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 Fluorescein labelled phosphoramidites

Details
Inventors: Brush, Charles K.;
Assignee: Pharmacia Biotech Inc. (Milwaukee, WI)
Primary Examiner: Kunz; Gary L.
Assistant Examiner:
Attorney, Agent or Firm: Quarles & Brady

Compounds useful to attach a fluorescein label to an oligonucleotide are disclosed. To create these compounds, oxygen groups on the fluorescein moiety are protected (e.g. with acyl groups). One then links a phosphoramidite to the fluorescein moiety via an amide or thiourea linkage to an active site on the fluorescein ring. The resulting compound can then be directly linked to an oligonucleotide as it is being formed in an automated synthesizer and then deprotected using the same deprotection conditions as are used to deprotect the oligonucleotides. Such compounds are, inter alia, useful to create labelled primers for DNA sequencing.

DETAILED DESCRIPTION In one aspect, the invention provides a compound of the following formula: ##STR1## wherein the substituent ##STR2## is linked to the fluorescein carbon 1, 2, 3, or 4 positions at B*, or when B* is absent at C*; B* is selected from the group consisting of NR.
sub.
1, O, S, and nothing; R.
sub.
1, R.
sub.
2 and R.
sub.
3 are selected from the group consisting of alkyl groups having 6 or less carbons and H; C*.
dbd.
Y is selected from the group consisting of C.
dbd.
O and C.
dbd.
S, and, when B* is absent, CH.
sub.
2 ; n is a number selected from the group 2-12; and Pam is a phosphoramidite.
The carbon numbering/lettering is as specified in FIG.
2.
Oxygens at the E and G positions in the fluorescein moiety are preferably protected by R.
sub.
4 and R.
sub.
5 each of which may be acyl groups, or other groups that are of the type that are readily removable by treatment with ammonia, such as groups of the structure CH.
sub.
2 CH.
sub.
2 X, where X is an electron-withdrawing moiety.
Examples of such groups are CH.
sub.
2 CH.
sub.
2 CN and CH.
sub.
2 CH.
sub.
2 SO.
sub.
2 .
phi.
.
R.
sub.
4 and R.
sub.
5 are preferably isobutyryl or pivaloyl groups.
In a preferred form, B* can be NH, C*.
dbd.
Y can be C.
dbd.
S, n can be 6, Pam can be a N,N-diisopropyl-beta-cyanoethylphosphoramidite, R.
sub.
2 and R.
sub.
3 can be H, and the substituent can be linked at the fluorescein carbon 3.
In another preferred form, B* is absent, C*.
dbd.
Y can be C.
dbd.
O, n can be 6, Pam can be a N,N-diisopropyl-beta-cyanoethyl-phosphoramidite, R.
sub.
2 and R.
sub.
3 can be H, and the substituent can be linked at the fluorescein carbon 3 and/or 4.
In yet another aspect, the invention provides a method of attaching a fluorescein label to an oligonucleotide.
One reacts one of the compounds of the present invention with an oligonucleotide such that the label becomes linked to the oligonucleotide.
An object of the present invention is therefore to provide a compound useful in fluorescently labelling an oligonucleotide.
Another object is to provide a method of labelling oligonucleotide where the technician merely has to add a compound of the present invention to an oligonucleotide in an automated DNA synthesis machine



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