The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry

Nucleic Acids Research

Volumn 41, Issue 9, 2013, Pages

  Adams, Nicholas M ^a,b   Olmsted, Ian R ^a   Haselton, Frederick R ^b   Bornhop, Darryl J ^b,c   Wright, David W ^a  

^a VANDERBILT UNIVERSITY   (United States)

^b VANDERBILT UNIVERSITY   (United States)

^c VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LOCKED NUCLEIC ACID; NUCLEOTIDE; VIRUS RNA;

ARTICLE; BACKSCATTERING INTERFEROMETRY; BASE PAIRING; COMPUTER PROGRAM; CONTROLLED STUDY; DNA PROBE; HYBRIDIZATION; INTERFEROMETRY; MOLECULAR INTERACTION; NONHUMAN; NUCLEIC ACID PROBE; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; RESPIRATORY SYNCYTIAL PNEUMOVIRUS; RNA ANALYSIS; RNA FOLDING; VIRUS NUCLEOCAPSID;

INTERFEROMETRY; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; NUCLEOCAPSID PROTEINS; OLIGONUCLEOTIDE PROBES; OLIGONUCLEOTIDES; RNA; RNA FOLDING; RNA, VIRAL;

EID: 84877256700     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt165     Document Type: Article

References (27)

1. Bordelon, H., Adams, N.M., Klemm, A.S., Russ, P.K., Williams, J.V., Talbot, H.K., Wright, D.W. and Haselton, F.R. (2011) Development of a low-resource RNA extraction cassette based on surface tension valves. ACS Appl. Mater. Interfaces, 3, 2161-2168.
2. Bae, H.-G., Nitsche, A., Teichmann, A., Biel, S.S. and Niedrig, M. (2003) Detection of yellow fever virus: a comparison of quantitative real-time PCR and plaque assay. J. Virol. Methods, 110, 185-191.
3. Jayagopal, A., Halfpenny, K.C., Perez, J.W. and Wright, D.W. (2010) Hairpin DNA-functionalized gold colloids for the imaging of mRNA in live cells. J. Am. Chem. Soc., 132, 9789-9796.
4. Mehlmann, M., Dawson, E.D., Townsend, M.B., Smagala, J.A., Moore, C.L., Smith, C.B., Cox, N.J., Kuchta, R.D. and Rowlen, K.L. (2006) Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus. J. Clin. Microbiol., 44, 2857-2862.
5. Marras, S.A.E., Tyagi, S. and Kramer, F.R. (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin. Chim. Acta, 363, 48-60.
6. Nam, J.-M., Stoeva, S.I. and Mirkin, C.A. (2004) Bio-Bar-Code-based DNA detection with PCR-like sensitivity. J. Am. Chem. Soc., 126, 5932-5933.
7. Zhang, J., Lang, H.P., Huber, F., Bietsch, A., Grange, W., Certa, U., McKendry, R., Guntherodt, H.J., Hegner, M. and Gerber, C. (2006) Rapid and label-free nanomechanical detection of biomarker transcripts in human RNA. Nat. Nanotechnol., 1, 214-220.
8. Springer, T., Piliarik, M. and Homola, J. (2010) Surface plasmon resonance sensor with dispersionless microfluidics for direct detection of nucleic acids at the low femtomole level. Sensor. Actuator. B Chem., 145, 588-591.
9. Bornhop, D.J., Latham, J.C., Kussrow, A., Markov, D.A., Jones, R.D. and Sorensen, H.S. (2007) Free-solution, label-free molecular interactions studied by back-scattering interferometry. Science, 317, 1732-1736.
10. Kussrow, A., Enders, C.S., Castro, A.R., Cox, D.L., Ballard, R.C. and Bornhop, D.J. (2010) The potential of backscattering interferometry as an in vitro clinical diagnostic tool for the serological diagnosis of infectious disease. Analyst, 135, 1535-1537.
