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BIO 3'-End Oligonucleotide Labeling Kit with Biotin-11-UTP

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APP-001 25 reactions x 50 μl (5 pmol each) 279,13 Add to Basket/Quote Add to Notepad

For research use only!

Shipping: shipped on blue ice

Storage Conditions: store at -20 °C
avoid freeze/thaw cycles

Shelf Life: 12 months

Description:
BIO 3'-End Oligonucleotide Labeling Kit with Biotin-11-UTP contains all reagents (except oligonucleotide template to be labeled and materials for Biotin detection) required for efficient 3'-End biotinylation of DNA oligonucleotides (length: 20 -100 bp, 5 pmol per reaction).

The labeling principle is based on Terminal deoxynucleotidyl Transferase (TdT) that template-independently transfers 1-3 Biotin-11-UTPs to the 3'-OH group of ssDNA (e.g. an oligonucleotide) in the presence of CoCl2. It is similar to the principle of Biotin 3'-End DNA Labeling Kit (Pierce/Thermo Scientific).

The resulting 3'-End biotinylated oligonucleotides are ideally suited for applications involving sequence-specific protein binding or hybridiziation such as EMSA, Northern or Southern blots. Compared to internal, random biotinylated probes, Biotin is located at the 3'-End only and less likely interferes with probe binding.

TdT possesses a preference for single-stranded DNA (ssDNA) over dsDNA with 3'-overhangs or blunt ends. For the preparation of labeled dsDNA complexes, label each complementary oligonucleotide separately and anneal them before use.

Content:
Terminal Deoxynucleotidyl Transferase (TdT)
30 μl (20 U/μl) in 100 mM potassium acetate (pH 6.8), 2 mM 2-mercaptoethanol, 0.01% Triton X-100 (v/v) and 50% glycerol (v/v)

5x TdT Reaction Buffer
400 μl containing 1 M potassium cacodylate, 0.125 M Tris, 0.05% Triton X-100 (v/v), 5 mM CoCl2, pH 7.2

Biotin-11-UTP
5 μl, 10 mM in 10 mM Tris-HCl, pH 7.5

Unlabeled Control Oligonucleotide (60 bp)
250 μl, 1 μM in 1x TE Buffer, pH 7.6

3'-Biotin-labeled Control Oligonucleotide (60 bp)
130 μl, 1 μM in 1x TE Buffer, pH 7.6

PCR-grade H2O
12.5 ml

1x TE Buffer, pH 7.6
100 ml containing 10 mM Tris-HCl, 1 mM EDTA, pH 7.6

Stop Buffer
400 μl, 0.5 M EDTA solution, pH 8


1. Preparation of working solutions

1.1 Preparation of Biotin-11-UTP stock solution (1 mM)

  • Thaw 10 mM Biotin-11-UTP solution (5 μl) on ice, voretex and spin-down briefly.
  • Add 45 μl 1x TE Buffer (1:10 dilution) to achieve a final concentration of 1 mM.
  • Store stock solution at -20 °C until use (see 1.2).

1.2 Preparation of Biotin-11-UTP working solution (10 μM)

  • Thaw 1 mM Biotin-11-UTP solution (see 1.1) on ice, voretex and spin-down briefly.
  • Prepare a 1:100 dilution with PCR-grade H2O to achieve a final concentration of 10 μM (e.g. 1 μl of 1 mM Biotin-11-UTP + 99 μl PCR-grade H2O).
  • Keep working solution (10 μM) on ice until use (see 2.).
  • Prepare Biotin-11-UTP working solution (10 μM) freshly for each experiment. Do not store for subsequent use.

2. 3' End Oligonucleotide labeling reaction

  • Store all components except of TdT on ice until use.
  • Store TdT at -20°C until use.
  • Final Assay volume: 50 μl
  • Template requirements: oligonucleotide/ssDNA purified by HPLC or gel electrophoresis, 20 – 100 bp
  • Add all components on ice exactly in the order listed below.
  • Mix reaction gently by pipetting up and down. Do not voretex!
  • Incubate 30 min at 37 °C.
  • Add 1 μl Stop Buffer (0.5 M EDTA solution, pH 8) to stop each reaction.
  • Store reactions on ice for subsequent use (see 3.) or -20 °C for long-term storage.


ComponentVolumeFinal concentrationFinal molar amount
PCR grade H2O31.5 μln/an/a
5x TdT Reaction Buffer10 μl1xn/a
oligo-nucleotide template
(1 μM)
5 μl100 nM5 pmol
Biotin-11-UTP (10 μM) (see 1.2)2.5 μl0.5 μM50 pmol
TdT (20 U/μl)1 μl0.4 U/μl20 U
Total volume50 μl


3. Estimation of Biotin labeling degree
Quantification of Biotin labeling degree is essential for reproducible downstream results. An oligonucleotide dilution series is immobilized on a positively-charged membrane (Dot Blot) followed by an indirect detection of the Biotin moiety using streptavidin-horseradish peroxidase (HRP) or streptavidin-alkaline phosphatase (AP) conjugates.

Recommended oligonucleotide starting amount for chromogenic detection: 100 fmol
Recommended oligonucleotide starting amount for chemiluminescent detection: 20 fmol

The following reagent amounts (3.1 – 3.5) are calculated for an oligonucleotide starting amount of 100 fmol.

