruses.
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.
Szymkowiak
Christopher
C
Department of Virus and Cell Biology, Merck and Co Inc, 44L-206B West Point, PA 19486, USA.
Kwan
Wan-Sang
WS
Su
Qin
Q
Toner
Timothy J
TJ
Shaw
Alan R
AR
Youil
Rima
R
D020413:3' Untranslated Regions / Q000737:chemistry*; D020121:5' Untranslated Regions / Q000737:chemistry*; D008828:Microbiological Techniques / Q000379:methods*; D009975:Orthomyxoviridae / Q000235:genetics*; D011118:Polynucleotide Ligases / Q000378:metabolism; D011130:RNA Ligase (ATP); D012367:RNA, Viral / Q000737:chemistry*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014764:Viral Proteins / Q000378:metabolism
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012367:RNA, Viral; D014764:Viral Proteins; D011118:Polynucleotide Ligases; D011130:RNA Ligase (ATP); C467724:bacteriophage T4 RNA ligase 2