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RNA Purification & Analysis

RNA Conformations
Simplified conformations of six common types of cellular RNA. Figure made in Biorender.
RNA purification is the process of preparing, isolating, extracting, and purifying RNA from a cell culture or tissue sample to obtain high-quality RNA for use in downstream applications. As biomolecules are first transcribed from DNA to RNA before becoming proteins, the functional complexity of various RNAs should not be understated.

Primal RNA (priRNA) and messenger RNA (mRNA) are active members in transcription while transfer and transfer messenger RNAs (tRNA and tmRNA) are involved in translation. Additionally, small nuclear RNA (snRNA) function in splicing, while short interfering RNA (siRNA) and microRNA (miRNA) operate in post-transcription.

Purified RNA is commonly used as starting material for a number of experiments, including real-time and digital PCR, transcriptome analysis using next generation sequencing (NGS), and for the construction of cDNA libraries. Likewise, purified RNA may also be used in Northern blot, microarray analysis, or for use in nuclease protection assays. RNAs play vital and intricate roles in biology but in general, however, are fragile and may be difficult to recover. Adequate RNA purification is therefore essential to the success of downstream applications.

Common Extraction Methods

Spin Column Extraction

Prepacked ReadiUse™ Bio-Gel P6 Spin Column.
Prepacked ReadiUse™ Bio-Gel P6 Spin Column. The column was packed with P-6 DG in PBS buffer for sample volume 50~100 uL.
The spin column method is a solid phase extraction technique that relies on the fact that nucleic acids bind to solid silica under ideal conditions. The spin column method is an adsorption-based technique; it is based on the ability of RNA to create linkages to specific surfaces in the presence of chaotropic salts, rather, GTC/ GITC. This method offers quick test times, easy, simple steps, and commercial availability in many kit formats.
  1. First, cells are lysed to free nucleic acids, then a binding solution, ethanol and the aqueous samples are added to the spin column.
  2. A centrifugation step then forces binding of the solution through a silica gel membrane inside the spin column. As the solution is forced through the gel membrane, the freed nucleic acids will bind to the silica if the pH and concentration of the binding solution is optimal.
  3. The nucleic acids will undergo a washing step, and then will undergo elution from the membrane where they can be collected from the bottom of the column.

Phenol:Chloroform Extraction

The phenol:chloroform extraction method is a common technique used to purify RNA. Though this technique offers a simple, straightforward, cost-effective method of RNA purification, care should be taken upon each step that involves separating mediums, as upper and lower phases may become cross-contaminated.
  1. Samples initially undergo a lysis step that utilizes a cationic detergent, commonly guanidinium thiocyanate or isothiocyanate (GTC or GITC) that effectively inactivates endogenous ribonucleases.

    Note: The addition of a low-pH phenol reagent, such as TRIzol or TRI, is used as a deproteinizing agent that further removes DNA from the sample.

  2. Next, the sample undergoes an organic extraction step through the addition of chloroform. As chloroform is a purely organic reagent, it does not mix well with the cell lysate and the solution must be interspersed and then centrifuged, to separate the upper and lower phases, which correlate to the cell lysate and chloroform, respectively.
  3. After, the cell lysate is isolated, isopropanol is added, and the sample will undergo another centrifugation step. In alcohol precipitation, the RNA will become pelleted towards the bottom of the test tube and the solution should be secondarily discarded. Multiple ethanol washes combined with additional centrifugation steps may be used to remove residual salts.
  4. Finally, the purified RNA can be dissolved in RNase-free water or buffer, and stored for later or used immediately.

Other Methods

Isopycnic Centrifugation
Illustration of the principles of isopycnic centrifugation, showing the transition of the starting mixed sample to the equilibrium state of sample particles settled into layers of equivalent density. Even if centrifugal spinning continues after the equilibrium point, the particles will not move out of these layers into a pellet, minimizing the risk and sample damage of 'overspinning'. Figure made in BioRender.

