Single molecule detection with surface-enhanced raman scattering and applications in DNA or RNA sequencing
First Claim
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1. A method for determining the presence of at least one analyte, comprising:
- providing a sample comprising a plurality of aggregates of size of at least about 500 nm adsorbing a plurality of analytes;
exposing the sample to electromagnetic radiation to cause surface-enhanced emission;
obtaining spectral information of the sample, wherein at least one spectral line of the information represents a single analyte adsorbed on one of the plurality of aggregates; and
determining the presence of the single analyte from the at least one spectral line.
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Abstract
Surface-enhanced spectroscopy, such as surface-enhanced Raman spectroscopy employs aggregates that are of a size that allows easy handling. The aggregates are generally at least about 500 nm in dimension. The aggregates can be made of metal particles of size less than 100 nm, allowing enhanced spectroscopic techniques that operate at high sensitivity. This allows the use of larger, easily-handleable aggregates. Signals are determined that are caused by single analytes adsorbed to single aggregates, or single analytes adsorbed on a surface. The single analytes can be DNA or RNA fragments comprising at least one base.
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Citations
195 Claims
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1. A method for determining the presence of at least one analyte, comprising:
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providing a sample comprising a plurality of aggregates of size of at least about 500 nm adsorbing a plurality of analytes;
exposing the sample to electromagnetic radiation to cause surface-enhanced emission;
obtaining spectral information of the sample, wherein at least one spectral line of the information represents a single analyte adsorbed on one of the plurality of aggregates; and
determining the presence of the single analyte from the at least one spectral line. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 172)
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23. A method for determining the presence of an analyte, comprising:
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providing a sample comprising a plurality of aggregates adsorbing a plurality of analytes, wherein at least one aggregate of the plurality of aggregates comprises a metal cluster of at least seven particles and adsorbs only one analyte;
exposing the sample to electromagnetic radiation to cause surface-enhanced emission;
obtaining spectral information of the sample, wherein the only one analyte contributes to the spectral information; and
determining the presence of the only one analyte from the spectral information. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45)
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46. A method for determining the presence of an analyte, comprising:
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providing a sample comprising a plurality of aggregates adsorbing a plurality of analytes, wherein each aggregate comprises a plurality of metal particles, each metal particle having a dimension of no more than about 100 nm and at least one aggregate adsorbs only one analyte;
exposing the sample to electromagnetic radiation to cause surface-enhanced emission;
obtaining spectral information of the sample, wherein the only one analyte contributes to the spectral information; and
determining the presence of the only one analyte from the spectral information. - View Dependent Claims (47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63)
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64. A method for determining the presence of at least one analyte, comprising:
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providing a sample comprising a plurality of aggregates, at least one aggregate adsorbing only one analyte that is free of an emission-enhancing aid;
exposing the sample to electromagnetic radiation; and
obtaining a spectrum, wherein the only one analyte contributes to at least one signal of the spectrum. - View Dependent Claims (65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77)
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78. A method for determining the presence of a single analyte, comprising:
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providing a sample comprising a plurality of surfaces, a portion of the plurality of surfaces adsorbing only one analyte; and
exposing the sample to electromagnetic radiation to cause the sample to emit radiation such that the sample is free of photobleaching. - View Dependent Claims (79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90)
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- 91. A method for determining the presence of at least one molecule, comprising providing at least one molecule, exposing the at least one molecule to electromagnetic radiation to cause Raman scattering, obtaining Raman spectral information and determining the presence of the at least one molecule from at least one anti-Stokes line.
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96. A method for sequencing at least a portion of DNA or RNA, comprising:
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cleaving the at least a portion of DNA or RNA into DNA or RNA fragments, wherein each fragment comprises at least one base;
allowing each DNA or RNA fragment to become surface-adsorbed;
exposing each fragment to electromagnetic radiation to cause surface-enhanced emission; and
obtaining unique surface-enhanced spectral information attributed to each fragment. - View Dependent Claims (97, 98, 99, 100, 101, 102, 103, 104, 105, 106)
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- 107. A method for general field enhancement, comprising providing a plurality of aggregates, exposing the plurality of aggregates to near infrared radiation and inducing at least one electromagnetic resonance in the plurality of aggregates to cause a surface-enhanced radiation.
