| NEW ENGLAND BIOLABS, INC. Patent applications |
| Patent application number | Title | Published |
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| 20120107877 | Methods and Compositions for Concentrating Secreted Recombinant Protein - Methods and compositions are described that relate to obtaining concentrated preparations of secreted recombinant proteins. These proteins are expressed in the form of fusion proteins with a chitin-binding domain (CBD). The fusion proteins are capable of being concentrated in the presence of chitin. Also described is: a shuttle vector that includes a modified LAC4 promoter; a chitinase-negative host cell; a CBD capable of eluting from chitin under non-denaturing conditions; and sterilized chitin, which can be optionally magnetized for facilitating recovery of recombinant protein. | 05-03-2012 |
| 20120088237 | Engineering a Novel Methylation-Specific Restriction Endonuclease - A restriction endonuclease is provided that has been engineered to have a cleavage specificity for a DNA recognition sequence containing a modified nucleotide. Methods for engineering enzymes to cleave DNA containing modified nucleotides at specific sequences are provided. | 04-12-2012 |
| 20120077230 | Removal of the Guanine Cap on the 5' Terminus of RNA - Methods and compositions are provided for efficiently removing a guanine cap from the 5′ end of an RNA using enzymes. Decapped RNA can be used for cloning, sequencing or other RNA manipulations. | 03-29-2012 |
| 20120040333 | Methods to Distinguish Different Disaccharide Products after Digestion with Heparinases - Methods are provided for determining stereochemistry for a component of a composition where the composition includes a glycosaminoglycan (GAG) where the method includes (a) cleaving the GAG with a lyase; (b) separating the products of the cleaved GAG by chromatography in the presence of one or more solvents wherein at least one solvent comprises an organic acid or organic acid derivative in an amount of no more than 50% v/v of solvent; and determining the stereochemistry of the component. | 02-16-2012 |
| 20120028305 | Solubilization and Purification of a Target Protein Fused to a Mutant Maltose-Binding Protein - Methods and compositions are provided that relate to a composition that includes a modified maltose-binding protein (MBP) which when fused to a protein results in an increase in binding affinity for maltodextrin compared with the wild type MBP fused to the protein, the modified MBP maintaining enhanced solubility, The modification includes a mutation selected from the group consisting of: F68L, I318V, Q326R, V344M, and T | 02-02-2012 |
| 20110269202 | Genetically Engineered Yeast for the Production of Biofuels - Compositions and methods are provided for generating biofuels by fermentation from carbon sources other than glucose using genetically engineered yeast strains. For example, a | 11-03-2011 |
| 20110262973 | Methods and Compositions for DNA Manipulation - single-stranded extension having a desired length and sequence composition. Methods for forming single-stranded extensions include: the use of a cassette containing at least one nicking site and at least one restriction site at a predetermined distance from each other and in a predetermined orientation; or primer-dependent amplification which introduces into a polynucleotide molecule, a modified nucleotide which is excised to create a nick using a nicking agent. The methods and compositions provided can be used to manipulate a DNA sequence including introducing site specific mutations into a polynucleotide molecule and for cloning any polynucleotide molecule or set of joined polynucleotide molecules in a recipient molecule such as a vector of choice. | 10-27-2011 |
| 20110256593 | Generation of Random Double-Strand Breaks in DNA Using Enzymes - An enzyme preparation is described that includes a non-specific nuclease and a T7 Endo I mutant in a unit ratio of less than 1:200. This enzyme preparation may be used to generate double-stranded DNA fragments of a size suitable for DNA sequencing. The ends of the fragments can be readily modified as necessary to ligate adaptors or individual nucleotides to one strand of the double-stranded DNA fragments. | 10-20-2011 |
| 20110201056 | Repair of Nucleic Acids for Improved Amplification - Methods and compositions are provided for repairing a polynucleotide so that it can be synthesized efficiently with improved fidelity and yield in, for example, an amplification reaction. This involves the use of a reaction mixture that includes a ligase and a cofactor selected from NAD+ or ATP and incubating the polynucleotide with the reaction mixture in the absence of Endonuclease VI. | 08-18-2011 |
