This work was supported by the National Science Foundation CAREER Award (0953583) and the National Institute of Health NCI/R21-CA116102, NCI/R21-CA125088, NIBIB/R01-EB012065, NCI/R01-CA157766.

In this protocol, one oligonucleotide (RBMB1) was labeled at its 5&#8217;-end with a CF640R reporter dye and has the sequence: 5&#8217;-mCmUmUmC mGmUmC mCmAmC mAmAmA mCmAmC mAmAmC mUmCmC mU mGmAmAmG mGmAmC mGmGmC mAmGmC mGmUmG mCmAmG mCmUmC mUmU-3&#8217;. Self-complementary domains, which drive the formation of the hairpin structure, are in bold. The second oligonucleotide (RBMB2) was labeled at the 3&#8217;-end with an Iowa Black RQ-Sp quencher and has the sequence: 5&#8217;-mGmAmG mCmUmG mCmAmC mGmCmU mGmCmC mGmUmC-3&#8217;.
1. Preparation of RBMBs
<ol>
	<li>Perform a quick spin of the tubes containing the RBMB1 and RBMB2 oligonucleotides, to ensure the dried oligonucleotide is at the bottom of the tube, and resuspend in DNase and RNase-free water to a final concentration of 100 &#956;M. For example, a 10 nmole sample of oligonucleotide should be resuspended in 100 &#956;l of water.</li>
	<li>Measure the exact concentration of RBMB1 and RBMB2 stock samples by UV-vis spectroscopy.
	<ol>
		<li>Mix 3 &#956;l of the RBMB sample with 117 &#956;l DPBS (without calcium and magnesium) in a microcentrifuge tube.</li>
		<li>Blank the spectrophotometer with DPBS and measure the absorbance from 200-800 nm. Note: Peak absorbances at 260 nm and 650 nm should be visible.</li>
		<li>Calculate the stock concentration of the RBMB samples based on the absorbance at 260 nm (or 650 nm for RBMB1), using the equation: 
		Stock Concentration (M) = A260* dilution factor/extinction coefficient where A260 is the absorbance at 260 nm and the Dilution factor is 40. 
		Note: The extinction coefficient for the RBMB can be found on the specification sheet provided by the oligonucleotide manufacturer. The extinction coefficient of CF640R at 650 nm is 103,000.</li>
	</ol>
	</li>
	<li>Mix 20 &#956;l of 100 &#956;M RBMB1, 30 &#956;l of 100 &#956;M RBMB2, 6 &#956;l 10x&#160;phosphate buffer (10x&#160;phosphate buffer: 480 mM K2HPO4, 45 mM KH2PO4, 140 mM NaH2PO4, pH 7.2) and 4 &#956;l DNase and RNase-free water. Incubate the mixture at room temperature for 30 min. Note: This is typically sufficient for approximately 50 studies.</li>
	<li>Prepare a liquid chromatography column using 75 prep grade Superdex to remove any unhybridized RBMB2 oligonucleotides. Use an 8 mL (0.7 x 20 cm) liquid chromatography column with a ~4 ml bed volume to purify the small volume of mixed probes.</li>
	<li>Wash and equilibrate the Superdex with ~50 ml of 1x&#160;phosphate buffer using a syringe pump running at a flow at a flow rate of 0.6 ml/min. Before all of the fluid enters the bed volume, stop the syringe pump, detach it, and let the remaining liquid go through the column by gravity.</li>
	<li>Load the RBMB mixture (60 &#956;l) onto the chromatography column.
	<ol>
		<li>After the RBMB sample has completely entered the bed, slowly add another 250 &#956;l of 1x&#160;phosphate buffer to the top of the bed to ensure that the entire sample has completely entered the column.</li>
		<li>Fill the column to the rim with 1x&#160;phosphate buffer. Close the top, and start the syringe pump - the syringe should be filled with ~50 ml 1x&#160;PBS and run at a flow rate of 0.6 ml/min.</li>
		<li>Once the RBMB nears the bottom of the column &#8211; the RBMB sample can typically be readily visualized due to the color of the dye incorporated into the probe &#8211; collect the flow-through at 2 drops per microcentrifuge tube (1.5 ml). Stop collecting the sample once the color within the microcentrifuge tubes becomes clear.</li>
	</ol>
	</li>
	<li>Combine the tubes containing the colored RBMB sample &#8211; typically 5-6 tubes - and load into a centrifugal filter device (10,000 MW cutoff). Centrifuge the sample at 10,000 RCF for 20 min or until the desired volume. Note: These speeds and times will typically yield a final volume of ~30 &#956;l.</li>
	<li>Measure the exact concentration of the purified RBMB sample by UV-Vis spectroscopy.
	<ol>
		<li>Take 3 &#956;l of the concentrated RBMB sample and mix with 117 &#956;l DPBS in a microcentrifuge tube.</li>
		<li>Blank the spectrophotometer with DPBS and measure the absorbance from 200-800 nm. Note: Peak absorbances at 260 nm and 650 nm should be visible.</li>
		<li>Calculate the stock concentration of the hybridized RBMB based on the absorbance at 650 nm, using the equation: 
		Stock Concentration (M) = A650* dilution factor/extinct coefficient where A650 is the absorbance at 650 nm, the Dilution factor is 40. 
		Note: The extinction coefficient for CF640R at 650nm is 103,000 and the extinction coefficient for Iowa Black RQ is ~20,000. The extinction coefficients are additive and are not sensitive to hybridization. Therefore, the stock RBMB sample has a combined extinction coefficient of approximately 123,000 at 650 nm.</li>
	</ol>
	</li>
	<li>Label the tube appropriately with name and concentration and store at -20 &#176;C for future use.</li>
</ol>
2. Preparation of Poly-d-lysine Coated 8-well Chambered Coverglass
<ol>
	<li>Prepare a 0.2 mg/ml solution of Poly-D-lysine by dissolving 5 mg of Poly-D-lysine (lyophilized powder, g-irradiated) in 25 ml of sterilized water in a sterile environment.</li>
	<li>Add 200 &#956;l of the 0.2 mg/ml Poly-D-lysine solution to each well of an 8-well chambered coverglass, in a sterile environment.</li>
	<li>Incubate at room temperature for 16-18 hr in the cell culture hood.</li>
	<li>Aspirate the Poly-D-lysine and wash the well 3 times with sterile distilled water. Note: The coated chamber slides can be stored at 4 &#176;C.</li>
