COMPOSITIONS, METHODS AND SYSTEMS FOR SINGLE MOLECULE SEQUENCING

• US 20110165652A1
• Filed: 01/14/2009
• Published: 07/07/2011
• Est. Priority Date: 01/14/2008
• Status: Abandoned Application

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Lincecum, Tommie Lloyd JR., Pan, Ivan, Stevens, Benjamin, Kraltcheva, Anelia, Nagaswamy, Uma, Deluge, Norha, Kim, Hye Eun, Reddy, Mitsu Sreedhar, Kincaid, Kristi, Volkov, Andrei, Wang, Hongyi, Bandekar, Alok N., Fa, Ming, Castillo, Amy, Bryant, Amy, Hardin, Susan H., Belosludtsev, Yuri
• Application Number:
  US12/812,952
• Publication Number:
  US 20110165652A1
• Time in Patent Office: Days
• US Class Current: 435/194
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/207 the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine adenine dinucleotide or nicotinamide-adenine dinucleotide
• CPC Class Codes: C12N 9/1252 DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
• CPC Class Codes: C12Q 1/6869 Methods for sequencing

Abstract

Compositions, systems and methods of sequencing are disclosed, where the compositions and systems include polymerase enzymes that have been genetically modified to more efficiently incorporate nucleotides including labels having a detectable properties that are released during incorporation, to augment a rate of labeled nucleotide incorporation, to augment a rate of pyrophosphate release, or to augment two or more of these properties and rates. Also disclosed are terminally labeled and dual labeled nucleotides, and click-chemistry based methods of synthesizing the same.

Claims

1-51. -51. (canceled)

52. An isolated variant of Phi-29 polymerase comprising the amino acid sequence shown in SEQ ID NO:

3, wherein the variant comprises an amino acid sequence that is at least 80% identical to SEQ ID NO;

3, and wherein the variant further comprises one or more mutations selected from the group consisting of;

V250A/E375Y, V250A/E375A/Q380A, V250A/E375C, V250A/E375Y, V250I/E375A/Q380A, V250I/E375C, V250A, V250I, E375A, E375C, E375Y, E375A/Q380A, Q380A, D456N, D456E, D456S, D458N, V250A/E375A/Q380A/D456E, E375Y/V250L, E375Y/V250P, E375Y/V250Q, E375Y/V250R, E375Y/V250Y, E375Y/V250F, E375Y/V250S, E375Y/V250C, E375Y/V250T, E375Y/V250K, E375Y/V250H, E375Y/V250N, E375Y/V250D, E375Y/V250G, E375Y/V250W, E375Y/S388G, E375Y/K512A, E375Y/K525A, Y254V/E375Y, K132A, K383A, K383R, K383P, K371A, K371T, Y254F, Y254V, Y254S, Y254V, Y254S, K379A, K525A, K135A, P255S, S388G, K512A, L384R, E486A, E486D, K478A, E375W, N387A, N387Y, V250A/E375W, D456N/D458N/L351P, Y254V/A377E, D456N/D458N, D169A, D12A/D66A/D169A, T15I, N62D, C22S, C290S, C448S, C530S, C290S/C448S/C530S, C22S/C448S/C530S, C22S/C290S/C530S and C22S/C290S/C448S.

65. A method for detecting one or more nucleotide incorporation events, comprising:

conducting a nucleotide polymerase reaction in the presence of one or more detectably labeled nucleotides and a mutant polymerase according to claim 52, which reaction results the production of a detectable signal before, after or during a nucleotide incorporation event; and

detecting the detectable signal, thereby determining if a nucleotide incorporation event has occurred.

66. The method of claim 65, further comprising the step of analyzing the signal to determine the identity of the nucleobase of the incorporated nucleotide.

67. The method of claim 66, wherein the detectable signal is a FRET signal.

53. An isolated variant of Phi-29 polymerase that comprises one or more mutations selected from the group consisting of:

V250A/E375Y, V250A/E375A/Q380A, V250A/E375C, V250A/E375Y, V250I/E375A/Q380A, V250I/E375C, V250A, V250I, E375A, E375C, E375Y, E375A′

Q380A, Q380A, D456N, D456E, D456S, D458N, V250A/E375A/Q380A/D456E, E375Y/V250L, E375Y/V250P, E375Y/V250Q, E375Y/V250R, E375Y/V250Y, E375Y/V250F, E375Y/V250S, E375Y/V250C, E375Y/V250T, E375Y/V250K, E375Y/V250H, E375Y/V250N, E375Y/V250D, E375Y/V250G, E375Y/V250W, E375Y/S388G, E375Y/K512A, E375Y/K525A, Y254V/E375Y, K132A, K383A, K383R, K383P, K371A, K371T, Y254F, Y254V, Y254S, Y254V, Y254S, K379A, K525A, K135A, P255S, S388G, K512A, L384R, E486A, E486D, K478A, E375W, N387A, N387Y, V250A/E375W, D456N/D458N/L351P, Y254V/A377E, D456N/D458N, D169A, D12A/D66A/D169A, T15I, N62D, C22S, C290S, C448S, C530S, C290S/C448S/C530S, C22S/C448S/C530S, C22S/C290S/C530S and C22S/C290S/C448S.

54. The isolated variant of claim 53, wherein the variant comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:

3.

55. The variant of claim 54, wherein the protein is operably linked to a FRET donor.

56. The protein of claim 55, wherein the FRET donor is a nanocrystal.

57. The variant of claim 56, wherein the FRET donor is capable of undergoing FRET with an acceptor attached to a nucleotide before, during or after the nucleotide is incorporated by the polymerase onto the terminal 3′

OH of a synthesized DNA molecule.

58-64. -64. (canceled)