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  Methods to increase nucleotide signals by raman scatteringUSPTO Application #: 20060166243Title: Methods to increase nucleotide signals by raman scattering Abstract: The methods and apparatus disclosed herein concern nucleic acid sequencing by enhanced Raman spectroscopy. In certain embodiments of the invention, nucleotides are covalently attached to Raman labels before incorporation into a nucleic acid. In other embodiments, unlabeled nucleic acids are used. Exonuclease treatment of the nucleic acid results in the release of labeled or unlabeled nucleotides that are detected by Raman spectroscopy. In alternative embodiments of the invention, nucleotides released from a nucleic acid by exonuclease treatment are covalently cross-linked to nanoparticles and detected by surface enhanced Raman spectroscopy (SERS), surface enhanced resonance Raman spectroscopy (SERRS) and/or coherent anti-Stokes Raman spectroscopy (CARS). Other embodiments of the invention concern apparatus for nucleic acid sequencing. (end of abstract) Agent: Dla Piper Rudnick Gray Cary US LLP Attorneys For Intel Coprporation - San Diego, CA, US Inventors: Xing Su, Andrew A. Berlin, Selena Chan, Steven J. Kirch, Tac-Woong Koo, Gabi Neubauer, Valluri Rao, Narayanan Sundararajan, Mineo Yamakawa USPTO Applicaton #: 20060166243 - Class: 435006000 (USPTO) Related Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Nucleic Acid The Patent Description & Claims data below is from USPTO Patent Application 20060166243. Brief Patent Description - Full Patent Description - Patent Application Claims
CROSS REFERENCE TO RELATED APPLICATIONS [0001] The present application is a continuation-in-part of U.S. patent application Ser. No. 10/099,287, filed on Mar. 14, 2002; and a continuation-in-part of U.S. patent application Ser. No. 09/962,555, filed Sep. 24, 2001. FIELD OF THE INVENTION [0002] The present methods and apparatus relate to the fields of molecular biology and genomics. More particularly, the methods and apparatus concern nucleic acid sequencing. BACKGROUND [0003] Genetic information is stored in the form of very long molecules of deoxyribonucleic acid (DNA), organized into chromosomes. The human genome contains approximately three billion bases of DNA sequence. This DNA sequence information determines multiple characteristics of each individual. Many common diseases are based at least in part on variations in DNA sequence. [0004] Determination of the entire sequence of the human genome has provided a foundation for identifying the genetic basis of such diseases. However, a great deal of work remains to be done to identify the genetic variations associated with each disease. That would require DNA sequencing of portions of chromosomes in individuals or families exhibiting each such disease, in order to identify specific changes in DNA sequence that promote the disease. Ribonucleic acid (RNA), an intermediary molecule in processing genetic information, may also be sequenced to identify the genetic bases of various diseases. [0005] Existing methods for nucleic acid sequencing, based on detection of fluorescently labeled nucleic acids that have been separated by size, are limited by the length of the nucleic acid that can be sequenced. Typically, only 500 to 1,000 bases of nucleic acid sequence can be determined at one time. This is much shorter than the length of the functional unit of DNA, referred to as a gene, which can be tens or even hundreds of thousands of bases in length. Using current methods, determination of a complete gene sequence requires that many copies of the gene be produced, cut into overlapping fragments and sequenced, after which the overlapping DNA sequences may be assembled into the complete gene. This process is laborious, expensive, inefficient and time-consuming. It also typically requires the use of fluorescent or radioactive labels, which can potentially pose safety and waste disposal problems. [0006] More recently, methods for nucleic acid sequencing have been developed involving hybridization to short oligonucleotides of defined sequenced, attached to specific locations on DNA chips. Such methods may be used to infer short nucleic acid sequences or to detect the presence of a specific nucleic acid in a sample, but are not suited for identifying long nucleic acid sequences. BRIEF DESCRIPTION OF THE DRAWINGS [0007] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the disclosed embodiments of the invention. The embodiments of the invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments of the invention presented herein. [0008] FIG. 1 illustrates an exemplary apparatus 10 (not to scale) and method for nucleic acid 13 sequencing, using nucleotides 16 covalently attached to Raman labels. [0009] FIG. 2 illustrates an exemplary apparatus 100 (not to scale) and method for nucleic acid 13 sequencing in which the released nucleotides 130 are covalently attached to nanoparticles 140 prior to detection by surface enhanced Raman spectroscopy (SERS) 180. [0010] FIG. 3 illustrates another exemplary apparatus 210 (not to scale) for nucleic acid 13 sequencing. [0011] FIG. 4 shows the Raman spectra of all four deoxynucleoside monophosphates (dNTPs) at 100 TM concentration, using a 100 millisecond data collection time. Characteristic Raman emission peaks for as shown for each different type of nucleotide. The data were collected without surface-enhancement or labeling of the nucleotides. [0012] FIG. 5 shows SERS detection of 1 nM guanine, obtained from dGMP by acid treatment according to Nucleic Acid Chemistry, Part 1, L. B. Townsend and R. S. Tipson (Eds.), Wiley-Interscience, New York, 1978. [0013] FIG. 6 shows SERS detection of 10 nM cytosine, obtained from dCMP by acid treatment. [0014] FIG. 7 shows SERS detection of 100 nM thymine, obtained from dTMP by acid treatment. [0015] FIG. 8 shows SERS detection of 100 pM adenine, obtained from dAMP by acid treatment. [0016] FIG. 9 shows a comparative SERS spectrum of a 500 nM solution of deoxyadenosine triphosphate covalently labeled with fluorescein (upper trace) and unlabeled dATP (lower trace). The dATP-fluorescein was obtained from Roche Applied Science (Indianapolis, Ind.). A strong increase in the SERS signal was detected in the fluorescein labeled dATP. [0017] FIG. 10 shows the SERS detection of a 0.9 nM (nanomolar) solution of adenine. The detection volume was 100 to 150 femtoliters, containing an estimated 60 molecules of adenine. [0018] FIG. 11 shows the SERS detection of a rolling circle amplification product, using a single-stranded, circular M13 DNA template. DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS [0019] The disclosed methods and apparatus are of use for the rapid, automated sequencing of nucleic acids. In particular embodiments of the invention, the methods and apparatus are suitable for obtaining the sequences of very long nucleic acid molecules of greater than 1,000, greater than 2,000, greater than 5,000, greater than 10,000 greater than 20,000, greater than 50,000, greater than 100,000 or even more bases in length. Advantages over prior art methods include the ability to read long nucleic acid sequences in a single sequencing run, greater speed of obtaining sequence data, decreased cost of sequencing and greater efficiency in operator time required per unit of sequence data. Continue reading... Full patent description for Methods to increase nucleotide signals by raman scattering Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Methods to increase nucleotide signals by raman scattering patent application. ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. Start now! - Receive info on patent apps like Methods to increase nucleotide signals by raman scattering or other areas of interest. ### Previous Patent Application: Methods to assess quality of microarrays Next Patent Application: Methods, compositions, and kits for forming labeled polynucleotides Industry Class: Chemistry: molecular biology and microbiology ### FreshPatents.com Support Thank you for viewing the Methods to increase nucleotide signals by raman scattering patent info. IP-related news and info Results in 0.47674 seconds Other interesting Feshpatents.com categories: Electronics: Semiconductor , Audio , Illumination , Connectors , Crypto , |
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