Other adsorption methods aside from spin column extraction exist as well, including those that utilize:
• magnetic beads
• polystyrene latex materials
• cellulose matrices
• glass fibers

In principle, the procedures are similar; the samples are lysed, exposed to an adsorbing material, mixed to facilitate binding, washed to remove contaminants, then sedimented.

These techniques also come with some drawbacks. Loss of the membrane or beads as well as overdrying must be carefully avoided, as these occurrences will result in a loss of RNA. Caution should also be taken when separating phases after centrifugation steps, and separation techniques should involve the use of a long flexible pipette over an aspirator.

Other techniques of RNA purification include the isopycnic gradient method, which is a density driven technique that similarly utilizes GTC/ GITC, a column, and centrifugation. This method may commonly be used for isolating RNA free of proteins, DNA, polysaccharides and other cellular components. It may be desired instead that mRNA be purified from the total RNA sample. To do so, the chemical structure of mRNA using the polyadenylate tail located at the 3' terminus is exploited, and mRNA may be obtained by chromatographic methods, or by the use of a magnetic field.

Additionally, various kits are commercially available for the extended purification of other RNA species from total RNA, including those for small RNAs (like miRNA and siRNAs), cell-free mRNAs, or even for the simultaneous co-purification of RNA and proteins together.

Common Analysis Methods

Ultraviolet (UV) Spectroscopy

Common analysis techniques involve the use of UV spectroscopy, where diluted RNA can be measured between 260-280 nm, representing a 260/280 nm ratio of absorbance. Nucleic acid concentration is calculated using the Beer-Lambert law, which predicts a linear relationship between absorbance and concentration.

Check out our Beer Lambert Law Calculator. The formula sets absorbance equal to extinction coefficient
(molar absorptivity) in M-1 cm-1 multiplied by path length and concentration.

UV spectroscopy does not discriminate between RNA and DNA, so a sample treatment step with RNase-free DNase to remove contaminating DNA prior to analysis is vital. It is important to note that other contaminants, including residual proteins and/or phenol, can interfere with absorbance readings, so optimal extraction and purification steps may be necessary.

The 260/280 nm absorbance ratio is dependent on both pH and ionic strength; as the pH of the sample increases, the 280 nm absorption decreases and the absorption at 260 nm is unaffected, leading to an increased ratio. Since water is often acidic, it may lower the 260/280 nm ratio, so a buffer with a slightly alkaline pH, like Tris-EDTA, is recommended for use as a diluent and blank to provide reproducible readings.

Click the button on the right to see a variety of buffer preparations and recipes.

Sample readings are also taken using quartz cuvettes, so care must be taken to ensure these apparatuses are cleaned thoroughly as dirt and dust may impact absorbance at 260 nm. Background corrections may also need to be performed using readings from a blank at 320, 260, and 280 nm.
Fluorescence Images
Fluorescence images of live and fixed HeLa cells stained with StrandBrite RNA Green (Green) and counter-stained with Hoechst 33342 or DAPI (Blue). Fluorescence signal were measured using a fluorescence microscope with FITC filter.

Fluorescent Dyes

Fluorescent dyes may also be used for analyzing RNA purification, which utilize the excitation, or binding, of fluorophores to RNA to evaluate the purity of the RNA test sample. Sample fluorescence can then be plotted against a standard curve formed from known concentrations at 260 nm. Detection and quantitation can be performed using a laboratory standard or filter fluorometer, or a fluorescence microplate reader.

Note: To ensure the accuracy of fluorometric readings, possible contaminants must be carefully assessed and removed where possible. For fluorometric methods, continuous freeze-thawing of the sample and experimental reagents must also be avoided.

Agarose/acrylamide Gel Electrophoresis

In agarose and acrylamide gel electrophoresis samples are loaded into precast gels then stained with fluorescent dyes that bind nucleic acids. After the addition of an electrical current, nucleic acid fragments move through the gel and are separated on the basis of size. Larger fragments move more slowly while smaller fragments move more quickly through the gel, and separated fragments may be visualized by exciting the fluorescent dye bound to the nucleic acid.

