Protected fluorescent reagent compounds

Patent metadata

Field	Value
Publication number	US-10800805-B2
Application number	US-201815966334-A
Country	US
Kind code	B2
Filing date	Apr 30, 2018
Priority date	Aug 5, 2013
Publication date	Oct 13, 2020
Grant date	Oct 13, 2020

Abstract

Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.

First claim

What is claimed is:

1. A compound of structural formula (I):
Z—[S′—B′] m   (I); wherein

Z is a multivalent central core element comprising a fluorescent dye element;
each S′ is independently an intermediate chemical group, wherein at least one S′ comprises a shield element, and wherein the shield element comprises a plurality of side chains;
each B′ is independently a terminal chemical group, wherein at least one B′ comprises a binding element, and wherein the binding element comprises a nucleotide, biotin, or a polyphosphate; and
m is an integer from 2 to 24.

2. The compound of claim 1 , wherein the shield element decreases photodamage of the compound or of a biomolecule associated with the binding element.

3. The compound of claim 1 , wherein the shield element decreases contact between the fluorescent dye element and the binding element.

4. The compound of claim 1 , wherein at least one side chain has a molecular weight of at least 300.

5. The compound of claim 1 , wherein all of the side chains have a molecular weight of at least 300.

6. The compound of claim 1 , wherein at least one side chain comprises a dendrimer.

7. The compound of claim 1 , wherein at least one side chain comprises a polyethylene glycol.

8. The compound of claim 1 , wherein at least one side chain comprises a negatively-charged component.

9. The compound of claim 8 , wherein the negatively-charged component comprises a sulfonic acid.

10. The compound of claim 1 , wherein at least one side chain comprises a substituted phenyl group.

11. The compound of claim 10 , wherein the at least one side chain comprises the structure:

wherein each x is independently an integer from 1 to 6.

12. The compound of claim 11 , wherein each x is independently an integer from 1 to 4.

13. The compound of claim 1 , wherein at least one side chain comprises a triazole.

14. The compound of claim 1 , wherein at least one side chain comprises the structure:

15. The compound of claim 1 , wherein at least one side chain comprises the structure:

16. The compound of claim 1 , wherein the shield element comprises the structure:

wherein each y is independently an integer from 1 to 6.

17. The compound of claim 1 , wherein the shield element comprises an inner layer and an outer layer.

18. The compound of claim 1 , wherein at least one S′—B′ group comprises the structure:

wherein R 1 and R 2 is each independently aside chain;
L is an alkyl, heteroalkyl, cycloalkyl, cycloheteroalkyl, aryl, or heteroaryl linker; and
Y is

19. The compound of claim 1 , wherein Z comprises a branching element.

20. The compound of claim 19 , wherein the branching element comprises a substituted phenyl group.

21. The compound of claim 19 , wherein the branching element comprises the structure:

wherein each z′ is independently 1 to 6.

22. The compound of claim 1 , wherein the fluorescent dye element is a cyanine dye.

23. The compound of claim 1 , wherein Z comprises a linker group.

24. The compound of claim 23 , wherein the linker group comprises a substituted phenyl group.

25. The compound of claim 24 , wherein the linker group comprises the structure:

wherein each z is independently an integer from 1 to 6.

26. The compound of claim 25 , wherein each z is independently an integer from 1 to 4.

27. The compound of claim 23 , wherein the linker group comprises a diaminoalkyl group.

Assignees

• Pacific Biosciences California Inc

Inventors

• Sebo Lubomir
• Hanes Jeremiah
• Shen Gene
• Brogley Louis
• Yue Stephen
• Zheng Frank
• Lapin Yuri
• Lyle John
• Osuna Honey
• Fedorov Andrei

Classifications

• C12Q1/6869

  Methods for sequencing · CPC title

• C09B23/06

  three >CH- groups, e.g. carbocyanines · CPC title

• C09B69/105

  containing a methine or polymethine dye · CPC title

• C07F9/65616

  containing the ring system [IMAGE cpc-sch-C07F-1006.gif] having three or more than three double bonds between ring members or between ring members and non-ring members, e.g. purine or analogs · CPC title

• C07H19/10 Primary

  with the saccharide radical esterified by phosphoric or polyphosphoric acids · CPC title