Multifunctional linking reagents for synthesis of branched oligomers
First Claim
1. A reagent which is capable of forming a oligomer with monomeric units, said reagent comprising a compound of the formula:
- ##STR12## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, and groups of the formula;
##STR13## wherein X4 is halogen or substituted amino,X5 is alkyl, alkoxy, aryloxy, or a cyano derivative thereof,X6 is halogen, amino or O, andX7 is alkyl, alkoxy or aryloxy, or may be H only if X6 is O, with the proviso that at least one of R1, R2 and R3 is not hydrogen;
Each of X1, X2, and X3 is independently selected from the group consisting of compounds of the formula
space="preserve" listing-type="equation">--X.sub.r --Y.sup.4 -- where r is an integer at least 1, each X is independently C or O, and each C can independently be substituted or unsubstituted, saturated or unsaturated, and Y4 is selected from the group consisting of O, S, NH, N═
N and a direct bond linking Xr with R1, R2, or R3 ; and
Each of Y1, Y2, and Y3 is independently O or S.
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Abstract
Reagents capable of forming branched oligomers with monomeric units are disclosed, together with oligomers incorporating such reagents, kits containing such reagents and methods for use of such reagents in forming oligomers with monomeric units. The present reagents can advantageously be used to introduce multiple labels or reporter molecules onto oligomers such as oligonucleotides and oligopeptides. In particular, non-nucleosidic phosphoramidites based on 1,3,5-tris(2-hydroxyethyl)cyanuric acid are disclosed. Multiply-labeled, branched DNA oligomer probes constructed using these phosphoramidite reagents showed increased signal intensity relative to singly-labeled oligomer probes.
64 Citations
26 Claims
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1. A reagent which is capable of forming a oligomer with monomeric units, said reagent comprising a compound of the formula:
- ##STR12## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, and groups of the formula;
##STR13## wherein X4 is halogen or substituted amino,X5 is alkyl, alkoxy, aryloxy, or a cyano derivative thereof, X6 is halogen, amino or O, and X7 is alkyl, alkoxy or aryloxy, or may be H only if X6 is O, with the proviso that at least one of R1, R2 and R3 is not hydrogen; Each of X1, X2, and X3 is independently selected from the group consisting of compounds of the formula
space="preserve" listing-type="equation">--X.sub.r --Y.sup.4 --where r is an integer at least 1, each X is independently C or O, and each C can independently be substituted or unsubstituted, saturated or unsaturated, and Y4 is selected from the group consisting of O, S, NH, N═
N and a direct bond linking Xr with R1, R2, or R3 ; andEach of Y1, Y2, and Y3 is independently O or S. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
- ##STR12## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, and groups of the formula;
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17. A nucleic acid oligomer having nucleotide and non-nucleotide monomeric units, at least one of said non-nucleotide units comprising a compound of the formula:
- ##STR14## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, linking groups, bonds to adjacent units and groups of the formula ##STR15## wherein X4 is halogen or substituted amino,
X5 is alkyl, alkoxy, aryloxy, or a cyano derivative thereof, X6 is halogen, amino or O, and X7 is alkyl, alkoxy or aryloxy, or may be H only if X6 is O, with the proviso that at least one of R1, R2 and R3 is not hydrogen; Each of X1, X2, and X3 is independently selected from the group consisting of compounds of the formula
space="preserve" listing-type="equation">--X.sub.r --Y.sup.4 --where r is an integer at least 1, each X is independently C or O, and each C can independently be substituted or unsubstituted, saturated or unsaturated, and Y4 is selected from the group consisting of, O, S, NH, N═
N and a direct bond linking Xr with R1, R2, or R3 ; andEach of Y1, Y2, and Y3 is independently O or S, said non-nucleotide unit bound to at least one nucleotide monomeric unit by a bond or linking group at either R1, R2 or R3.