Qualitative RNA concentrations may be measured by comparing the fluorescent intensity of the sample RNA bands to the known standards, run alongside the test samples. Quantitative assessment may be performed by equipment with built-in software to analyze an image of the gel, a technique called gel densitometry.

Table 1. Nucleic acid stains for agarose and polyacrylamide gel electrophoresis

Ex (nm)¹
Unit Size
Cat No.
Helixyte™ Green Nucleic Acid Gel Stain *10,000X DMSO Solution*254 mnLong path green filter1 mL17590
Helixyte™ Green Nucleic Acid Gel Stain *10,000X DMSO Solution*254 mnLong path green filter100 µL17604
Helixyte™ Gold Nucleic Acid Gel Stain *10,000X DMSO Solution*254 mnLong path green filter1 mL17595
Gelite™ Green Nucleic Acid Gel Staining Kit254 nm or 300 nmLong path green filter1 Kit17589
Gelite™ Orange Nucleic Acid Gel Staining Kit254 nm or 300 nmLong path green filter1 Kit17594
Gelite™ Safe DNA Gel Stain *10,000X Water Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters100 µL17700
Gelite™ Safe DNA Gel Stain *10,000X Water Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters500 µL17701
Gelite™ Safe DNA Gel Stain *10,000X Water Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters1 mL17702
Gelite™ Safe DNA Gel Stain *10,000X Water Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters10 mL17703
Gelite™ Safe DNA Gel Stain *10,000X DMSO Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters100 µL17704
Gelite™ Safe DNA Gel Stain *10,000X DMSO Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters500 µL17705
Gelite™ Safe DNA Gel Stain *10,000X DMSO Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters1 mL17706
Gelite™ Safe DNA Gel Stain *10,000X DMSO Solution*254 nm, 300 nm or 520 nmEthidium Bromide, Gel Star, Gel Green, Gel Red and SYBR filters10 mL17707

Use our RNA Concentration Calculator to determine the concentration of RNA in a solution.

Real-Time Quantitative PCR (qPCR) and reverse transcriptase PCR (RT-qPCR)

One-step RT-PCR diagram
One-step RT-PCR diagram. In one-step RT-PCR, cDNA synthesis via reverse transcription (RT) and subsequent PCR amplification occur in the same reaction vessel (figure made in BioRender).

In qPCR the amount of amplified product is measured at the end of each cycle after amplification, or in real-time during the exponential phase of amplification. The incorporation of a reverse transcriptase step to qPCR allows the qualitative measurement of the amount of each specific RNA species in a sample.

Here, amplified products are also measured through use of fluorescent probes. Adequate primer design is crucial to the success of the experiment, and RNA-specific primers that flank an intron of the target sequence should be used for cDNA detection. Primers within an intron can also be used to detect DNA contamination in an RNA sample. The use of multiple fluorophores, separately labeled to different primers may also be preferred. This technique allows researchers to analyze multiple targets in a single reaction and examine samples for the presence of PCR inhibitors.

Table 2. Fluorescent reporter dyes for labeling the 5' end or 3' end on sequence-specific qPCR probes.