| 20110189753 | Intracellular Production of a Nuclease - Methods and compositions are provided that relate to obtaining a recombinant DNA and RNA cleaving nuclease. This involves the over-expression of a fusion protein between maltose-binding protein and a truncated nuclease in a soluble form in the cytoplasm of a host cell from which it can be readily extracted. | 08-04-2011 |
| 20110151450 | High Fidelity Restriction Endonucleases - Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer. | 06-23-2011 |
| 20110097737 | Methods and Compositions for Targeting Proteins of Interest to the Host Cell Envelope - Methods and compositions are provided for producing membrane proteins or toxic proteins from recombinant DNA introduced into a prokaryotic host cell by targeting the expressed proteins to the envelope of the host cell. The methods and compositions utilize a protein vehicle fused to a protein of interest. The fusion protein may contain one or more protease cleavage sites to separate the protein of interest from the protein vehicle either in vivo or in vitro. The protein vehicle is characterized by a membrane-tar peptide and a trans-membrane segment separated by a cytoplasmic amino acid sequence that includes a cytoplasmic affinity-binding domain. | 04-28-2011 |
| 20110071280 | Methods and Compositions for Concentrating Secreted Recombinant Proteins - Methods and compositions are described that relate to obtaining concentrated preparations of secreted recombinant proteins. These proteins are expressed in the form of fusion proteins with a chitin-binding domain (CBD). The fusion proteins are capable of being concentrated in the presence of chitin. Also described is: a shuttle vector that includes a modified LAC4 promoter; a chitinase-negative host cell; a CBD capable of eluting from chitin under non-denaturing conditions; and sterilized chitin, which can be optionally magnetized for facilitating recovery of recombinant protein. | 03-24-2011 |
| 20110065182 | Modified DNA Cleavage and Methods for Use - Compositions and methods are provided that relate to a modified DNA cleaving enzyme having at least 35% amino acid sequence identity with T7 Endo I. The modified enzyme includes two catalytic centers separated by a β-bridge where the β-bridge contains at least one mutation having an effect of altering enzyme cleavage activity compared to the unmodified enzyme. Activities associated with the modified DNA cleaving enzyme that can be modulated in different reaction conditions include at least one of: (a) non-sequence specific nicking activity; (b) cleaving the second strand of a duplex DNA at a preexisting nick site to produce a linear duplex with a single strand overhang; (c) non-sequence specific DNA cleavage; (d) cleaving DNA flanking a mismatch; and (e) cleavage at a cruciform structure in a DNA duplex. | 03-17-2011 |
| 20110060135 | Selective Purification of Small RNAs from Mixtures - Methods and kits are provided for obtaining small RNAs from a mixture of RNAs of varying sizes such as can be found in a cell lysate or an enzyme-digested RNA. The methods and kits utilize magnetic beads and require the addition of one or more alcohols to bind small RNAs effectively to the beads. | 03-10-2011 |
| 20110053215 | Endoglycosidases that Cleave O-linked Glycans - Methods and compositions have been described that relate to a newly identified polypeptide family wherein each member has O-glycosidase activity and specified sequence characteristics. This family of enzymes can be used for example for cleaving O-linked glycans and for synthesis of neoglycopeptides or neoglycoproteins. | 03-03-2011 |
| 20110045489 | Polymerases for Incorporating Modified Nucleotides - Compositions and methods are provided that relate to a recombinant protein with DNA polymerase activity in which one or more amino acids are mutated compared with the corresponding wild type protein. The recombinant protein is capable of incorporating one or more modified nucleotides into a nucleic acid substrate with a specific activity greater than 200. | 02-24-2011 |
| 20110039306 | Reagent Containing a Thermostable Endonuclease - Compositions and methods are provided for preserving the thermostability of an endonuclease in the presence of DNA for uses that include DNA repair. The compositions and methods include the presence of zinc ions. | 02-17-2011 |
| 20110020911 | SOLUBILIZATION AND PURIFICATION OF A TARGET PROTEIN FUSED TO A MUTANT MALTOSE-BINDING PROTEIN - Methods and compositions are provided for increasing at least one of: (i) binding affinity of a target protein for a maltodextrin substrate and/or (ii) solubility of a target protein. The methods and compositions relate to a modified maltose-binding protein. | 01-27-2011 |