</ol>
3. Probe Delivery
Note: The cell system used should contain an integrated gene construct that expresses RNA with at least 4-sequential binding sites for the RBMB in the 3&#8217;-untranslated region (UTR). The target sequences should be complementary to the loop of the RBMB. It is advised that as a negative control, the same cell line be engineered to express the same gene construct, but without the tandem repeats. In this protocol, a human fibrosarcoma cell line, HT1080, was engineered to express gfp RNA with 96-tandem repeats of the RBMB target sequence in the 3&#8217;-UTR. The control cell line was engineered to express wild-type gfp RNA.
<ol>
	<li>Plate cells in a T25 flask at 40-50% confluency one day before probe delivery. Culture the cells with DMEM media supplemented with 1% pen/strep and 10% fetal bovine serum (FBS), and incubate at 37 &#176;C with 5% CO2. </li>
	<li>The next day, turn on the microporator and set up the microporation parameters to 950 V, 2 pulses, 25 msec. Note: These parameters have been optimized for HT1080 cells, but they are cell-type dependent and can be adjusted for other cell types as described in the manufacturer&#8217;s instructions.</li>
	<li>Fill the microporation tube with 4 ml electrolytic buffer and place it on the microporation station.</li>
	<li>Take out the stock sample of purified RBMB and defrost it. Dilute several microliters to a final concentration of 12 &#956;M with 1x&#160;phosphate buffer. 1 &#956;l is needed for each microporation.</li>
	<li>Pipette 1 ml of culture medium with FBS but without antibiotics into a microcentrifuge tube. Note: This will be used to suspend the cells immediately after microporation and can be set aside, near the microporation device, for the time being. The inclusion of antibiotics in culture media will decrease the cell viability after microporation.</li>
	<li>Remove the cell culture media from the engineered HT1080 cells (60-80% confluent), wash the cells with 1 ml Ca2+ and Mg2+-free DPBS once, and incubate with 1 ml trypsin for 1-2 min.</li>
	<li>Stop the trypsinization by adding 1 ml DMEM media supplemented with 10% fetal bovine serum, without antibiotics and phenol red, and transfer the cells into two 1.5 ml microcentrifuge tubes.</li>
	<li>Spin down the cells in the microcentrifuge tube at 200 x g for 5 min. Remove the supernatant, resuspend and combine the cell pellets in a final volume of 1 ml DPBS.</li>
	<li>Take 10 &#956;l from the well-mixed cell suspension and count the cells.</li>
	<li>Pipette the cells up and down several times to make sure they are well dispersed and transfer 300,000 cells with DPBS into a new 1.5 ml microcentrifuge tube and spin down at 200 x g for 5 min.</li>
	<li>Remove the supernatant, being careful not to disturb the cell pellet. Resuspend the pellet in 11 &#956;l resuspension buffer and pipette up and down several times to ensure that the cells are well dispersed. Be sure not to generate any air bubbles. Note: Air bubbles will cause a spark during microporation and result in poor RBMB delivery and cell death.</li>
	<li>Add 1 &#956;l of the diluted RBMB (12 &#956;M) and mix well by pipetting up and down several times. Again be careful not to generate any air bubbles.</li>
	<li>Aspirate 10 &#956;l of the RBMB-cell mixture, using the microporation pipette, and insert the pipette into the microporation tube. Push the start button to start the microporation. Note: There should be no visible air bubbles in the tip.</li>
	<li>When the screen of the microporator shows completion, remove the pipette from the station, expel the 10 &#956;l mixture into the microcentrifuge tube that was prepared earlier, with 1 ml culture medium with FBS but without antibiotics. Mix gently by rocking the tube side-to-side several times.</li>
	<li>Spin the cells at 200 x g for 5 min and wash the cells two more times, in 1 ml phenol red free culture medium with FBS but without antibiotics, to remove any RBMBs that were not delivered into the cells. Resuspend with 400 &#956;l phenol red free culture medium with FBS but without antibiotics.</li>
	<li>Plate the microporated cells into the Poly-D-lysine coated 8-well chambered coverglass at 200 &#956;l per well or at the desired confluency.</li>
	<li>Optional: If it is desirable to image the nucleus, add Hoescht 33342 to the cells at a final concentration of 0.01 mg/ml.</li>
	<li>Place the chambered coverglass into a cell culture incubator. Incubate the cells for 1-2 hr prior to imaging, so that the cells have adequate time to settle down on the coverglass surface. Note: Imaging can be performed as soon as 30 min post-microporation.</li>
</ol>
4. Image Acquisition
<ol>
	<li>Turn on the live cell stage top incubation system and equilibrate it until it reaches 37 &#176;C, 5% CO2, and 75% humidity.</li>
	<li>Turn on the microscope and fluorescent light source and open the Metamorph software. Note: Other similar software packages for microscope control and image acquisition can also be used.</li>
	<li>Apply Immersol oil to the objective.</li>
	<li>Transfer the chambered coverglass with microporated cells to the live cell stage top incubation system. Incubate the stage top system until the temperature and CO2 levels are stabilized.</li>
	<li>Open the Acquire tab, in Metamorph software. Click the Show Live button to find the field, adjust the focus under white light and click the Stop Live button.</li>
	<li>Under the Acquire tab, click and open the stream acquisition pop-up button, and set up the desired movie acquisition parameters. Acquire 150 frames using the Cy5/CF640R filter and save the images to the hard drive.</li>
</ol>