Ex (nm)
Em (nm)
Unit Size
Cat No.
EDANS acid [5-((2-Aminoethyl)amino)naphthalene-1-sulfonic acid] *CAS 50402-56-7*3364551 g610
EDANS acid [5-((2-Aminoethyl)amino)naphthalene-1-sulfonic acid] *CAS 50402-56-7*33645510 g611
EDANS C5 maleimide3364555 mg619
EDANS sodium salt [5-((2-Aminoethyl)aminonaphthalene-1-sulfonic acid, sodium salt] *CAS 100900-07-0*3364551 g615
EDANS sodium salt [5-((2-Aminoethyl)aminonaphthalene-1-sulfonic acid, sodium salt] *CAS 100900-07-0*33645510 g616
Tide Fluor™ 1 acid [TF1 acid] *Superior replacement for EDANS*341448100 mg2238
Tide Fluor™ 1 alkyne [TF1 alkyne]3414485 mg2237
Tide Fluor™ 1 amine [TF1 amine] *Superior replacement for EDANS*3414485 mg2239
Tide Fluor™ 1 azide [TF1 azide]3414485 mg2236
Tide Fluor™ 1 CPG [TF1 CPG] *500 Å*341448100 mg2240
Tide Fluor™ 1 CPG [TF1 CPG] *1000 Å*341448100 mg2241
Tide Fluor™ 1 maleimide [TF1 maleimide] *Superior replacement for EDANS*3414485 mg2242
Tide Fluor™ 1 succinimidyl ester [TF1 SE] *Superior replacement for EDANS*3414485 mg2244
5(6)-FAM [5-(and-6)-Carboxyfluorescein] *CAS 72088-94-9*4935171 g100
5(6)-FAM [5-(and-6)-Carboxyfluorescein] *CAS 72088-94-9*49351710 g101
5(6)-FAM [5-(and-6)-Carboxyfluorescein] *CAS 72088-94-9*49351725 g102
5(6)-FAM cadaverine493517100 mg127
5(6)-FAM ethylenediamine493517100 mg123
5(6)-FAM, SE [5-(and-6)-Carboxyfluorescein, succinimidyl ester] *CAS 117548-22-8*49351725 mg110
5(6)-FAM, SE [5-(and-6)-Carboxyfluorescein, succinimidyl ester] *CAS 117548-22-8*493517100 mg111
5(6)-FAM, SE [5-(and-6)-Carboxyfluorescein, succinimidyl ester] *CAS 117548-22-8*4935171 g112
6-FAM [6-Carboxyfluorescein]493517100 mg106
6-FAM [6-Carboxyfluorescein]4935171 g107
6-FAM [6-Carboxyfluorescein]4935175 g108
6-FAM Alkyne49351710 mg134
6-FAM Alkyne493517100 mg956
6-FAM Azide49351710 mg133
6-FAM Azide493517100 mg955
FAM-xtra™ Phosphoramidite 49351750 µmoles6037
6-FAM phosphoramidite [5'-Fluorescein phosphoramidite]493517100 µmoles6016
6-FAM phosphoramidite [5'-Fluorescein phosphoramidite]49351710x100 µmoles6017
6-FAM, SE [6-Carboxyfluorescein, succinimidyl ester] *CAS 92557-81-8*49351710 mg116
6-FAM, SE [6-Carboxyfluorescein, succinimidyl ester] *CAS 92557-81-8*493517100 mg117
6-FAM, SE [6-Carboxyfluorescein, succinimidyl ester] *CAS 92557-81-8*4935171 g118
6-Fluorescein phosphoramidite498517100 µmoles6018
6-Fluorescein phosphoramidite49851710x100 µmoles6019
3'-(6-Fluorescein) CPG *1000 Å*4985171 g6014
Tide Fluor™ 2 acid [TF2 acid] *Superior replacement for fluorescein*50352525 mg2245
Tide Fluor™ 2 alkyne [TF2 alkyne] *Superior replacement for fluorescein*5035251 mg2253
Tide Fluor™ 2 amine [TF2 amine] *Superior replacement for fluorescein*5035251 mg2246
