making and using an oligo probe labeled with alkaline phosphatase
DESCRIPTION
Making and Using an Oligo Probe Labeled with Alkaline Phosphatase. Alk-Phos Direct Amersham Life Technologies. Outline. Basic idea of the labeled probe The probe labeling reaction = linking of an oligonucleotide to the enzyme alkaline phosphatase Hybridization and rinse considerations - PowerPoint PPT PresentationTRANSCRIPT
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Making and Using an Oligo Probe Labeled withAlkaline Phosphatase
Alk-Phos Direct
Amersham Life Technologies
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Outline
Basic idea of the labeled probe The probe labeling reaction = linking of an
oligonucleotide to the enzyme alkaline phosphatase
Hybridization and rinse considerations Visualization – light production by action of
the enzyme alkaline phosphatase on the substrate CDP-Star
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The basics The enzyme alkaline phosphatase (alk phos) can
produce light given an appropriate substrate. Alk phos can be covalently linked to a nucleic acid
probe and remain active. The probe labeled with alk phos can hybridize to
target DNA on a membrane. The alk phos stays active even after hybridization. Addition of substrate to the blot and recording of the
light produced on film shows where on the blot hybridization occurred!
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The labeling reaction
Oligonucleotide or polynucleotide probe Alkaline phosphatase enzyme
specially developed thermostable enzyme thermostability allows a broader range of temperatures
for establishing appropriate hybridization stringency Formaldehyde crosslinker
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Chemistry of the formaldehyde cross-linking reaction Proteins can be covalently cross-linked to nucleic
acids by formaldehyde. Formaldehyde can also cross-link proteins to each
other. Formaldehyde is a highly reactive dipolar compound. Carbon atom of formaldehyde acts as nucleophilic
center. Amino or imino group + formaldehyde Schiff base Schiff base intermediate + 2nd amino group cross-
link Reaction is reversible at low pH.
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Lysine
Arginine
Histidine
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Note available amino group on each of the bases adenine and cytosine.
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Formaldehyde crosslinking
Protein Formaldehyde
A or C of Nucleic Acid oligo- or polymer
Schiff base or imine
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Hyb and rinse considerations The presence of AlkPhos interferes with base pairing
So, in any given hybridization solution, probe labeled with alkaline phosphatase will have more difficulty hybridizing than a probe labeled with radioactivity or a less bulky label
i.e., the presence of Alk Phos has lowered the Tm of the probe. Think of needing a new mathematical term in the Tm
equation
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Hyb and rinse considerations AlkPhos Direct hybridization and 1o wash solutions
contain urea, a denaturant. Why? Background: You would like to be able to hybridize at
a temperature low enough to preserve the activity of the Alk Phos enzyme. Denaturant lowered Tm, so inclusion of a denaturant
means you can lower the temperature and thereby preserve enzyme activity.
Urea is less damaging to AlkPhos than formamide, the traditional denaturant in hybridization solutions.
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Hyb and rinse considerations (cont’d)
At or near the Tm, a perfectly complementary oligonucleotide is essentially completely bound, or completely free (no bubbles in the hybrid). During hybridization, in high [probe], when an
oligonucleotide separates from the target, it can be replaced by another probe
During rinse, in the absence of additional probe, when an oligonucleotide separates from target, it won’t be replaced by another probe
Short rinses required to avoid losing hybrids between target and probe!
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The light producing reaction: Occurs in alkaline conditions
Caution: Low pH will inhibit alkaline phosphatase enzyme activity. reverse the cross-links formed during the
formaldehyde driven cross-linking reaction! Uses dioxetane substrates
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Light producing reaction[2’spiroadamantane]-4-methoxy-3-[3”-(phosphoryl)phenyl]1,2,-dioxetane
Excited anion
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Dioxetane substrates
can detect < 100 fg of nucleic acid in a single band radioactivity is still more sensitive
half-life of excited molecule ranges from 2 minutes - several hours - several days depends on specific dioxetane molecule and
environment in which the excited molecule is found
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Dioxetane substrates (cont’d)
nylon membranes stabilize decay excited anion stabilized by hydrophobic pocket hydrophobic interactions blue shift to 466 nm
chlorinated dioxetanes (CSPD) minimize both hydrophobic interactions and self-aggregation to cause more rapid decay
AMPPD, CSPD, CDP- Star don’t work with nitrocellulose Nitrocellulose is insufficiently hydrophobic
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CDP-Star is a stabilized dioxetane has short lag phase fast results
The turnover rate for various enzyme/substrate combinations varies. The higher the turnover rate, the shorter the lag phase. Turnover rate = the number of enzymatic reaction
repetitions/unit time yields maximum light by 4 hours and continues light
production for several days allows multiple exposures to film, so the user
can optimize signal to noise can more accurately compare intensities of sample in different
lanes = more accurate relative quantitation
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P.S.
10-3 = milli 10-6 = micro 10-9 = nano 10-12 = pico 10-15 = femto 10-18 = ??? 10-21 = zepto