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J., Pinto, M., Schanze, K., Tan, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+synthesis+of+an+oligonucleotide-poly(phenylene+ethynylene)+conjugate+with+a+precise+one-to-one+molecular+ratio.">Direct synthesis of an oligonucleotide-poly(phenylene ethynylene) conjugate with a precise one-to-one molecular ratio.</a> Angew Chem Int Ed Engl. 44 (17), 2572-2576 (2005).</li><li>Lu, J., Tsourkas, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+individual+microRNAs+in+single+mammalian+cells+in+situ.">Imaging individual microRNAs in single mammalian cells in situ.</a> Nucleic Acids Res. 37 (14), e100 (2009).</li><li>Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., Tyagi, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stochastic+mRNA+synthesis+in+mammalian+cells.">Stochastic mRNA synthesis in mammalian cells.</a> PLoS Biol. 4 (10), e309 (2006).</li></ol>

Dr. Mark Behlke and Dr. Ling Huang are employed by IDT which offers oligonucleotides for sale similar to some of the compounds described in the manuscript. IDT is, however, not a publicly traded company and they personally do not own any shares/equity in IDT.

The ability to image single engineered RNA transcripts in living cells using a conventional wide-field microscope requires a bright and photostable fluorescent signal to be associated with each RNA transcript and a low fluorescent background emanating from unbound fluorescent probes. In this method, a bright fluorescent signal is achieved by hybridizing multiple (up to 96) oligonucleotide-based fluorescent probes, i.e. RBMBs, onto each RNA transcript. However, as few as four bindings sites are sufficient16<...

The expression and regulation of RNA transcripts is a complex and dynamic process that is largely responsible for controlling cell behavior and fate.&#160; Although the importance of RNA in dictating cell function has been known for some time, it is often difficult to draw clear connections between the two since most RNA analysis tools lack the spatial and temporal resolution required to capture important regulatory events such as transcription bursting, RNA trafficking, and localized RNA processing. This has led to the advent of several techniques that allow individual RNA transcripts to be visualized in living cells in real-time1. Perhaps, the most prominent of these techniques utilizes a GFP-MS2 fusion protein to target RNA that has been engineered to contain tandem repeats of the MS2 binding site in the 3&#8217;-UTR2,3. By bringing multiple GFP molecules into close proximity, individual RNA transcripts appear as bright fluorescent spots via fluorescence microscopy. The GFP-MS2 system has provided unprecedented insight into RNA behavior, including direct visualization and measurements of transcriptional bursting4,5, detection of unique sub-cellular localization and processing6-9, and real-time imaging of RNA transport10. However, despite the tremendous potential of the GFP-MS2 system, unbound GFP-MS2 fusion proteins can create a high background fluorescent signal that limits the versatility and dynamic range of this technique.&#160; Several approaches have been developed to limit this background signal, including subcellular compartmentalization of unbound GFP-MS210, protein fragment complementation11, and alternative RNA binding proteins and targets12.&#160; However, all of these approaches remain sensitive to the relative and total expression of the RNA target and GFP-MS2 fusion protein.

As an alternative to the GFP-MS2 systems, molecular beacons have also been used to detect engineered RNA transcripts with tandem repeats of the complementary binding site in the 3&#8217;-UTR13,14. Molecular beacons are hairpin-forming oligonucleotide probes that are labeled at one end with a quencher and at the other end with a fluorescent reporter. When not bound to target RNA the fluorescent reporter and quencher remain in close proximity, resulting in a low-fluorescent state. Upon hybridization, the fluorescent reporter and quencher are forced apart and fluorescence is restored. Similar to the GFP-MS2 system, the binding of multiple molecular beacons onto a single RNA transcript results in a bright fluorescent spot that can be identified by fluorescence microscopy; however, the background fluorescence is expected to be much lower, due to the quenched configuration of unbound molecular beacons. Unfortunately, despite the clever activation mechanism that is incorporated into the molecular beacon design, there is now growing evidence that unhybridized molecular beacons do not remain in the hairpin conformation when introduced into living cells.&#160; Consequently, they generate a false-positive signal that significantly reduces the signal-to-background. To overcome this shortcoming, we recently developed a new synthetic probe for imaging RNA in living cells, ratiometric bimolecular beacons (RBMBs; Figure 1A)15,16. RBMBs are composed of two 2&#8217;-O-methyl oligonucleotide strands that form a hybrid structure with features from both short hairpin RNA (shRNA) and molecular beacons.&#160; The loop and fluorescence activation mechanism is similar to the molecular beacon, while the long double stranded domain with a 3&#8217;-UU overhang is more characteristic of shRNA.&#160; The shRNA features are designed to drive nuclear export, which we have found increases intracellular lifetime to &#62;24 hr, with minimal observable degradation, and prevents non-specific opening of the loop. As a result RBMBs exhibit a significantly higher signal-to-background than molecular beacons.