Tide Fluor™ 2 azide [TF2 azide] *Superior replacement for fluorescein*5035251 mg2252
Tide Fluor™ 2 maleimide [TF2 maleimide] *Superior replacement for fluorescein*5035251 mg2247
Tide Fluor™ 2, succinimidyl ester [TF2 SE] *Superior replacement for fluorescein*5035255 mg2248
Tide Fluor™ 2WS acid [TF2WS acid] *Superior replacement for FITC*50352510 mg2348
Tide Fluor™ 2WS amine [TF2WS amine] *Superior replacement for FITC*5035251 mg2351
Tide Fluor™ 2WS maleimide [TF2WS maleimide] *Superior replacement for FITC*5035251 mg2350
Tide Fluor™ 2WS succinimidyl ester [TF2WS SE] *Superior replacement for FITC*5035255 mg2349
6-TET alkyne5215435 mg245
6-TET azide5215435 mg244
6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite]52154350 µmoles6021
6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite]521543100 µmoles6027
6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite]52154310x100 µmoles6025
6-TET, SE [6-Carboxy-2',4,7',7-tetrachlorofluorescein, succinimidyl ester]5215435 mg211
Helix Fluor™ 545, succinimidyl ester5265431 mg250
VIC phosphoramidite52654350 µmoles6080
VIC phosphoramidite526543100 µmoles6081
VIC phosphoramidite5265431 g6082
5-VIC phosphoramidite52654350 µmoles6083
5-VIC phosphoramidite526543100 µmoles6084
5-VIC phosphoramidite5265431 g6085
6-VIC, SE [6-VIC NHS ester]5265431 mg212
6-VIC, SE [6-VIC NHS ester]5265435 mg213
6-HEX alkyne5335595 mg241
6-HEX azide5335595 mg240
6-HEX, SE [6-Carboxy-2',4,4',5',7,7'-hexachlorofluorescein, succinimidyl ester]5335595 mg202
6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite]533559100 µmoles6026
6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite]53355910x100 µmoles6024
6-NED alkyne5455671 mg216
6-NED azide5455671 mg217
6-NED maleimide5455671 mg218
6-NED, SE [6-NED NHS ester]5455671 mg214
6-NED, SE [6-NED NHS ester]5455671 mg215
Helix Fluor™ 575, succinimidyl ester5535701 mg251
Tide Fluor™ 3 acid [TF3 acid] *Superior replacement for Cy3*54657125 mg2268
Tide Fluor™ 3 alkyne [TF3 alkyne] *Superior replacement for Cy3*5465711 mg2255
Tide Fluor™ 3 amine [TF3 amine] *Superior replacement for Cy3*5465711 mg2269
Tide Fluor™ 3 azide [TF3 azide] *Superior replacement for Cy3*5465711 mg2254
Tide Fluor™ 3 maleimide [TF3 maleimide] *Superior replacement for Cy3*5465711 mg2270
Tide Fluor™ 3 succinimidyl ester [TF3 SE] *Superior replacement for Cy3*5465711 mg2271
Tide Fluor™ 3 phosphoramidite [TF3 CEP] *Superior replacement to Cy3 phosphoramidite*546571100 µmoles2274
Tide Fluor™ 3WS acid [TF3WS acid] *Superior replacement for Cy3*55156310 mg2268
Tide Fluor™ 3WS amine [TF3 amine] *Superior replacement for Cy3*5515631 mg2347
Tide Fluor™ 3WS maleimide [TF3 maleimide] *Superior replacement for Cy3*5515631 mg2344