11. Kussrow, A., Enders, C.S. and Bornhop, D.J. (2011) Interferometric methods for label-free molecular interaction studies. Anal. Chem., 84, 779-792.
12. Olmsted, I.R., Xiao, Y., Cho, M., Csordas, A.T., Sheehan, J.H., Meiler, J., Soh, H.T. and Bornhop, D.J. (2011) Measurement of aptamer-protein interactions with back-scattering interferometry. Anal. Chem., 83, 8867-8870.
13. Latham, J.C., Markov, D.A., Sorensen, H.S. and Bornhop, D.J. (2005) Photobiotin surface chemistry improves label-free interferometric sensing of biochemical interactions. Angew. Chem., 118, 969-972.
14. Baksh, M.M., Kussrow, A.K., Mileni, M., Finn, M. and Bornhop, D.J. (2011) Label-free quantification of membrane-ligand interactions using backscattering interferometry. Nat. Biotechnol., 29, 357-360.
15. Pesciotta, E.N., Bornhop, D.J. and Flowers, R.A. II (2011) Back-scattering interferometry: a versatile platform for the study of free-solution versus surface-immobilized hybridization. Chem.-Asian J., 6, 70-73.
16. Perez, J.W., Vargis, E.A., Russ, P.K., Haselton, F.R. and Wright, D.W. (2011) Detection of respiratory syncytial virus using nanoparticle amplified immuno-polymerase chain reaction. Anal. Biochem., 410, 141-148.
17. Perez, J.W., Haselton, F.R. and Wright, D.W. (2009) Viral detection using DNA functionalized gold filaments. Analyst, 134, 1548-1553.
18. Markov, D., Begari, D. and Bornhop, D.J. (2002) Breaking the 10-7 barrier for RI measurements in nanoliter volumes. Anal. Chem., 74, 5438-5441.
19. Vester, B. and Wengel, J. (2004) LNA (Locked Nucleic Acid): high-affinity targeting of complementary RNA and DNA. Biochemistry, 43, 13233-13241.
20. Petersen, M., Bondensgaard, K., Wengel, J. and Jacobsen, J.P. (2002) Locked Nucleic Acid (LNA) Recognition of RNA: NMR solution structures of LNA:RNA hybrids. J. Am. Chem. Soc., 124, 5974-5982.
21. Ivanov, V.I., Minchenkova, L.E., Minyat, E.E., Frank-Kamenetskii, M.D. and Schyolkina, A.K. (1974) The B to A transition of DNA in solution. J. Mol. Biol., 87, 817-833.
22. Kypr, J., Kejnovska, I., Renciuk, D. and Vorlickova, M. (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res., 37, 1713-1725.
23. Wiese, K.C. and Hendriks, A. (2006) Comparison of P-RnaPredict and mfold-algorithms for RNA secondary structure prediction. Bioinformatics, 22, 934-942.
24. Braasch, D.A. and Corey, D.R. (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem. Biol., 8, 1-7.
25. Robertson, K.L. and Thach, D.C. (2009) LNA flow-FISH: a flow cytometry-fluorescence in situ hybridization method to detect messenger RNA using locked nucleic acid probes. Anal. Biochem., 390, 109-114.
26. Tran Tan, T., Pawestri, H., My, N., Minh, H., Syahrial, H., Vu, T., van Doorn, H.R., Wertheim, H., Van Vinh, C., Quang, H. et al. (2010) A real-time RT-PCR for detection of clade 1 and 2 H5N1 influenza A virus using Locked Nucleic Acid (LNA) TaqMan probes. Virol. J., 7, 46.
27. Nielsen, K.E., Rasmussen, J., Kumar, R., Wengel, J., Jacobsen, J.P. and Petersen, M. (2004) NMR studies of fully modified Locked Nucleic Acid (LNA) hybrids: solution structure of an LNA:RNA hybrid and characterization of an LNA:DNA hybrid. Bioconjugate Chem., 15, 449-457.