It should be noted that RBMBs cannot be prepared using DNA oligonucleotides, since DNA-based probes do not possess the same nuclear export capabilities as RNA-based probes. Structurally, the RBMB loop is typically designed to be between 15 and 21 bases long, to create a balance between specificity and selectivity upon RNA hybridization.&#160; The short stem that forms from the two self-complementary domains is usually designed to be 4 bases.&#160; If a longer stem is selected, the rate of hybridization between the RBMB loop and target RNA is significantly slowed17,18. Conversely, when a shorter stem sequence is selected the melting temperature is often too low to sustain the stem-loop structure at 37 &#176;C, leading to a high background signal. The specificity of the RBMB is also reduced as the stem length is shortened. Since the sequence of the RBMB stem-loop can also influence RBMB performance, it must be carefully selected19. In particular, ideal loop sequences should have minimal secondary structure, hybridize to RNA sequences with minimal secondary structure, avoid protein binding sites, and avoid off-target binding. Predictions of both RBMB and RNA secondary structure can be obtained using software such as mfold20. Complementary off-target sites can identified using a nucleotide Basic Local Assignment Search Tool (BLAST).&#160; However, because of inconsistencies in model predictions and the difficulty in identifying protein-biding sites, the specificity of all RBMBs must ultimately be validated experimentally.

If desirable, an unquenched reference dye that is insensitive to the hybridization state can be added to the RBMB15.&#160; The addition of a reference dye can provide a marker for probe delivery and be used for ratiometric imaging, if more accurate measurements of total cellular fluorescence are required.&#160; The reference dyes allows measurements to be adjusted for differences in background owing to cell-to-cell variations in delivery.&#160; However, when imaging individual RNA transcripts the reference dye is not necessary. Notably, some reference dyes can interfere with the export of RBMBs from the nucleus, leading to a slightly higher background signal in the nucleus.

When designed properly, RBMBs can be used to image individual RNA transcripts in single living cells, if the target RNA is engineered to contain at least four RBMB binding sites (Figure 1B)16. RBMBs can be efficiently delivered into a wide range of cells types via microporation, with little to no effect on cell viability21, and quantitative measurements of gene expression can be acquired within 30 min.&#160; Moreover, the methodology is fairly insensitive to RBMB concentration and target RNA levels, since fluorescence from unbound RBMBs is efficiently quenched. Here we provide a detailed description of the methodology used to prepare and purify RBMBs, as well as a general procedure for the delivery of RBMBs into live-cells via microporation and the imaging of single RNA transcripts in real-time.

<table border="0" cellpadding="0" cellspacing="0" width="977">
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			<td style="width:220px;">AM9932</td>
			<td style="width:244px;">no DEPC-treated</td>
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			<td height="21" style="height:21px;width:307px;">DPBS</td>
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			<td>14190-144</td>
			<td>No Ca2+ and Mg2+</td>
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			<td height="21" style="height:21px;width:307px;">Cary 100 UV-Vis Spectrophotometer</td>
			<td style="width:207px;">Agilent Technologies</td>
			<td style="width:220px;"></td>
			<td></td>
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			<td height="21" style="height:21px;width:307px;">Potassium Phosphate Dibasic</td>
			<td style="width:207px;">Fisher Scientific</td>
			<td style="width:220px;">P290-500</td>
			<td></td>
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			<td height="21" style="height:21px;width:307px;">Potassium Phosphate Monobasic</td>
			<td style="width:207px;">Fisher Scientific</td>
			<td style="width:220px;">P284-500&#160;</td>
			<td></td>
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			<td height="21" style="height:21px;width:307px;">Sodium Phosphate Monobasic</td>
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			<td style="width:220px;">S381-500</td>
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		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Microcentrifuge tubes</td>
			<td style="width:207px;">Eppendorf</td>
			<td style="width:220px;">22364111</td>
			<td>1.5mL</td>
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			<td height="21" style="height:21px;width:307px;">Chromatography Column</td>
			<td style="width:207px;">Kimble Chase Life Science</td>
			<td style="width:220px;">420400-0720</td>
			<td>0.7x20cm</td>
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			<td height="21" style="height:21px;width:307px;">Superdex 75 Prep Grade</td>
			<td style="width:207px;">GE healthcare</td>
			<td style="width:220px;">17-1044-01&#160;</td>
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			<td height="21" style="height:21px;width:307px;">Syringe Pump</td>
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			<td height="21" style="height:21px;width:307px;">Centrifugal Filter Units</td>
			<td style="width:207px;">Millipore</td>
			<td style="width:220px;">UFC501096</td>
			<td>Mw 10,000 cutoff</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Centrifuge 5418</td>
			<td style="width:207px;">Eppendorf</td>
			<td style="width:220px;"></td>
			<td></td>
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			<td height="21" style="height:21px;width:307px;">Poly-D-lysine</td>
			<td>Sigma-Aldrich</td>
			<td style="width:220px;">P7280-5MG</td>
			<td>lyophilized powder, g-irradiated</td>
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			<td height="21" style="height:21px;width:307px;">8-well chambered coverglass</td>
			<td style="width:207px;">Fisher Scientific</td>
			<td style="width:220px;">155409</td>
			<td>Working volume 0.2-0.5mL</td>
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			<td height="21" style="height:21px;width:307px;">HT1080</td>
			<td style="width:207px;">ATCC</td>
			<td style="width:220px;">CCL-121</td>
			<td>Human Fibrosarcoma cell line</td>
		</tr>
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			<td height="21" style="height:21px;width:307px;">Cell Culture Flask</td>
			<td style="width:207px;">Corning</td>
			<td style="width:220px;">430639</td>
			<td>25cm2</td>
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			<td height="21" style="height:21px;width:307px;">DMEM</td>
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			<td>High glucose</td>
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			<td height="21" style="height:21px;width:307px;">DMEM without Phenol Red</td>
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			<td style="width:220px;">21063029</td>
			<td>High glucose</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Fetal Bovine Serum</td>
			<td style="width:207px;">Sigma-Aldrich</td>
			<td style="width:220px;">F2442-500ML&#160;</td>
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			<td height="21" style="height:21px;width:307px;">Penecillin/Streptomycin</td>
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			<td style="width:220px;">15140122</td>
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			<td height="21" style="height:21px;width:307px;">Trypsin</td>
			<td style="width:207px;">Life Technologies</td>
			<td style="width:220px;">25300054</td>
			<td>0.05% Trypsin-EDTA</td>
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		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Neon transfection system</td>
			<td style="width:207px;">Life Technologies</td>
			<td style="width:220px;">MPK5000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Neon transfection system kit&#160;</td>
			<td style="width:207px;">Life Technologies</td>
			<td style="width:220px;">MPK1096</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:307px;">Hemacytometer</td>
			<td style="width:207px;">Fisher Scientific</td>
			<td style="width:220px;">02-671-10&#160;</td>
			<td></td>
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			<td height="21" style="height:21px;">Hoescht 33342</td>
			<td style="width:207px;">Life Technologies</td>
			<td style="width:220px;">H1399</td>
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			<td height="21" style="height:21px;width:307px;">IX-81 Inverted fluorescence microscope&#160;</td>
			<td style="width:207px;">Olympus</td>
			<td style="width:220px;"></td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:307px;">SOLA light engine</td>
			<td style="width:207px;">Lumencor</td>
			<td style="width:220px;"></td>
			<td></td>
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			<td height="21" style="height:21px;width:307px;">Metamorph</td>
			<td style="width:207px;">Molecular Devices</td>
			<td style="width:220px;"></td>
			<td>Software controlling microscope</td>
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			<td height="21" style="height:21px;">Immersol oil 518F</td>
			<td style="width:207px;">Fisher Scientific</td>
			<td style="width:220px;">12-624-66B&#160;</td>
			<td></td>
		</tr>
	</tbody>
</table>