Tide Fluor™ 3WS succinimidyl ester [TF3WS SE] *Superior replacement for Cy3*5515631 mg2346
Tide Fluor™ 4 acid [TF4 acid] *Superior replacement for ROX and Texas Red*57860210 mg2285
Tide Fluor™ 4 alkyne [TF4 alkyne] *Superior replacement for ROX and Texas Red*5786021 mg2301
Tide Fluor™ 4 amine [TF4 amine] *Superior replacement for ROX and Texas Red*5786021 mg2286
Tide Fluor™ 4 azide [TF4 azide] *Superior replacement for ROX and Texas Red*5786021 mg2300
Tide Fluor™ 4 maleimide [TF4 maleimide] *Superior replacement for ROX and Texas Red*5786021 mg2287
Tide Fluor™ 4, succinimidyl ester [TF4 SE] *Superior replacement for ROX and Texas Red*5786025 mg2289
Tide Fluor™ 5WS acid [TF5WS acid] *Superior replacement for Cy5*64966410 mg2278
Tide Fluor™ 5WS alkyne [TF5WS alkyne] *Superior replacement for Cy5*6496641 mg2276
Tide Fluor™ 5WS amine [TF5WS amine] *Superior replacement for Cy5*6496641 mg2279
Tide Fluor™ 5WS azide [TF5WS azide] *Superior replacement for Cy5*6496641 mg2275
Tide Fluor™ 5WS maleimide [TF5WS maleimide] *Superior replacement for Cy5*6496641 mg2280
Tide Fluor™ 5WS succinimidyl ester [TF5WS SE] *Superior replacement for Cy5*6496645 mg2281
Tide Fluor™ 6WS acid [TF6WS acid] *Superior replacement for Cy5.5*68270110 mg2291
Tide Fluor™ 6WS alkyne [TF6WS alkyne] *Superior replacement for Cy5.5*6827011 mg2303
Tide Fluor™ 6WS amine [TF6WS amine] *Superior replacement for Cy5.5*6827011 mg2292
Tide Fluor™ 6WS azide [TF6WS azide] *Superior replacement for Cy5.5*6827011 mg2302
Tide Fluor™ 6WS maleimide [TF6WS maleimide] *Superior replacement for Cy5.5*6827011 mg2293
Tide Fluor™ 6WS succinimidyl ester [TF6WS SE] *Superior replacement for Cy5.5*6827011 mg2294
Tide Fluor™ 7WS acid [TF7WS acid] *Superior replacement for Cy7*75678010 mg2330
Tide Fluor™ 7WS alkyne [TF7WS alkyne] *Superior replacement for Cy7*7567801 mg2305
Tide Fluor™ 7WS amine [TF7WS amine] *Superior replacement for Cy7*7567801 mg2331
Tide Fluor™ 7WS azide [TF7WS azide] *Superior replacement for Cy7*7567801 mg2304
Tide Fluor™ 7WS maleimide [TF7WS maleimide] *Superior replacement for Cy7*7567801 mg2332
Tide Fluor™ 7WS succinimidyl ester [TF7WS SE] *Superior replacement for Cy7*7567801 mg2333
Tide Fluor™ 8WS acid [TF8WS acid] *Near Infrared Emission*78580110 mg2335
Tide Fluor™ 8WS alkyne [TF8WS alkyne] *Near Infrared Emission*7858011 mg2307
Tide Fluor™ 8WS amine [TF8WS amine] *Near Infrared Emission*7858011 mg2336
Tide Fluor™ 8WS azide [TF8WS azide] *Near Infrared Emission*7858011 mg2306
Tide Fluor™ 8WS maleimide [TF8WS maleimide] *Near Infrared Emission*7858011 mg2337
Tide Fluor™ 8WS succinimidyl ester [TF8WS SE] *Near Infrared Emission*7858011 mg2338