3.1 Preparation of Unlabeled control oligonucleotide (Unlab. oligo)
working solution (500 nM)

  • Thaw 1 μM unlabeled control oligonucleotide solution on ice, voretex and spin-down briefly.
  • Prepare a 1: 2 dilution with 1x TE Buffer, pH 7.6 to achieve a final concentration of 500 nM (e.g. 5 μl of 1 μM unlabeled control oligonucleotide + 5 μl 1x TE Buffer, pH 7.6).
  • Keep the working solution (500 nM) on ice until use (see 2.).
  • Prepare unlabeled control oligonucleotide working solution (500 nM) freshly for each experiment. Do not store for subsequent use.

3.2 Preparation of 3'-Biotin-labeled control oligonucleotide
(3'-BIO oligo) working solution (500 nM)

  • Thaw 1 μM 3'-Biotin-labeled control oligonucleotide solution on ice, voretex and spin-down briefly.
  • Prepare a 1:2 dilution with 1x TE Buffer, pH 7.6 to achieve a final concentration of 500 nM (e.g. 5 μl of 1 μM 3'-Biotin-labeled control oligonucleotide solution + 5 μl 1x TE Buffer, pH 7.6).
  • Keep the working solution (500 nM) on ice until use (see 2.)
  • Prepare 3'-Biotin-labeled control oligonucleotide working solution (500 nM) freshly for each experiment. Do not store for subsequent use.

3.3 Preparation of Biotin oligonucleotide standard solutions
(50 fmol/μl)

  • Prepare Biotin oligonucleotide standard solutions (S1 – S5) with varying degrees of oligonucleotide biotinylation as follows.
  • Total oligonucleotide concentration (S1-S5): 50 fmol/μl
  • Degree of dioxygenylation: S1=100 %, S2=75 %, S3= 50 %, S4= 25 %, S5= 0 %
  • Voretex and spin-down briefly.


S1S2S3S4S5
3'-BIO oligo (500nM) (s. 3.2)2 μl1.5 μl1 μl0.5 μl0 μl
Unlab. oligo (500nM) (s. 3.1)0 μl0.5 μl1 μl1.5 μl2 μl
1x TE Buffer pH 7.68 μl8 μl8 μl8 μl8 μl
Total Volume10 μl10 μl10 μl10 μl10 μl

3.4 Preparation of sample dilutions (50 fmol/μl)

  • Dilute sample labeling reaction(s) (see 1) 1:2 to a final oligonucleotide concentration of 50 nM (e.g. 5 μl sample labeling reaction + 5 μl 1x TE Buffer, pH 7.6.)
  • Voretex and spin-down briefly.

3.5 Preparation oligonucleotide standard and sample dilution series

  • Transfer 10 μl of each Biotin oligonucleotide standard solution S1 – S5 (see 2.1) to well A1 – A5 of a low absorption 96-well PCR plate, respectively (e.g. 96-well Multiply® PCR plate, Sarstedt, #72.1979.102).
  • Transfer 10 μl of sample dilution(s) (see 2.2) to the remaining "A" wells (A6 to A…)
  • Prepare a two-fold dilution series with 1x TE Buffer as follows:


123456
A10μl of S110μl of S210μl of S310μl of S410μl of S510μl sample
B5μl A1 + 5μl TE5μl A2 + 5μl TE5μl A3 + 5μl TE5μl A4 + 5μl TE5μl A5 + 5μl TE5μl A6 + 5μl TE
C5μl B1 + 5μl TE5μl B2 + 5μl TE5μl B3 + 5μl TE5μl B4 + 5μl TE5μl B5 + 5μl TE5μl B6 + 5μl TE
D5μl C1 + 5μl TE5μl C2 + 5μl TE5μl C3 + 5μl TE5μl C4 + 5μl TE5μl C5 + 5μl TE5μl C6 + 5μl TE
E5μl D1 + 5μl TE5μl D2 + 5μl TE5μl D3 + 5μl TE5μl D4 + 5μl TE5μl D5 + 5μl TE5μl D6 + 5μl TE
F5μl E1 + 5μl TE5μl E2 + 5μl TE5μl E3 + 5μl TE5μl E4 + 5μl TE5μl E5 + 5μl TE5μl E6 + 5μl TE

3.6 Dot Blot and UV crosslinking

  • Equilibrate a positively-charged membrane of appropriate size for at least 10 minutes in 1x TE Buffer, pH 7.6 (e.g. Biorad Zeta-Probe® Membrane, #1620159).
  • Place the equilibrated membrane onto a clean dry Whatman® paper. Allow excess buffer to absorb into the membrane, but do not let the membrane dry out.
  • Spot 2 μl of each dilution onto the membrane.

3'-OH [fmol]100% BIO75% BIO50% BIO25% BIO0% BIOSample
1002μl A12μl A2.........2μl A6
502μl B1......
25...
12.5
6.25
3.125

  • Allow samples to absorb into the membrane.
  • Immediately fix the oligonucleotide to the membrane by crosslinking with UV-light using a commercial UV-light crosslinking instrument according to the manufacturers instructions (e.g. 120 mJ/cm2, 254 nm bulbs, 45-60 second exposure).
  • Proceed immediately with detection (see 3.7) or store the membrane dry at room-temperature.

3.7 Biotin detection with Streptavidin-Alkaline Phosphatase (AP)

  • Perform Biotin detection with an appropriate Streptavidin-AP or -HRP conjugate e.g. according to "Chromogenic Biotin Detection Kit" (Thermo Scientific) with the following modification: Extend Streptavidin incubation from 30 min at room temperature to overnight at room temperature.
  • Compare spot intensities of sample lanes to those of control oligonucleotide template and Biotin oligonucleotide standard.
    Please note: Biotin labeling degree may vary depending on the template (e.g. purity, length or overall sequence).