| 20100330551 | Novel Restriction Endonucleases, DNA Encoding These Endonucleases and Methods for Identifying New Endonucleases with the Same or Varied Specificity - Specified restriction endonucleases have been characterized for the first time by their amino acid and DNA sequences. These sequences and those with at least 90% identity thereto have been used as probes in sequence similarity analyses to identify sequence matches in a sequence database that corresponds to novel restriction endonucleases or isoschizomers. The sequence similarity analyses includes selecting a positive sequence match from any sequence producing an expectation value of less than or equal to e-02. | 12-30-2010 |
| 20100240099 | rBSA from K. lactis Expression, Secretion and Purification of Recombinant Bovine Serum Albumin (rBSA) from K. lactis and uses thereof - A recombinant BSA (rBSA) that (a) substantially lacks deoxyribonuclease activity as determined by incubating rBSA with linear DNA overnight and gel electrophoresis, (b) lacks animal viruses associated with animal-derived cell growth supplements; and (c) is capable of stabilizing DNA proteins is provided. Methods for making the rBSA and using it to stabilize enzymes are also provided. | 09-23-2010 |
| 20100173364 | Repair of Nucleic Acids for Improved Amplification - Methods and compositions are provided for repairing a polynucleotide so that it can be copied with improved fidelity and/o yield in, for example, an amplification reaction. This involves the use of a reaction mixture that includes a DNA ligase and an effective amount of at least one endonuclease as well as a cofactor selected from NAD | 07-08-2010 |
| 20100167942 | Compositions, Methods and Related Uses for Cleaving Modified DNA - Compositions, methods and related uses are provided relating to cleaving modified DNA. For example, a set of DNA fragments obtainable by enzymatic cleavage of a large DNA is described where at least 50% are similarly sized and have a centrally positioned modified nucleotide. In addition, an enzyme preparation is provided that includes one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide. The one or more enzymes are further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology to WXD(X) | 07-01-2010 |
| 20100159534 | Recombinant Type II Restriction Endonuclease, NmeAIII, and a Process for Producing the Same - A protein is described that has an amino acid sequence characterized by at least 90% sequence identity with SEQ ID NO: 24, the protein being capable of recognizing a sequence consisting of 5′-GCCGAG-3′ within the double-stranded DNA and cleaving the substrate predominantly at 21/19 nucleotides from the recognition site. A method is also described that utilizes the protein for creating a DNA tag for use as a unique identifier for paired end sequencing of DNA or serial analysis of gene expression. | 06-24-2010 |
| 20100129916 | Expression of Toxic Genes In Vivo in a Non-Natural Host - Compositions and methods are provided for expression of a toxic protein in a host cell preferably a bacterial host cell where at least one T7 RNA polymerase gene Is contained on the host cell chromosome and one or more genes encoding a T7 RNA polymerase inhibitor is located on an F′ plasmid or on the chromosome. | 05-27-2010 |
| 20100112585 | Method for Enriching Methylated CpG Sequences - Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease. | 05-06-2010 |
| 20100075384 | Helicase-dependent amplification of circular nucleic acids - A helicase-mediated amplification method for circular DNA templates and target DNA sequences within the templates is provided. The method combines a DNA polymerase and a helicase preparation to amplify a target sequence as well as the entire circular DNA template. | 03-25-2010 |
| 20090305342 | Solubilization and Purification of a Target Protein fused to a Mutant Maltose-Binding Protein - Methods and compositions are provided for increasing at least one of: (i) binding affinity of a target protein for a maltodextrin substrate and/or (ii) solubility of a target protein. The methods and compositions relate to a modified maltose-binding protein. | 12-10-2009 |
| 20090286251 | Enzyme Reagents for Amplification of Polynucleotides in the Presence of Inhibitors - Compositions and methods are provided for amplifying polynucletoides from samples containing inhibitors that normally inhibit amplification using an enzyme blend containing a plurality of polymerases. The ability to amplify polynucleotides efficiently in the presence of inhibitors allows the enzyme reagent to be used in both routine amplification and real-time amplification from inhibitor-containing samples. | 11-19-2009 |
