Pyrimidine derivatives for labeled binding partners

• US 7,511,125 B2
• Filed: 08/19/2004
• Issued: 03/31/2009
• Est. Priority Date: 11/07/1997
• Status: Expired due to Fees

• Current Assignee: Carlsbad Technology Incorporated (Yung Shin Pharmaceuticals Industrial)
• Original Assignee: Carlsbad Technology Incorporated (Yung Shin Pharmaceuticals Industrial)
• Inventors: Matteucci, Mark D., Lin, Kuei-Ying
• Primary Examiner(s): Lewis; Patrick T
• Application Number:
  US10/921,734
• Publication Number:
  US 20050020826A1
• Time in Patent Office: 1,685 Days
• Field of Search: 536/22.1, 536/23.1, 536/25.3, 536/25.31, 536/25.32, 536/25.33, 536/25.34, 536/25.4, 544/245, 544/242, 544/249
• US Class Current: 536/22.1
• 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)

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. An oligonucleotide having the formula:

2. The oligonucleotide of claim 1 wherein R² is —

O(CH₂)₂—

NH₂, —

O(CH₂)₃—

NH₂, —

CH₂—

(CH₂)_tN(R³)₂, —

N(R⁵)—

(CH₂)_tN(R³)₂, —

S—

(CH₂)_tN(R³)₂, —

O(CH₂N(R³)₂, —

O(CH₂)₂—

N(CH₃)₂, —

O(CH₂)₃—

N(CH₃)₂, —

O(CH₂)₂—

NHCH₃, —

O(CH₂)₃—

NHCH₃, —

O—

CH₂—

CH(CH₃)—

NH₂, —

CH₂—

O(CH₂)₂—

NH₂, —

CH₂—

O(CH₂)₃—

NH₂ or —

(CH₂)₂—

O(CH₂)₂—

NH₂.

3. The oligonucleotide of claim 1 wherein each B not having structure II is selected from the group consisting of adenine, guanine, thymine, uracil, cytosine, 5-methylcytosine, 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine, 5-(1-butynyl)uracil and 5-(1-butynyl)cytosine).

4. The oligonucleotide of claim 1 wherein R² is —

R⁶(CH₂)_tN(R⁵)C(NR⁵)N(R³)₂, —

O(CH₂)₂NH₂, —

O(CH₂)₃NH₂, or —

R⁶(R⁷)_vN(R³)₂.

5. The compound of claim 4 wherein R² is —

R⁶(CH₂)_tN(R⁵)C(NR⁵)N(R³)₂.

6. The compound of claim 4 wherein R² is —

R⁶(R⁷)_vN(R³)₂.