- ##STR14## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, linking groups, bonds to adjacent units and groups of the formula ##STR15## wherein X4 is halogen or substituted amino,
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18. A method for preparing a nucleic acid oligomer having both nucleotide and non-nucleotide units, comprising
coupling at least one unit comprising a compound of the formula: - ##STR16## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, linking groups, bonds to adjacent units, and groups of the formula ##STR17## wherein X4 is halogen or substituted amino,
X5 is alkyl, alkoxy, aryloxy, or a cyano derivative thereof, X6 is halogen, amino or O, and X7 is alkyl, alkoxy or aryloxy, or may be H only if X6 is O, with the proviso that at least one of R1, R2 and R3 is not hydrogen; Each of X1, X2, and X3 is independently selected from the group consisting of compounds of the formula
space="preserve" listing-type="equation">--X.sub.r --Y.sup.4 --where r is an integer at least 1, each X is independently C or O, and each C can independently be substituted or unsubstituted, saturated or unsaturated, and Y4 is selected from the group consisting of, O, S, NH N═
N and a direct bond linking Xr with R1, R2, or R3 ; andEach of Y1, Y2, and Y3 is independently O or S, to at least one nucleotide unit by a bond or linking group at either R1, R2 or R3. - View Dependent Claims (19)
- ##STR16## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, linking groups, bonds to adjacent units, and groups of the formula ##STR17## wherein X4 is halogen or substituted amino,
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20. A kit for preparing a nucleic acid oligomer having both nucleotide and non-nucleotide units, comprising
a receptacle adapted to hold one or more individual reagent containers; - and
a first container containing a reagent in accordance with the formula;
##STR18## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, and groups of the formula ##STR19## wherein X4 is halogen or substituted amino,X5 is alkyl, alkoxy, aryloxy, or a cyano derivative thereof, X6 is halogen, amino or O, and X7 is alkyl, alkoxy or aryloxy, or may be H only if X6 is O, with the proviso that at least one of R1, R2 and R3 is not hydrogen; Each of X1, X2, and X3 is independently selected from the group consisting of compounds of the formula
space="preserve" listing-type="equation">--X.sub.r --Y.sup.4 --where r is an integer at least 1, each X is independently C or O, and each C can independently be substituted or unsubstituted, saturated or unsaturated, and Y4 is selected from the group consisting of, O, S, NH, N═
N and a direct bond linking Xr with R1, R2, or R3 ; andEach of Y1, Y2, and Y3 is independently selected from the group consisting of O and S. - View Dependent Claims (21, 22)
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23. A method for detecting the presence or amount of an analyte in a sample comprising
providing a sample suspected of containing an analyte of interest; -
providing a nucleic acid oligomer having both nucleotide and non-nucleotide units, at least one of said non-nucleotide units comprising a compound of the formula;
##STR20## wherein Each of R1, R2 and R3 is independently selected from the group consisting of hydrogen, blocking groups, capping groups, labels, linking groups, bonds to adjacent units, and groups of the formula ##STR21## wherein X4 is halogen or substituted amino,X5 is alkyl, alkoxy, aryloxy, or a cyano derivative thereof, X6 is halogen, amino or O, and X7 is alkyl, alkoxy or aryloxy, or may be H only if X6 is O, with the proviso that at least one of R1, R2 and R3 further comprises a detectable label, Each of X1, X2, and X3 is independently selected from the group consisting of compounds of the formula
space="preserve" listing-type="equation">--X.sub.r --Y.sup.4 --where r is an integer at least 1, each X is independently C or O, and each C can independently be substituted or unsubstituted, saturated or unsaturated, and Y4 is selected from the group consisting of, O, S, NH, N═
N and a direct bond linking Xr with R1, R2, or R3 ; andEach of Y1, Y2, and Y3 is independently O or S, said non-nucleotide unit bound to at least one nucleotide monomeric unit by a bond or a linking group at either R1, R2 or R3, and wherein said oligomer is configured so as to be able to hybridize with said analyte; exposing said sample to said oligomer for a time and under conditions which permit said oligomer to hybridize with any analyte present in said sample; and detecting the presence or amount of said analyte in said sample. - View Dependent Claims (24, 25, 26)
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Specification