Pyrimidine derivatives for labeled binding partners

• US 6,007,992 A
• Filed: 11/10/1997
• Issued: 12/28/1999
• Est. Priority Date: 11/10/1997
• Status: Expired due to Term

• Current Assignee: Daryl D. Muenchau, Ionis Pharmaceuticals, Inc.
• Original Assignee: Gilead Sciences Inc.
• Inventors: Lin, Kuei-Ying, Matteucci, Mark D.
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/966,875
• Time in Patent Office: 778 Days
• Field of Search: 536/22.1, 536/23.1, 536/25.3, 536/25.31, 536/25.32, 536/25.34, 536/25.4, 435/6, 435/87, 435/90, 435/91.1
• US Class Current: 435/6.12
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Compounds having structure (1) ##STR1## wherein R¹ is --H a protecting group, a linker or a binding partner; and R² and R³⁴ are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.

Claims

1. A method comprising mixing a compound having the structure (1):

##STR37## and tautomers, solvates and salts thereof, wherein R¹ is an oligonucleotide, a protecting group, a linker, or H;

R² is A(Z)_X1, wherein A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R² is not amine, protected amine, nitro or cyano;

R²⁷ is independently --CH═

, --N═

, --C(C₁ -C₈ alkyl)═

or --C(halogen)═

, but no adjacent R²⁷ are both --N═

, or two adjacent R²⁷ are taken together to form a ring having the structure, ##STR38## where Ra is independently --CH═

, --N═

, --C(C₁ -C₈ alkyl)═

or --C(halogen)═

, but no adjacent Ra are both --N═

,

R³⁴ is --O--, --S--, or --N(CH₃)--; and

X1 is 1, 2 or 3;

with a sample suspected of containing a target nucleic acid having a base sequence that is substantially complementary or complementary to the compound'"'"'s base sequence to form a mixture and optionally incubating the mixture to form a complex.

2. The method of claim 1 wherein the compound and the target nucleic acid form a complex having a Tm of about 85 to 95°

C., optionally heating the complex to about 85 to 95 °

C. to provide a heated complex, and optionally mixing the heated complex with a DNA polymerase.

3. The method of claim 1 wherein R¹ has the structure:

##STR39## wherein D is --OH, protected --OH, an oligonucleotide coupling group or a solid support;

D¹ is an oligonucleotide coupling group, --OH, protected --OH, or a solid support, wherein D¹ is bonded to one 2'"'"' or 3'"'"' position in the oligonucleotide of structure (2) and the adjacent 2'"'"' or 3'"'"' position in structure (2) is substituted with R²¹, provided that D and D¹ are not both an oligonucleotide coupling group or they are not both a solid support;

R⁴ is independently a phosphodiester linkage or a phosphodiester substitute linkage, wherein R⁴ is bonded to one 2'"'"' or 3'"'"' position in the structure (2) oligonucleotide and the adjacent 2'"'"' or 3'"'"' position in structure (2) is substituted with R²¹ ;

R²¹ is independently --H, --OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage;

R³⁷ is independently --O--, --CH₂ -- or --CF₂ --;

n is at least about 7; and

B independently is a purine or pyrimidine base or a protected derivative thereof, provided that at least one B is a base of structure (3), ##STR40## .