| 20090280528 | Method for Cloning and Expression of NruI Restriction Endonuclease - Recombinant DNA encoding NruI- and SboI-like restriction endonucleases and methylases and their amino acid sequences are provided as well as methods for expressing the enzymes in transformed host cells and purifying the enzymes. | 11-12-2009 |
| 20090142811 | Discovery, Cloning and Purification of Thermococccus sp. (Strain 9 Degrees N-7) Dna Ligase - Compositions that describe a thermostable DNA ligase isolated from | 06-04-2009 |
| 20090042258 | Methods and Compositions for DNA Manipulation - Methods and compositions are provided for generating a single-stranded extension on a polynucleotide molecule, the single-stranded extension having a desired length and sequence composition. Methods for forming single-stranded extensions include: the use of a cassette containing at least one nicking site and at least one restriction site at a predetermined distance from each other and in a predetermined orientation; or primer-dependent amplification which introduces into a polynucleotide molecule, a modified nucleotide which is excised to create a nick using a nicking agent. The methods and compositions provided can be used to manipulate a DNA sequence including introducing site specific mutations into a polynucleotide molecule and for cloning any polynucleotide molecule or set of joined polynucleotide molecules in a recipient molecule such as a vector of choice. | 02-12-2009 |
| 20090036320 | Rational Design of Binding Proteins That Recognize Desired Specific Sequences - Methods and compositions are provided for creating a binding protein that recognizes a rationally chosen recognition sequence in which a first amino acid has been substituted for a second amino acid using site-directed mutagenesis of a member protein of a set of proteins at an identified position or positions correlated with recognition of a chosen specified target module in the recognition sequence. A system is provided for automating the storage and manipulation of the correlations between positions and types of amino acid residues in the binding protein with specific modules at specified positions in the target recognition sequence and for designing and creating proteins with novel specificities. | 02-05-2009 |
| 20090029418 | METHOD FOR CLONING AND EXPRESSION OF STUI RESTRICTION ENDONUCLEASE AND STUI METHYLASE IN E. COLI - The present invention relates to compositions including: (1) isolated DNA encoding the Stul restriction endonuclease and isolated DNA encoding cognate and non-cognate methylase; (2) vectors and cells containing the isolated DNA; and (3) methods for producing the Stul restriction endonuclease. | 01-29-2009 |
| 20090029376 | High Fidelity Restriction Endonucleases - Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions include restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor. | 01-29-2009 |
| 20080227133 | KpnI Restriction Endonucleases with Reduced Star Activity - Methods are provided for making restriction endonucleases with reduced star activity by one or more targeted mutations to a catalytic site within the restriction endonuclease. Examples of modifications to restriction endonucleases with significant sequence identity with KpnI are provided and reduced star activity demonstrated. | 09-18-2008 |
| 20080213860 | Nicking Endonuclease Methods and Compositions - A nicking endonuclease is described which has an amino acid sequence with at least 70% identity to SEQ ID NO:6 and comprising a mutation at least one of an arginine or gutamic acid corresponding to position 507 and position 546 respectively in SEQ ID NO:6. | 09-04-2008 |
| 20080206835 | Methods and Compositions Relating to Gene Silencing - A method for obtaining a mixture of heterogenous short double-stranded RNA molecules suitable for use in gene silencing (hsiRNA) by subjecting large double-stranded RNA to enzymatic cleavage under specified conditions. The resulting mixture consistently includes enhanced representation of fragments having a size of 21-22 nucleotides absent any fractionation step. The fragments contain sequences that collectively span the entire length of the large double-stranded RNA from which they are derived. Double-stranded RNA with sequences that individually represent segments of a target mRNA may be analyzed using the methods described herein to identify the most active subset of hsiRNA fragments or individual siRNA fragments for achieving gene silencing for any gene or transcribed sequences. A method is additionally provided for preparing and cloning DNA encoding selected siRNA, hsiRNA mixtures or hairpin sequences to provide a continuous supply of a gene silencing reagent derived from any long double-stranded RNA. | 08-28-2008 |
| 20080206832 | Selection and Enrichment of Proteins Using in vitro Compartmentalization - Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer. | 08-28-2008 |
