Phosphoroamidate esters, and use and synthesis thereof
Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed, including compounds having the following structure: wherein R 1 , R 2 , R 3 and R 4 are as defined herein. These compounds include nucleotide phosphoramidates analogs that are modified on the alpha-phosphate to enable attachment of a variety of application-specific substituents such as tether molecules
1. A compound of the formula:
wherein
R 1 is
an alkyl group which terminates in —C≡CH;
R 3 is R 5 ,
or
R 5 is H or G 1 ;
R 6 is:
an adenosine analog of formula
a guanosine analog of formula
a uridine analog of formula
or
a cytidine analog of formula
R 13 is
an alkyl group which terminates in —C≡CH;
R 8 is OR 11 or —O-SS, wherein SS represents a solid support;
R 11 is H or G 3 ;
G 1 is H or a protecting group for a hydroxyl group that is bonded to a phosphorous atom; and
G 3 is a protecting group for a hydroxyl group that is bonded to a carbon atom.
2. The compound of claim 1 wherein R 1 is —(CH 2 ) q —C≡CH and q is an integer selected from 2-10.
3. The compound of claim 1 wherein R 13 is —C≡C—(CH 2 ) 4 —C≡CH.
4. The compound of claim 1 having the formula:
5. The compound of claim 1 having the formula:
6. The compound of claim 1 having the formula:
7. The compound of claim 6 having the formula (4c).
8. The compound of claim 6 having the formula (4d).
9. The compound of claim 6 having the formula (4e).
10. The compound of claim 6 having the formula (4f).