Direct sequence detection of structured H5 influenza viral RNA

Journal of Molecular Diagnostics

Volumn 10, Issue 3, 2008, Pages 225-235

  Kerby, Matthew B ^a   Freeman, Sarah ^a   Prachanronarong, Kristina ^a   Artenstein, Andrew W ^a,c   Opal, Steven M ^a,c   Tripathi, Anubhav ^a,b,c  

^a BROWN UNIVERSITY   (United States)

^b MEMORIAL HOSPITAL OF RHODE ISLAND   (United States)

^c BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE (MAGNESIUM); COMPLEMENTARY DNA; HEMAGGLUTININ; SIALIC ACID; VIRUS RNA;

ARTICLE; BINDING KINETICS; DNA CLEAVAGE; DNA PROBE; DNA TEMPLATE; FLUORESCENCE; GENE SEQUENCE; GENE TARGETING; HOST; HUMAN; INFLUENZA VIRUS A H5N1; MOLECULAR BEACON; MOLECULAR CLONING; MOLECULAR RECOGNITION; NONHUMAN; POINT MUTATION; PROTEIN MOTIF; RNA HYBRIDIZATION; RNA STRUCTURE; RNA TRANSCRIPTION; SENSITIVITY AND SPECIFICITY; TEMPERATURE; THERMODYNAMICS; VIRUS IDENTIFICATION; VIRUS ISOLATION;

EID: 43749096611     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2008.070094     Document Type: Article

References (53)

