Methods and compositions for analyzing polymers using chimeric tags
First Claim
1. A method for analyzing a polymer comprising contacting the polymer with a conjugate comprising a nucleic acid tag molecule and a nucleic acid binding agent, allowing the nucleic acid binding agent to bind to the polymer non-specifically, and allowing the nucleic acid tag molecule to bind specifically to the polymer, and determining a pattern of binding of the conjugate to the polymer.
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Abstract
The invention relates to the use of conjugates of nucleic acid tag molecules and nucleic acid binding agents for labeling polymers such as nucleic acid molecules. The nucleic acid binding agents are nucleic acid binding enzymes that bind nucleic acid molecules non-specifically, in some embodiments. The conjugate can be formed by directly or indirectly binding the nucleic acid tag molecules to the nucleic acid binding agents. The invention provides conjugate compositions as well as methods and systems for using the conjugates to label and analyze polymers such as nucleic acid molecules.
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Citations
128 Claims
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1. A method for analyzing a polymer comprising
contacting the polymer with a conjugate comprising a nucleic acid tag molecule and a nucleic acid binding agent, allowing the nucleic acid binding agent to bind to the polymer non-specifically, and allowing the nucleic acid tag molecule to bind specifically to the polymer, and determining a pattern of binding of the conjugate to the polymer.
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35. A system for optically analyzing a polymer comprising:
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an optical source for emitting optical radiation;
an interaction station for receiving the optical radiation and for receiving a polymer that is exposed to the optical radiation to produce detectable signals; and
a processor constructed and arranged to analyze the polymer based on the detected radiation including the signals, wherein the polymer is bound to a conjugate comprising a nucleic acid tag molecule and a nucleic acid binding agent. - View Dependent Claims (36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67)
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68. A method for analyzing a polymer comprising:
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generating optical radiation of a known wavelength to produce a localized radiation spot;
passing a polymer through a microchannel;
irradiating the polymer at the localized radiation spot;
sequentially detecting radiation resulting from interaction of the polymer with the optical radiation at the localized radiation spot; and
analyzing the polymer based on the detected radiation, wherein the polymer is bound to a conjugate of a nucleic acid tag molecule and a nucleic acid binding agent. - View Dependent Claims (69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90)
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91. A method for analyzing a nucleic acid molecule, comprising:
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exposing a nucleic acid molecule to a conjugate of a nucleic acid tag molecule and a nucleic acid binding enzyme, allowing the nucleic acid binding enzyme to bind to the nucleic acid molecule, allowing the nucleic acid tag molecule to bind to the nucleic acid molecule in a sequence-specific manner, and determining a pattern of binding of the conjugate to the nucleic acid molecule. - View Dependent Claims (92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111)
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112. A composition comprising
a conjugate of a nucleic acid tag molecule and a nucleic acid binding enzyme, wherein a detectable moiety is present on the nucleic acid binding enzyme.
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113. A composition comprising
a conjugate of a nucleic acid tag molecule and a nucleic acid binding enzyme, wherein a detectable moiety is present on the nucleic acid tag molecule and wherein the nucleic acid binding enzyme is not the detectable moiety.
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125. A method for analyzing a polymer comprising
contacting the polymer with a conjugate comprising a nucleic acid tag molecule and a nucleic acid binding agent, allowing the nucleic acid binding agent to bind to the polymer, and allowing the nucleic acid tag molecule to bind specifically to the polymer, wherein the nucleic acid binding agent is selected from the group consisting of a DNA repair enzyme, a helicase, a nuclease, and a ligase.
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126. A method for labeling a polymer comprising
contacting the polymer with a conjugate comprising a nucleic acid tag molecule and a nucleic acid binding agent, allowing the nucleic acid binding agent to bind to and translocate along the polymer, and allowing the nucleic acid tag molecule to bind specifically to the polymer.
Specification