Thong H Nguyen

US Patent:

20060141498, Jun 29, 2006

Filed:

Nov 14, 2005

Appl. No.:

11/273964

Inventors:

Kai Wu - Mountain View CA, US
Charles Miyada - San Jose CA, US
Thong Nguyen - San Jose CA, US

Assignee:

Affymetrix, INC. - Santa Clara CA

International Classification:

C12Q 1/68
C12P 19/34
C12N 9/22

US Classification:

435006000, 435091200, 435199000

Abstract:

Methods for using an apurinic/apyrimidinic endonuclease, capable of cleaving both single- and double-stranded cDNA, for fragmentation and labeling of single stranded or double stranded DNA molecules are provided. Amplification methods that generate single-stranded amplified cDNA are also disclosed. In the subject methods AP sites in a population of nucleic acids are cleaved by an AP endonuclease that is active on both double and single stranded DNA. Fragments may be end labeled. In preferred embodiments APE 1 is used. The methods may be used in a variety of applications where end-labeling single or double stranded DNA is desired.

US Patent:

20070218478, Sep 20, 2007

Filed:

Dec 18, 2006

Appl. No.:

11/612454

Inventors:

Qing Bai - Santa Clara CA, US
Susana Salceda - San Jose CA, US
Kai Wu - Mountain View CA, US
Thong Nguyen - San Jose CA, US
Charles Miyada - San Jose CA, US

Assignee:

Affymetrix, INC. - Santa Clara CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435006000, 435091200

Abstract:

Methods for fragmenting and labeling DNA in a single reaction volume and incubation step using a uracil DNA glycosylase, an apurinic/apyrimidinic endonuclease, and a terminal transferase are disclosed. In a preferred embodiment the UDG, AP and TdT activities are first mixed together to form an enzyme mixture and then the enzyme mixture is mixed with the uracil containing DNA. The fragmentation and labeling reactions thus take place simultaneously as part of the same reaction. The methods may be used in a variety of applications where fragmenting and end-labeling single or double stranded DNA is desired.