1. JKMD Taubenberger Influenza: the mother of all pandemics Emerg Infect Dis 2006 1918 15 22
2. LA Mermel Pandemic avian influenza Lancet Infect Dis 11 2005 666 667
3. EG Brown Influenza virus genetics Biomed Pharmacother 54 2000 196 209
4. RAMV Fouchier A Wallensten TM Bestebroer S Herfst D Smith GF Rimmelzwaan B Olsen AD Osterhaus Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls J Virol 79 2005 2814 2822
5. MT Osterholm Preparing for the next pandemic N Engl J Med 2005 1839 1842
6. AS Fauci Pandemic influenza threat and preparedness Emerg Infect Dis 2006 73 77
7. ED Dawson CL Moore JA Smagala DM Dankbar M Mehlmann MB Townsend CB Smith NJ Cox RD Kuchta KL Rowlen MChip: a tool for influenza surveillance Anal Chem 78 2006 7610 7615
8. N Kessler O Ferraris K Palmer W Marsh A Steel Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses J Clin Microbiol 42 2004 2173 2185
9. JP Li S Chen DH Evans Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR J Clin Microbiol 39 2001 696 704
10. JE Larkin BC Frank H Gavras R Sultana J Quackenbush Independence and reproducibility across microarray platforms Nature Methods 2 2005 337 343
11. M Mehlmann ED Dawson MB Townsend JA Smagala CL Moore CB Smith NJ Cox RD Kuchta KL Rowlen Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus J Clin Microbiol 44 2006 2857 2862
12. S Sengupta K Onodera A Lai U Melcher Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization J Clin Microbiol 41 2003 4542 4550
13. J Stevens O Blixt JC Paulson IA Wilson Glycan microarray technologies: tools to survey host specificity of influenza viruses Nature Rev Microbiol 4 2006 857 864
14. L Di Trani B Bedini I Donatelli L Campitelli B Chiappini MA De Marco M Delogu C Buonavoglia G Vaccari A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control BMC Infect Dis 6 2006 87 95
15. LFP Ng I Barr T Nguyen SM Noor RSP Tan LV Agathe S Gupta H Khalil TL To SS Hassan EC Ren Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay BMC Infect Dis 6 2006 40 46
16. S Payungporn S Chutinimitkul A Chaisingh S Damrongwantanapokin C Buranathai A Amonsin A Theamboonlers Y Poovorawan Single step multiplex real-time RT-PCR for H5N1 influenza A virus detection J Virol Methods 131 2006 143 147
17. N Pourmand L Diamond R Garten JP Erickson J Kumm RO Donis RW Davis Rapid and highly informative diagnostic assay for H5N1 influenza viruses PLoS ONE 1 2006 e95
18. HL Wei GR Bai AS Mweene YC Zhou YL Cong J Pu SH Wang H Kida JH Liu Rapid detection of avian influenza virus a and subtype H5N1 by single step multiplex reverse transcription-polymerase chain reaction Virus Genes 32 2006 261 267
19. C Yea D Adachi G Johnson E Nagy F Gharabaghi M Petric SE Richardson R Tellier Design of a single tube RT-PCR assay for the diagnosis of human infection with highly pathogenic influenza A(H5) viruses J Virol Methods 139 2006 220 226
20. G Bonnet S Tyagi A Libchaber FR Kramer Thermodynamic basis of the enhanced specificity of structured DNA probes Proc Natl Acad Sci USA 96 1999 6171 6176
21. JF Hopkins SA Woodson Molecular beacons as probes of RNA unfolding under native conditions Nucleic Acids Res 33 2005 5763 5770
22. SA Marras S Tyagi FR Kramer Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes Clin Chim Acta 363 2006 48 60
23. S Tyagi FR Kramer Molecular beacons: probes that fluoresce upon hybridization Nature Biotechnol 14 1996 303 308
24. DH Mathews DH Turner Prediction of RNA secondary structure by free energy minimization Curr Opin Struct Biol 16 2006 270 278
25. DH Mathews Revolutions in RNA secondary structure prediction J Mol Biol 359 2006 526 532
26. P Schuster Prediction of RNA secondary structures: from theory to models and real molecules Rep Progress Physics 69 2006 1419 1477
27. M Szemes CD Schoen Design of molecular beacons for AmpliDet RNA assay: characterization of binding stability and probe specificity Anal Biochem 315 2003 189 201
28. G Leone H van Schijndel B van Gemen FR Kramer CD Schoen Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA Nucleic Acids Res 26 1998 2150 2155
29. A Tsourkas MA Behlke G Bao Hybridization of 2′-O-methyl and 2′-deoxy molecular beacons to RNA and DNA targets Nucleic Acids Res 30 2002 5168 5174
30. VK Misra DE Draper A thermodynamic framework for Mg2+ binding to RNA Proc Natl Acad Sci USA 98 2001 12456 12461
31. VK Misra R Shiman DE Draper A thermodynamic framework for the magnesium-dependent folding of RNA Biopolymers 69 2003 118 136
32. S Hibbitts A Rahman R John D Westmoreland JD Fox Development and evaluation of NucliSen (R) Basic Kit NASBA for diagnosis of parainfluenza virus infection with “end-point” and “real-time” detection J Virol Methods 108 2003 145 155
33. GR Bai Y Sakoda AS Mweene N Fujii H Minakawa H Kida Improvement of a rapid diagnosis kit to detect either influenza A or B virus infections J Vet Med Sci 68 2006 35 40
34. MB Kerby RS Legge A Tripathi Measurements of kinetic parameters in a microfluidic reactor Anal Chem 78 2006 8273 8280
35. GW Chen SC Chang CK Mok YL Lo YN Kung JH Huang YH Shih JY Wang C Chiang CJ Chen SR Shih Genomic signatures of human versus avian influenza a viruses Emerg Infect Dis 12 2006 1353 1360
36. DM Whiley TP Sloots A 5′-nuclease real-time reverse transcriptase-polymerase chain reaction assay for the detection of a broad range of influenza A subtypes, including H5N1 Diagn Microbiol Infect Dis 53 2005 335 337
37. RM Hall GM Air Variation in nucleotide sequences coding for the N-terminal regions of the matrix and nonstructural proteins of influenza A viruses J Virol 38 1981 1 7
38. A Vines K Wells M Matrosovich MR Castrucci T Ito Y Kawaoka The role of influenza a virus hemagglutinin residues 226 and 228 in receptor specificity and host range restriction J Virol 72 1998 7626 7631
39. Y Ha DJ Stevens JJ Skehel DC Wiley X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs Proc Natl Acad Sci USA 98 2001 11181 11186
40. J Stevens O Blixt TM Tumpey JK Taubenberger JC Paulson IA Wilson Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus Science 312 2006 404 410
41. S Payungporn S Chutinimitkul A Chaisingh S Damrongwantanapokin B Nuansrichay W Pinyochon A Amonsin RO Donis A Theamboonlers Y Poovorawan Discrimination between highly pathogenic and low pathogenic H5 avian influenza A viruses Emerg Infect Dis 12 2006 700 701
42. M Hatta P Gao P Halfmann Y Kawaoka Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses Science 293 2001 1840 1842
43. SAE Marras FR Kramer S Tyagi Multiplex detection of single-nucleotide variations using molecular beacons Genet Anal Biomol Eng 14 1999 151 156
44. DH Mathews J Sabina M Zuker DH Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J Mol Biol 288 1999 911 940
45. M Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 31 2003 3406 3415
46. R Russell IS Millettt MW Tate LW Kwok B Nakatani SM Gruner SGJ Mochrie V Pande S Doniach D Herschlag L Pollack Rapid compaction during RNA folding Proc Natl Acad Sci USA 99 2002 4266 4271
47. DL Sokol XL Zhang PZ Lu AM Gewitz Real time detection of DNA RNA hybridization in living cells Proc Natl Acad Sci USA 95 1998 11538 11543
48. J Dai XF Fan J Fang ZR Xu Study on temperature measurement and control for microfluidic systems Spectroscopy Spectral Anal 28 2008 148 152
49. V Barsky A Perov S Tokalov A Chudinov E Kreindlin A Sharonov E Kotova A Mirzabekov Fluorescence data analysis on gel-based biochips J Biomol Screening 7 2002 247 257
50. SC Karm YG Ju HG Joo Portable antigen detector using blue laser diodes and quantum dots Japn J Appl Phys Part 1 46 2007 1763 1767
51. YH Kim KS Shin JY Kang EG Yang KK Paek DS Seo BK Ju Poly(dimethylsiloxane)-based packaging technique for microchip fluorescence detection system applications J Microelectromech Systems 15 2006 1152 1158
52. KS Shin YH Kim JA Min SM Kwak SK Kim EG Yang JH Park BK Ju TS Kim JY Kang Miniaturized fluorescence detection chip for capillary electrophoresis immunoassay of agricultural herbicide atrazine Anal Chim Acta 573 2006 164 171
53. A Tibuzzi G Rea G Pezzotti D Esposito U Johanningmeier MT Giardi A new miniaturized multiarray biosensor system for fluore scence detection J Physics Condensed Matter 19 2007 10.1088/0953–8984/19/39/395006 395006