DR. FEI CHEN
Student, Health Care at Archer Rd, Gainesville, FL

8034923, Oct 11, 2011

Mar 27, 2009

12/383776

Steven Albert Benner - Gainesville FL, US
Daniel Hutter - Gainesville FL, US
Nicole Aurora Leal - Gainesville FL, US
Fei Chen - Gainesville FL, US

C07H 21/02, C07H 21/04, C07H 19/04, C07H 19/048, C07H 19/067, C07H 19/073, C07H 19/167, C07H 19/173

536 251, 536 253, 536 2531, 536 256, 536 261, 536 262, 536 2626

Processes are disclosed that use 3′-reversibly terminated nucleoside triphosphates to analyze DNA for purposes other than sequencing using cyclic reversible termination. These processes are based on the unexpected ability of terminal transferase to accept these triphosphates as substrates, the unexpected ability of polymerases to add reversibly and irreversibly terminated triphosphates in competition with each other, the development of cleavage conditions to remove the terminating group rapidly, in high yield, and without substantial damage to the terminated oligonucleotide product, and the ability of reversibly terminated primer extension products to capture groups. The presently preferred embodiments of the disclosed processes use a triphosphate having its 3′-OH group blocked as a 3′-ONHgroup, which can be removed in buffered NaNOand use variants of Taq DNA polymerase, including one that has a replacement (LA).

2011012, May 26, 2011

Jun 16, 2009

12/999138

Steven Albert Benner - Gainesville FL, US
Fei Chen - Gainesville FL, US
Zunyi Yang - Gainesville FL, US

C12P 19/34

435 912

The disclosed invention teaches processes to amplify oligonucleotides by contacting templates and primers with DNA polymerases and triphosphates of non-standard nucleotides, which form nucleobase pairs fitting the standard Watson-Crick geometry, but joined by hydrogen bonding patterns different from those that join standard A:T and G:C pairs. Thus, this invention relates to nucleotide analogs and their derivatives that, when incorporated into DNA and RNA, expand the number of replicatable nucleotides beyond the four found in standard DNA and RNA. The invention further relates to polymerases that incorporate those non-standard nucleotide analogs into oligonucleotide products using the corresponding triphosphate derivatives, and more specifically, polymerases and non-standard nucleoside triphosphates that support the polymerase chain reaction (PCR), including PCR where the products contain more than one non-standard nucleotide unit. Examples are provides that show this process using 6-amino-5-nitro-3-(1′-beta-D-2′-deoxyribofuranosyl)-2(1H)-pyridone to implement the non-standard “small” donor-donor-acceptor (pyDDA) hydrogen bonding pattern, and 2-amino-8-(r-beta-D-2′-deoxyribofuranosyl)-imidazo[1,2-α]-1,3,5-triazin-4(8H)-one to implement the “large” acceptor-acceptor-donor (puADD) pattern.

2011027, Nov 10, 2011

Mar 23, 2009

12/383306

Steven A. Benner - Gainesville FL, US
Daniel Hutter - Gainesville FL, US
Nicole Aurora Leal - Gainesville FL, US
Fei Chen - Gainesville FL, US

C12P 19/34, C07H 19/14, C07H 19/20, C07H 19/10, C07H 19/073

435 911, 536 2626, 536 2852, 536 272

This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions of matter that comprise triphosphates of modified 2′-deoxynucleosides and oligonucleotides that are formed when these are appended to the 3′-end of a primer, wherein said modifications comprise NHmoiety attached to their 3′-hydroxyl group and a fluorescent species in a form of a tag affixed to the nucleobase via a linker that can be cleaved. Such compositions and their associated processes enable and improve the sequencing of oligonucleotides using a strategy of cyclic reversible termination, as outlined in U.S. Pat. No. 6,664,079. Most specifically, the invention concerns compositions of matter that are 5′-triphosphates of ribo- and 2′-deoxyribonucleosides carrying detectable tags and oligonucleotides that might be derived from them. The invention also concerns processes wherein a DNA polymerase, RNA polymerase, or reverse transcriptase synthesizes said oligonucleotides via addition of said triphosphates to a primer.