real-time imaging of single engineered rna transcripts in living cells using ratiometric bimolecular beacons

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3&#8217;-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.

Shortly following the microporation of HT1080 cells in the presence of RBMBs, individual RNA transcripts that were engineered to contain multiple RBMB binding sites in their 3&#8217;-UTR appear as bright fluorescent spots when imaged by wide-field fluorescence microscopy (Figure 2). While individual RNA transcripts with as few as four RBMB binding sites can be imaged in live-cells, the more RBMB binding sites in the 3&#8217;-UTR, the stronger the fluorescent signal.&#160; Moreover, the more RBMBs that ar...

Watch this Scientific Journal Video about Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons at JoVE.com

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Ratiometric bimolecular beacons (RBMBs) can be used to image single engineered RNA transcripts in living cells. Here, we describe the preparation and purification of RBMBs, delivery of RBMBs into cells by microporation and fluorescent imaging of single RNA transcripts in real-time.

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the ...

real-time-imaging-single-engineered-rna-transcripts-living-cells

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Biology

11.7K Views.  University of Pennsylvania. Ratiometric bimolecular beacons (RBMBs) can be used to image single engineered RNA transcripts in living cells. Here, we describe the preparation and purification of RBMBs, delivery of RBMBs into cells by microporation and fluorescent imaging of single RNA transcripts in real-time.

Video: Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Imaging Cell Shape Change in Living Drosophila Embryos

The developing Drosophila melanogaster embryo undergoes a number of cell shape changes that are highly amenable to live confocal imaging. Cell shape changes in the fly are analogous to those in higher organisms, and they drive tissue morphogenesis. So, in many cases, their study has direct implications for understanding human disease (Table 1)1-5. On the sub-cellular scale, these cell shape changes are the product of activities ranging from gene expression to signal transduction, cell polarity, cytoskeletal remodeling and membrane trafficking. Thus, the Drosophila embryo provides not only the context to evaluate cell shape changes as they relate to tissue morphogenesis, but also offers a completely physiological environment to study the sub-cellular activities that shape cells.
The protocol described here is designed to image a specific cell shape change called cellularization. Cellularization is a process of dramatic plasma membrane growth, and it ultimately converts the syncytial embryo into the cellular blastoderm. That is, at interphase of mitotic cycle 14, the plasma membrane simultaneously invaginates around each of ~6000 cortically anchored nuclei to generate a sheet of primary epithelial cells. Counter to previous suggestions, cellularization is not driven by Myosin-2 contractility6, but is instead fueled largely by exocytosis of membrane from internal stores7. Thus, cellularization is an excellent system for studying membrane trafficking during cell shape changes that require plasma membrane invagination or expansion, such as cytokinesis or transverse-tubule (T-tubule) morphogenesis in muscle.
Note that this protocol is easily applied to the imaging of other cell shape changes in the fly embryo, and only requires slight adaptations such as changing the stage of embryo collection, or using "embryo glue" to mount the embryo in a specific orientation (Table 1)8-19. In all cases, the workflow is basically the same (Figure 1). Standard methods for cloning and Drosophila transgenesis are used to prepare stable fly stocks that express a protein of interest, fused to Green Fluorescent Protein (GFP) or its variants, and these flies provide a renewable source of embryos. Alternatively, fluorescent proteins/probes are directly introduced into fly embryos via straightforward micro-injection techniques9-10. Then, depending on the developmental event and cell shape change to be imaged, embryos are collected and staged by morphology on a dissecting microscope, and finally positioned and mounted for time-lapse imaging on a confocal microscope.