Product Ordering Information


Table 3. Available RNA quantifying reagents and kits.

Product Name
Ex (nm)
Em (nm)
Unit Size
Cat No.
StrandBrite™ Green Fluorimetric RNA Quantitation Kit490545100 Tests17656
StrandBrite™ Green Fluorimetric RNA Quantitation Kit *High Selectivity*490540100 Tests17657
StrandBrite™ Green Fluorimetric RNA Quantitation Kit *Optimized for Microplate Readers*4905451000 Tests17655
StrandBrite™ Green RNA Quantifying Reagent *200X DMSO Solution*4905251 mL17610
StrandBrite™ Green RNA Quantifying Reagent *200X DMSO Solution*49052510 mL17611
Portelite™ Fluorimetric RNA Quantitation Kit *Optimized for Cytocite™ and Qubit™ Fluorometers*490525100 Tests17658
Portelite™ Fluorimetric RNA Quantitation Kit *Optimized for Cytocite™ and Qubit™ Fluorometers*490525500 Tests17659
Cell Navigator® Live Cell RNA Imaging Kit *Optimized for Fluorescence Microscope*490520100 Tests22630

Table 4. Aldehyde-reactive molecular probes potentially suitable for 3’-end labeling of RNA oligos.

Ex (nm)
Em (nm)
Unit Size
Cat No.
Biocytin hydrazide *CAS 102743-85-1*  25 mg3086
Biotin hydrazide *CAS 66640-86-6*  25 mg3007
Cyanine 3 hydrazide [equivalent to Cy3® hydrazide]5555691 mg146
Cyanine 5 hydrazide [equivalent to Cy5® hydrazide]6516701 mg156
Cyanine 5.5 hydrazide [equivalent to Cy5.5® hydrazide]6837031 mg177
Cyanine 7 hydrazide [equivalent to Cy7® hydrazide]7567791 mg166
ICG hydrazide7898141 mg987
iFluor™ 350 hydrazide3454501 mg1080
iFluor™ 405 hydrazide4034271 mg1081
iFluor™ 488 hydrazide4915161 mg1082
iFluor™ 555 hydrazide5575701 mg1083
iFluor™ 647 hydrazide6566701 mg1085
iFluor™ 680 hydrazide6847011 mg1086
iFluor™ 700 hydrazide6907131 mg1087
iFluor™ 750 hydrazide7577791 mg1088
iFluor™ 790 hydrazide7878121 mg1364
ReadiView™ biotin hydrazide  5 mg3055
Texas Red® hydrazide *Single Isomer*5866035 mg481

Table 5. Probe-labeled nucleotides potentially suitable for 3’-end labeling of RNA or DNA oligos.

