target RNA. Nucleic Acids Res 36(12):e69.
doi:10.1093/nar/gkn331
- Wu Y, Yang CJ, Moroz LL, Tan W (2008)
Nucleic acid beacons for long-term real-time
intracellular monitoring. Anal Chem 80
(8):3025–3028. doi:10.1021/ac702637w
- Rhee WJ, Bao G (2009) Simultaneous detec-
tion of mRNA and protein stem cell markers in
live cells. BMC Biotechnol 9:30. doi:10.1186/
1472-6750-9-30
- Catrina IE, Marras SA, Bratu DP (2012) Tiny
molecular beacons: LNA/2^0 -O-methyl RNA
chimeric probes for imaging dynamic mRNA
processes in living cells. ACS Chem Biol 7
(9):1586–1595. doi:10.1021/cb300178a
- Santangelo P, Nitin N, LaConte L, Woolums
A, Bao G (2006) Live-cell characterization and
analysis of a clinical isolate of bovine respiratory
syncytial virus, using molecular beacons. J Virol
80(2):682–688. doi:10.1128/JVI.80.2.682-
688.2006
- Wang A, Salazar AM, Yates MV, Mulchandani
A, Chen W (2005) Visualization and detection
of infectious coxsackievirus replication using a
combined cell culture-molecular beacon assay.
Appl Environ Microbiol 71(12):8397–8401.
doi:10.1128/AEM.71.12.8397-8401.2005
- Wang W, Cui ZQ, Han H, Zhang ZP, Wei HP,
Zhou YF, Chen Z, Zhang XE (2008) Imaging
and characterizing influenza A virus mRNA
transport in living cells. Nucleic Acids Res 36
(15):4913–4928. doi:10.1093/nar/gkn475
- Yeh HY, Yates MV, Mulchandani A, Chen W
(2008) Visualizing the dynamics of viral repli-
cation in living cells via Tat peptide delivery of
nuclease-resistant molecular beacons. Proc
Natl Acad Sci U S A 105(45):17522–17525.
doi:10.1073/pnas.0807066105
- Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S,
Etkin LD (2005) Potential structural role of
non-coding and coding RNAs in the organiza-
tion of the cytoskeleton at the vegetal cortex of
Xenopus oocytes. Development 132
(15):3445–3457. doi:10.1242/dev.01919
- Yang L, Lin C, Liu W, Zhang J, Ohgi KA,
Grinstein JD, Dorrestein PC, Rosenfeld MG
(2011) ncRNA- and Pc2 methylation-
dependent gene relocation between nuclear
structures mediates gene activation programs.
Cell 147(4):773–788. doi:10.1016/j.cell.
2011.08.054
- Chen AK, Behlke MA, Tsourkas A (2009) Sub-
cellular trafficking and functionality of 2^0 -O-
methyl and 2^0 -O-methyl-phosphorothioate
molecular beacons. Nucleic Acids Res 37(22):
e149. doi:10.1093/nar/gkp837
- Zhao D, Yang Y, Qu N, Chen M, Ma Z, Krue-
ger CJ, Behlke MA, Chen AK (2016) Single-
molecule detection and tracking of RNA tran-
scripts in living cells using phosphorothioate-
optimized 2^0 -O-methyl RNA molecular bea-
cons. Biomaterials 100:172–183. doi:10.
1016/j.biomaterials.2016.05.022
- Chen AK, Cheng Z, Behlke MA, Tsourkas A
(2008) Assessing the sensitivity of commer-
cially available fluorophores to the intracellular
environment. Anal Chem 80(19):7437–7444.
doi:10.1021/ac8011347
Optimizing Molecular Beacons 257