Imaging Cell Shape Change in Living Drosophila Embryos

Early development of the fruit fly, Drosophila melanogaster, is characterized by a number of cell shape changes that are well suited for imaging approaches. This article will describe basic tools and methods required for live confocal imaging of Drosophila embryos, and will focus on a cell shape change called cellularization.

The developing Drosophila melanogaster embryo undergoes a number of cell shape changes that are highly amenable to live confocal imaging.  Cell shape ...

Measuring the Kinetics of mRNA Transcription in Single Living Cells

The transcriptional activity of RNA polymerase II (Pol II) is a dynamic process and therefore measuring the kinetics of the transcriptional process in vivo is of importance. Pol II kinetics have been measured using biochemical or molecular methods.1-3 In recent years, with the development of new visualization methods, it has become possible to follow transcription as it occurs in real time in single living cells.4 Herein we describe how to perform analysis of Pol II elongation kinetics on a specific gene in living cells.5, 6 Using a cell line in which a specific gene locus (DNA), its mRNA product, and the final protein product can be fluorescently labeled and visualized in vivo, it is possible to detect the actual transcription of mRNAs on the gene of interest.7, 8 The mRNA is fluorescently tagged using the MS2 system for tagging mRNAs in vivo, where the 3'UTR of the mRNA transcripts contain 24 MS2 stem-loop repeats, which provide highly specific binding sites for the YFP-MS2 coat protein that labels the mRNA as it is transcribed.9 To monitor the kinetics of transcription we use the Fluorescence Recovery After Photobleaching (FRAP) method. By photobleaching the YFP-MS2-tagged nascent transcripts at the site of transcription and then following the recovery of this signal over time, we obtain the synthesis rate of the newly made mRNAs.5 In other words, YFP-MS2 fluorescence recovery reflects the generation of new MS2 stem-loops in the nascent transcripts and their binding by fluorescent free YFP-MS2 molecules entering from the surrounding nucleoplasm. The FRAP recovery curves are then analyzed using mathematical mechanistic models formalized by a series of differential equations, in order to retrieve the kinetic time parameters of transcription.

RNA polymerase II transcriptional kinetics are measured on specific genes in living cells. mRNAs transcribed from the gene of interest are fluorescently tagged and using Fluorescence Recovery After Photobleaching (FRAP) the in vivo kinetics of transcriptional elongation are obtained.

The transcriptional activity of RNA polymerase II (Pol II) is a dynamic process and therefore measuring the kinetics of the transcriptional process in ...

FRET Microscopy for Real-time Monitoring of Signaling Events in Live Cells Using Unimolecular Biosensors

F&ouml;rster resonance energy transfer (FRET) microscopy continues to gain increasing interest as a technique for real-time monitoring of biochemical and signaling events in live cells and tissues. Compared to classical biochemical methods, this novel technology is characterized by high temporal and spatial resolution. FRET experiments use various genetically-encoded biosensors which can be expressed and imaged over time in situ or in vivo1-2. Typical biosensors can either report protein-protein interactions by measuring FRET between a fluorophore-tagged pair of proteins or conformational changes in a single protein which harbors donor and acceptor fluorophores interconnected with a binding moiety for a molecule of interest3-4. Bimolecular biosensors for protein-protein interactions include, for example, constructs designed to monitor G-protein activation in cells5, while the unimolecular sensors measuring conformational changes are widely used to image second messengers such as calcium6, cAMP7-8, inositol phosphates9 and cGMP10-11. Here we describe how to build a customized epifluorescence FRET imaging system from single commercially available components and how to control the whole setup using the Micro-Manager freeware. This simple but powerful instrument is designed for routine or more sophisticated FRET measurements in live cells. Acquired images are processed using self-written plug-ins to visualize changes in FRET ratio in real-time during any experiments before being stored in a graphics format compatible with the build-in ImageJ freeware used for subsequent data analysis. This low-cost system is characterized by high flexibility and can be successfully used to monitor various biochemical events and signaling molecules by a plethora of available FRET biosensors in live cells and tissues. As an example, we demonstrate how to use this imaging system to perform real-time monitoring of cAMP in live 293A cells upon stimulation with a &beta;-adrenergic receptor agonist and blocker.

F&#246;rster resonance energy transfer (FRET) microscopy is a powerful technique for real-time monitoring of signaling events in live cells using various biosensors as reporters. Here we describe how to build a customized epifluorescence FRET imaging system from commercially available components and how to use it for FRET experiments.

F&ouml;rster resonance energy transfer (FRET) microscopy  continues to gain increasing interest as a technique for real-time monitoring  of biochemical ...

Quantitative, Real-time Analysis of Base Excision Repair Activity in Cell Lysates Utilizing Lesion-specific Molecular Beacons

We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates using base excision repair (BER) molecular beacons. The substrate (beacon) is comprised of a deoxyoligonucleotide containing a single base lesion with a 6-Carboxyfluorescein (6-FAM) moiety conjugated to the 5'end and a Dabcyl moiety conjugated to the 3' end of the oligonucleotide. The BER molecular beacon is 43 bases in length and the sequence is designed to promote the formation of a stem-loop structure with 13 nucleotides in the loop and 15 base pairs in the stem1,2. When folded in this configuration the 6-FAM moiety is quenched by Dabcyl in a non-fluorescent manner via F&ouml;rster Resonance Energy Transfer (FRET)3,4. The lesion is positioned such that following base lesion removal and strand scission the remaining 5 base oligonucleotide containing the 6-FAM moiety is released from the stem. Release and detachment from the quencher (Dabcyl) results in an increase of fluorescence that is proportionate to the level of DNA repair. By collecting multiple reads of the fluorescence values, real-time assessment of BER activity is possible. The use of standard quantitative real-time PCR instruments allows the simultaneous analysis of numerous samples. The design of these BER molecular beacons, with a single base lesion, is amenable to kinetic analyses, BER quantification and inhibitor validation and is adaptable for quantification of DNA Repair activity in tissue and tumor cell lysates or with purified proteins. The analysis of BER activity in tumor lysates or tissue aspirates using these molecular beacons may be applicable to functional biomarker measurements. Further, the analysis of BER activity with purified proteins using this quantitative assay provides a rapid, high-throughput method for the discovery and validation of BER inhibitors.