Unit Size
Cat No.
2-Aminoethoxypropargyl ddATP1 µmoles17084
2-Aminoethoxypropargyl ddCTP1 µmoles17080
2-Aminoethoxypropargyl ddGTP1 µmoles17086
2-Aminoethoxypropargyl ddTTP1 µmoles17082
5-Propargylamino-3'-azidomethyl-dCTP50 nmoles17091
5-Propargylamino-3'-azidomethyl-dUTP50 nmoles17093
7-Deaza-7-Propargylamino-3'-azidomethyl-dATP50 nmoles17090
7-Deaza-7-Propargylamino-3'-azidomethyl-dGTP50 nmoles17092
AA-dUTP [Aminoallyl dUTP sodium salt] *4 mM in Tris Buffer (pH 7.5)* *CAS 936327-10-5*1 µmole17004
AA-dUTP [Aminoallyl dUTP sodium salt] *4 mM in Tris Buffer (pH 7.5)* *CAS 936327-10-5*2.5 µmole17005
AA-UTP [Aminoallyl UTP sodium salt] *4 mM in TE buffer* *CAS 75221-88-4*250 µL17021
Aminopropargyl dATP [7-Deaza-7-Propargylamino-2'-deoxyadenosine-5'-triphosphate]10 µmoles17056
Aminopropargyl dCTP [5-Propargylamino-2'-deoxycytidine-5'-triphosphate]10 µmoles17050
Aminopropargyl ddATP [7-Deaza-7-Propargylamino-2',3'-dideoxyadenosine-5'-triphosphate]10 µmoles17074
Aminopropargyl ddCTP [5-Propargylamino-2',3'-dideoxycytidine-5'-triphosphate]10 µmoles17070
Aminopropargyl ddGTP [7-Deaza-7-Propargylamino-2',3'-dideoxyguanosine-5'-triphosphate]10 µmoles17076
Aminopropargyl ddTTP [5-Propargylamino-2',3'-dideoxyuridine-5'-triphosphate]10 µmoles17072
Aminopropargyl dGTP [5-Propargylamino-2'-deoxyguanosine-5'-triphosphate]10 µmoles17059
Aminopropargyl dUTP [5-Propargylamino-2'-deoxyuridine-5'-triphosphate]10 µmoles17053
Biotin-11-dATP25 nmoles17014
Biotin-11-dGTP25 nmoles17015
Biotin-11-dUTP *1 mM in Tris Buffer (pH 7.5)* *CAS 86303-25-5*25 nmoles17016
Biotin-14-dCTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17019
Biotin-16-dUTP *1 mM in Tris Buffer (pH 7.5)* *CAS 136632-31-0*25 nmoles17017
Biotin-20-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17018
Cyanine 5-dATP [Cy5-dATP]25 nmoles17038
Cyanine-3- dUTP [Cy3-dUTP]  *1 mM in Tris Buffer (pH 7.5)*25 nmoles17025
Cyanine-5- dUTP [Cy5-dUTP]  *1 mM in Tris Buffer (pH 7.5)*25 nmoles17026
ddATP [2',3'-Dideoxyadenosine-5'-triphosphate]1 µmole17209
ddCTP [2',3'-Dideoxycytidine-5'-triphosphate]1 µmole17207
ddGTP [2',3'-Dideoxyguanosine-5'-triphosphate]1 µmole17210
ddTTP [2',3'-Dideoxythymidine-5'-triphosphate]1 µmole17208
DEAC-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17024
Digoxigenin-11-dUTP *1 mM solution in water*25 nmoles17012
Fluorescein-12-dUTP (Perkin-Elmer) *1 mM in Tris Buffer (pH 7.5)*25 nmoles17027
Fluorescein-12-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17028
Fluorescein-12-dUTP *1 mM in Tris Buffer (pH 7.5)* *CAS 214154-36-6*25 nmoles17022
iFluor® 440-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17029
iFluor®488-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17039
MagaDye™ 535-ddGTP5 nmoles17063
MagaDye™ 535-ddGTP50 nmoles17067
MagaDye™ 561-ddATP5 nmoles17062
MagaDye™ 561-ddATP50 nmoles17066
MagaDye™ 588-ddTTP5 nmoles17061
MagaDye™ 588-ddTTP50 nmoles17065
MagaDye™ 613-ddCTP5 nmoles17060
MagaDye™ 613-ddCTP50 nmoles17064
mFluor™ Violet 450-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17011
Tetramethylrhodamine-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17023
TF1-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17006
TF2-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17007
TF3-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17008
TF4-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17009
TF5-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17010
XFD™488-dUTP *1 mM in Tris Buffer (pH 7.5)*25 nmoles17040

Table 6. Phosphorothiolate-reactive maleimides potentially suitable for 5’-end labeling of RNA or DNA oligos.

Superior Alternative to
Excitation Max (nm)
Emission Max (nm)
Tide Fluor™ 1 Maleimide [TF1 Maleimide]EDANS341448
Tide Fluor™ 2 Maleimide [TF2 Maleimide]Fluoresceins (FAM and FITC)503525
Tide Fluor™ 2WS Maleimide [TF2WS Maleimide]Fluoresceins (FAM and FITC)503525
Tide Fluor™ 3 Maleimide [TF3 Maleimide]Cy3®554578
Tide Fluor™ 3WS Maleimide [TF3WS Maleimide]Cy3®551563
Tide Fluor™ 4 Maleimide [TF4 Maleimide]ROX/Texas Red®578602
Tide Fluor™ 5WS Maleimide [TF5WS Maleimide]Cy5®649664
Tide Fluor™ 6WS Maleimide [TF6WS Maleimide]Cy5.5682701
Tide Fluor™ 7WS Maleimide [TF7WS Maleimide]Cy7®756780
Tide Fluor™ 8WS Maleimide [TF8WS Maleimide]IRDye® 800785801



Methods of RNA Purification. All Ways (Should) Lead to Rome
Importance of RNA isolation methods for analysis of exosomal RNA: Evaluation of different methods
RNA Purification and Isolation
RNA Purification and Analysis: Sample Preparation, Extraction, Chromatography
Methods of RNA Quality Assessment