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118. A method for selecting a spectral range, comprising:
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providing a sample;
positioning at least one filter in association with an optical excitation and detection system, wherein the system is free of a spectrograph and the optical excitation system produces electromagnetic radiation in a first range;
exposing the sample to electromagnetic radiation via the system; and
obtaining a Raman spectrum of the sample having a second range wherein the second range is shifted from the first range. - View Dependent Claims (119, 120, 121)
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122. A method for determining the presence of an analyte, comprising:
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providing a sample comprising a rough metal film including a plurality of protrusions and indentations;
absorbing a plurality of analytes on a surface of the film;
exposing the sample to electromagnetic radiation to cause Raman scattering; and
obtaining a unique Raman signal attributed to a single analyte.
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123. A system for determining the presence of at least one analyte, comprising:
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a sample;
a source of electromagnetic radiation positioned to irradiate the sample; and
a detector positioned to detect surface-enhanced emission from the sample, wherein the sample comprises a plurality of aggregates of size of at least about 500 nm. - View Dependent Claims (124)
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125. A method comprising:
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a) sequentially removing nucleotides from one end of at least one nucleic acid;
b) attaching each nucleotide to at least one nanoparticle;
c) identifying said nucleotides; and
d) determining the sequence of said nucleic acid. - View Dependent Claims (126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137)
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138. A method comprising:
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a) obtaining nucleotides that are attached to Raman labels;
b) providing a nucleic acid comprising labeled nucleotides;
c) removing nucleotides from one end of the nucleic acid;
d) identifying nucleotides by Raman spectroscopy; and
e) determining the sequence of the nucleic acid. - View Dependent Claims (139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149)
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150. An apparatus comprising:
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a) a reaction site for immobilizing a DNA fragment onto an aggregate;
b) a first channel carrying a liquid stream, the first channel in fluid communication with said reaction site;
c) a second channel carrying the liquid stream, the second channel in fluid communication with said first channel;
d) a detection site in fluid communication with said first and second channels; and
e) a detection unit operably coupled to said detection site. - View Dependent Claims (151, 152)
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153. A method comprising:
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a) sequentially removing nucleotides from one end of at least one nucleic acid;
b) moving the nucleotides in a stream packed with nanoparticles;
c) identifying the nucleotides by Raman spectroscopy; and
d) determining the sequence of the nucleic acid. - View Dependent Claims (154, 155, 156, 157, 158, 159, 160, 161)
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162. A method comprising:
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a) preparing a nucleic acid comprising labeled nucleotides;
b) sequentially removing nucleotides from one end of the nucleic acid;
c) moving the nucleotides in a stream packed with nanoparticles;
d) identifying the nucleotides by Raman spectroscopy; and
e) determining the sequence of the nucleic acid. - View Dependent Claims (163, 164, 165, 166, 167, 168, 169, 170, 171)
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173. An apparatus comprising:
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a) a reaction site for immobilizing a DNA fragment onto an aggregate;
b) a first channel carrying a liquid stream, the first channel in fluid communication with said reaction site;
c) a second channel carrying the liquid stream, the second channel in fluid communication with said first channel;
d) a multiplicity of nanoparticles in said second channel; and
e) a Raman detector operably coupled to said second channel. - View Dependent Claims (174, 175, 176, 177, 178)
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179. A method comprising:
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a) removing one or more nucleotides from a nucleic acid;
b) attaching each of the one or more nucleotides to at least one nanoparticle;
c) identifying said nucleotides; and
d) determining the sequence of said nucleic acid. - View Dependent Claims (180, 181, 182, 183, 184, 185, 186, 187)
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188. A method comprising:
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a) removing one or more nucleotides from a nucleic acid;
b) identifying each of the one or more nucleotides by Raman spectroscopy; and
c) determining the sequence of the nucleic acid. - View Dependent Claims (189, 190, 191, 192, 193, 194, 195)
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Specification