We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates. The assay yields rates of DNA Repair activity amenable to kinetic analysis and is adaptable for quantification of DNA Repair activity in tissue and tumor lysates or with purified proteins.

We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates using base ...

Fluorescence Imaging with One-nanometer Accuracy (FIONA)

Fluorescence imaging with one-nanometer accuracy (FIONA) is a simple but useful technique for localizing single fluorophores with nanometer precision in the x-y plane. Here a summary of the FIONA technique is reported and examples of research that have been performed using FIONA are briefly described. First, how to set up the required equipment for FIONA experiments, i.e., a total internal reflection fluorescence microscopy (TIRFM), with details on aligning the optics, is described. Then how to carry out a simple FIONA experiment on localizing immobilized Cy3-DNA single molecules using appropriate protocols, followed by the use of FIONA to measure the 36 nm step size of a single truncated myosin Va motor labeled with a quantum dot, is illustrated. Lastly, recent effort to extend the application of FIONA to thick samples is reported. It is shown that, using a water immersion objective and quantum dots soaked deep in sol-gels and rabbit eye corneas (&#62;200 &#181;m), localization precision of 2-3 nm can be achieved.

Fluorescence Imaging with One-nanometer Accuracy FIONA

Single fluorophores can be localized with nanometer precision using FIONA. Here a summary of the FIONA technique is reported, and how to carry out FIONA experiments is described.

Fluorescence imaging with one-nanometer accuracy (FIONA) is a simple but useful technique for localizing single fluorophores with nanometer precision in ...

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes within individual endothelial cells (ECs). These processes are critical for homeostatic maintenance such as wound healing, and are also crucial in promoting tumor growth and metastasis. EC morphology is defined by the organization of the cytoskeleton, a tightly regulated system of actin and microtubule (MT) dynamics that is known to control EC branching, polarity and directional migration, essential components of angiogenesis. To study MT dynamics, we used high-resolution fluorescence microscopy coupled with computational image analysis of fluorescently-labeled MT plus-ends to investigate MT growth dynamics and the regulation of EC branching morphology and directional migration. Time-lapse imaging of living Human Umbilical Vein Endothelial Cells (HUVECs) was performed following transfection with fluorescently-labeled MT End Binding protein 3 (EB3) and Mitotic Centromere Associated Kinesin (MCAK)-specific cDNA constructs to evaluate effects on MT dynamics. PlusTipTracker software was used to track EB3-labeled MT plus ends in order to measure MT growth speeds and MT growth lifetimes in time-lapse images. This methodology allows for the study of MT dynamics and the identification of how localized regulation of MT dynamics within sub-cellular regions contributes to the angiogenic processes of EC branching and migration.

Protocols for Human Umbilical Vein Endothelial Cell (HUVEC) culture, transient transfection of fluorescently-labeled markers of microtubule growth, live-cell imaging and automated analysis of interphase microtubule growth dynamics are detailed.

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes ...

Application of Genetically Encoded Fluorescent Nitric Oxide (NO&#8226;) Probes, the geNOps, for Real-time Imaging of NO&#8226; Signals in Single Cells

Nitric Oxide (NO&#8226;) is a small radical, which mediates multiple important cellular functions in mammals, bacteria and plants. Despite the existence of a large number of methods for detecting NO&#8226; in vivo and in vitro, the real-time monitoring of NO&#8226; at the single-cell level is very challenging. The physiological or pathological effects of NO&#8226; are determined by the actual concentration and dwell time of this radical. Accordingly, methods that allow the single-cell detection of NO&#8226; are highly desirable. Recently, we expanded the pallet of NO&#8226; indicators by introducing single fluorescent protein-based genetically encoded nitric oxide (NO&#8226;) probes (geNOps) that directly respond to cellular NO&#8226; fluctuations and, hence, addresses this need. Here we demonstrate the usage of geNOps to assess intracellular NO&#8226; signals in response to two different chemical NO&#8226;-liberating molecules. Our results also confirm that freshly prepared 3-(2-hydroxy-1-methyl-2-nitrosohydrazino)-N-methyl-1-propanamine (NOC-7) has a much higher potential to evoke change in intracellular NO&#8226; levels as compared with the inorganic NO&#8226; donor sodium nitroprusside (SNP). Furthermore, dual-color live-cell imaging using the green geNOps (G-geNOp) and the chemical Ca2+ indicator fura-2 was performed to visualize the tight regulation of Ca2+-dependent NO&#8226; formation in single endothelial cells. These representative experiments demonstrate that geNOps are suitable tools to investigate the real-time generation and degradation of single-cell NO&#8226; signals in diverse experimental setups.

Application of Genetically Encoded Fluorescent Nitric Oxide (NO&amp;#8226;) Probes, the geNOps, for Real-time Imaging of NO&amp;#8226; Signals in Single Cells

This manuscript presents protocols for the application of novel genetically encoded nitric oxide (NO&#8226;) probes (geNOps) to monitor single cell NO&#8226; fluctuations in real-time using fluorescence microscopy. The Ca2+-triggered NO&#8226; formation on the level of individual endothelial cells was visualized by combining geNOps with a chemical Ca2+ sensor.

