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Sequencing-Related US Patents, Granted June — July 2007

US Patent 7,247,434. Methods and compositions for determining the sequence of nucleic acid molecules. Inventors: Jeffrey Van Ness, John C. Tabone, J Jeffry Howbert, John T Mulligan. Assignee: Operon Biotechnologies.
Protects methods and compounds for determining the sequence of nucleic acid molecules. The methods “permit the determination of multiple nucleic acid sequences simultaneously,” according to the patent abstract, and the compounds are used as tags to generate tagged nucleic acid fragments that are complementary to a selected target nucleic acid molecule. In a preferred embodiment, the tags are detected by mass spectrometry and the sequence of the nucleic acid molecule is determined.

US Patent 7,244,567. Double ended sequencing. Inventors: Yi-Ju Chen, John H. Leamon, Kenton L. Lohman, Michael T. Ronan, Jonathan M. Rothberg, Maithreyan Srinivasan, Michael P. Weiner. Assignee: 454 Life Sciences.
Covers methods of sequencing both the sense and antisense strands of DNA through the use of blocked and unblocked sequencing primers. These methods include the steps of “annealing an unblocked primer to a first strand of nucleic acid; annealing a second blocked primer to a second strand of nucleic acid; elongating the nucleic acid along the first strand with a polymerase; terminating the first sequencing primer; deblocking the second primer; and elongating the nucleic acid along the second strand,” according to the patent abstract.

US Patent 7,244,559. Method of sequencing a nucleic acid. Inventors: Jonathan M. Rothberg, Joel S. Bader, Scott B. Dewell, Keith McDade, John W. Simpson, Jan Berka, Christopher M. Colangelo. Assignee: 454 Life Sciences.
Covers methods for sequencing a nucleic acid that permit “a very large number” of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of more than 10,000 different oligonucleotides, the patent abstract states.

US Patent 7,238,530. Isolation and amplification of nucleic acid materials. Inventors: Jaap Goudsmit, Cornelis Johannes Andreas Sol, Marcellinus Gualbertus Hubertus Maria Beld, Willem Rene Boom. Assignee: bioMerieux.
Protects methods for separating single-stranded nucleic acid material from double-stranded nucleic acid material in a sample containing both. According to the patent abstract, “by the right choice of at lease one chaotropic agent, preferably a guanidine salt, at a selected concentration and other suitable conditions such a chelating agents, pH and the like, it is possible to bind double-stranded material to a solid phase such as silica particles, whereas single-stranded material will not bind under those circumstances.” The double-stranded material can be removed by separating the silica particles from the sample and eluting the silica particles. Following the separation of the two kinds of nucleic acid, either kind may be amplified. “Methods of amplification are provided which do not need sequence data of the material to be amplified,” the abstract states. “In these methods a primer will be provided with an amplification motif and a random hybridization motif.”

US Patent 7,238,485. Methods and apparatus for characterizing polynucleotides. Inventors: Mark Akeson; Daniel Branton, David W. Deamer, Jeffrey R. Sampson. Assignee: President and Fellows of Harvard College, Regents of the University of California, Agilent Technologies.
Protects systems and methods for analyzing polymers such as polynucleotides at a specified rate. One such system includes a structure having a nanopore aperture and a molecular motor, such as a polymerase, adjacent the nanopore aperture.

US Patent 7,238,323. Microfluidic sequencing systems. Inventors: Michael Knapp, John Wallace Parce, Luc J. Bousse, Anne R. Kopf-Sill. Assignee: Caliper Life Sciences.
Covers integrated microfluidic systems, apparatus, software, and methods for performing biochemical analysis, including DNA sequencing, genomic screening, purification of nucleic acids and other biological components, and drug screening. “The devices and systems of are used in performing fluid operations which require a large number of iterative, successive or parallel fluid manipulations, in a microscale, or sealed and readily automated format,” according to the patent abstract.

US Patent 7,238,321. Method for rapid thermal cycling of biological samples.
Covers a thermal cycling method and device that includes a sample chamber whose temperature can be “rapidly and accurately modulated over a range of temperatures needed to carry out a number of biological procedures, such a DNA polymerase chain reaction,” according to the patent abstract.
Inventors: Carl T. Wittwer, David R. Hillyard. Assignee: University of Utah Research Foundation.

US Patent 7,235,387. Method for mutation detection in HIV-1 using pol sequencing. Inventors: Brendan Larder, Sharon Kemp, Stuart Bloor, Ann Brophy. Assignee: Virco.
Protects a method for mutation analysis of the HIV pol gene of HIV virions that comprises amplifying virion RNA or DNA via nested PCR using outer primers, amplifying the PCR product via nested PCR using a 5' and 3' primer chosen from the inner primers, and sequencing this secondary PCR product. “The benefit of the sequences present in the invention resides in the fact that, with the aid of the oligonucleotides, the sequences of all presently known HIV subtypes and all mutations of the pol gene presently known to yield resistance towards antiretroviral therapy can be determined,” according to the patent abstract.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.