Nitric Oxide (NO&#8226;) is a small radical, which mediates multiple important cellular functions in mammals, bacteria and plants. Despite the existence ...

Method for Labeling Transcripts in Individual Escherichia coli Cells for Single-molecule Fluorescence In Situ Hybridization Experiments

A method is described for labeling individual messenger RNA (mRNA) transcripts in fixed bacteria for use in single-molecule fluorescence in situ hybridization (smFISH) experiments in E. coli. smFISH allows the measurement of cell-to-cell variability in mRNA copy number of genes of interest, as well as the subcellular location of the transcripts. The main steps involved are fixation of the bacterial cell culture, permeabilization of cell membranes, and hybridization of the target transcripts with sets of commercially available short fluorescently-labeled oligonucleotide probes. smFISH can allow the imaging of the transcripts of multiple genes in the same cell, with limitations imposed by the spectral overlap between different fluorescent markers. Following completion of the protocol illustrated below, cells can be readily imaged using a microscope coupled with a camera suitable for low-intensity fluorescence. These images, together with cell contours obtained from segmentation of phase contrast frames, or from cell membrane staining, allow the calculation of the mRNA copy number distribution of a sample of cells using open-source or custom-written software. The labeling method described here can also be applied to image transcripts with stochastic optical reconstruction microscopy (STORM).

Method for Labeling Transcripts in Individual Escherichia coli Cells for Single-molecule Fluorescence In Situ Hybridization Experiments

This manuscript describes a method for labeling individual messenger RNA (mRNA) transcripts with fluorescently-labeled DNA probes, for use in single-molecule fluorescence in situ hybridization (smFISH) experiments in E. coli. smFISH is a visualization method that allows the simultaneous detection, localization, and quantification of single mRNA molecules in fixed individual cells.

A method is described for labeling individual messenger RNA (mRNA) transcripts in fixed bacteria for use in single-molecule fluorescence in situ ...

Oligomerization Dynamics of Cell Surface Receptors in Living Cells by Total Internal Reflection Fluorescence Microscopy Combined with Number and Brightness Analysis

Despite the importance and ubiquity of receptor oligomerization, few methods are applicable for detecting clustering events and measuring the degree of clustering. Here, we describe an imaging approach to determine the average oligomeric state of mEGFP-tagged-receptor homocomplexes in the membrane of living cells. The protocol is based on Total Internal Reflection Fluorescence (TIRF) microscopy combined with Number and Brightness (N&#38;B) analysis. N&#38;B is a method similar to fluorescence-correlation spectroscopy (FCS) and photon counting histogram (PCH), which are based on the statistical analysis of the fluctuations of the fluorescence intensity of fluorophores diffusing in and out of an illumination volume during an observation time. In particular, N&#38;B is a simplification of PCH to obtain information on the average number of proteins in oligomeric mixtures. The intensity fluctuation amplitudes are described by the molecular brightness of the fluorophore and the average number of fluorophores within the illumination volume. Thus, N&#38;B considers only the first and second moments of the amplitude distribution, namely, the mean intensity and the variance. This is, at the same time, the strength and the weakness of the method. Because only two moments are considered, N&#38;B cannot determine the molar fraction of unknown oligomers in a mixture, but it only estimates the average oligomerization state of the mixture. Nevertheless, it can be applied to relatively small time series (compared to other moment methods) of images of live cells on a pixel-by-pixel basis, simply by monitoring the time fluctuations of the fluorescence intensity. It reduces the effective time-per-pixel to a few microseconds, allowing acquisition in the time range of seconds to milliseconds, which is necessary for fast oligomerization kinetics. Finally, large cell areas as well as sub-cellular compartments can be explored.

We describe an imaging approach for the determination of the average oligomeric state of mEGFP-tagged-receptor oligomers induced by ligand binding in the plasma membrane of living cells. The protocol is based on Total Internal Reflection Fluorescence (TIRF) microscopy combined with Number and Brightness (N&#38;B) analysis.

Despite the importance and ubiquity of receptor oligomerization, few methods are applicable for detecting clustering events and measuring the degree of ...

Probing mRNA Kinetics in Space and Time in Escherichia coli using Two-Color Single-Molecule Fluorescence In Situ Hybridization

Single-molecule fluorescence in situ hybridization (smFISH) allows for counting the absolute number of mRNAs in individual cells. Here, we describe an application of smFISH to measure the rates of transcription and mRNA degradation in Escherichia coli. As smFISH is based on fixed cells, we perform smFISH at multiple time points during a time-course experiment, i.e., when cells are undergoing synchronized changes upon induction or repression of gene expression. At each time point, sub-regions of an mRNA are spectrally distinguished to probe transcription elongation and premature termination. The outcome of this protocol also allows for analyzing intracellular localization of mRNAs and heterogeneity in mRNA copy numbers among cells. Using this protocol many samples (~50) can be processed within 8 h, like the amount of time needed for just a few samples. We discuss how to apply this protocol to study the transcription and degradation kinetics of different mRNAs in bacterial cells.

Probing mRNA Kinetics in Space and Time in Escherichia coli using Two-Color Single-Molecule Fluorescence In Situ Hybridization

This protocol describes an application of single-molecule fluorescence in situ hybridization (smFISH) to measure the in vivo kinetics of mRNA synthesis and degradation.

Single-molecule fluorescence in situ hybridization (smFISH) allows for counting the absolute number of mRNAs in individual cells. Here, we describe an ...