On the feasibility of using network processors for DNA processing
... fields suffer from poorly performing software when run on common processors, which to a large extent can be attributed to the fact that the hardware is not geared for high throughput or the exploitation of parallelism. For example, in our lab the performance of the Blast algorithm was improved signi ...
... fields suffer from poorly performing software when run on common processors, which to a large extent can be attributed to the fact that the hardware is not geared for high throughput or the exploitation of parallelism. For example, in our lab the performance of the Blast algorithm was improved signi ...
Bloom`s Syndrome and BLM
... BLM helicase is a caretaker tumor suppressor Proposed to act in HR pathway Homologous recombination exists to repair double strand breaks and damaged replication forks Sister chromatid exchanges arise during HR from the crossing over of chromatid arms BS cells have high frequency of SCE ...
... BLM helicase is a caretaker tumor suppressor Proposed to act in HR pathway Homologous recombination exists to repair double strand breaks and damaged replication forks Sister chromatid exchanges arise during HR from the crossing over of chromatid arms BS cells have high frequency of SCE ...
the three dynamic levels of dna consciousness
... dynamic levels of DNA consciousness testable models can then be proposed. At this point, both concepts of the theory of DNA consciousness will be able to be subjected to scientific investigation and applied to the science of consciousness studies. The Three Dynamic Levels of DNA Consciousness I have ...
... dynamic levels of DNA consciousness testable models can then be proposed. At this point, both concepts of the theory of DNA consciousness will be able to be subjected to scientific investigation and applied to the science of consciousness studies. The Three Dynamic Levels of DNA Consciousness I have ...
The Expression in Staphylococcus aureus of Cloned DNA Encoding
... al., 1987). Construction of the shuttle vector pGC2 (a hybrid of the S. aureus chloramphenicol-resistance plasmid pC194 opened at its HindIII site and inserted into the PvuII site of the E. coli vector pGEM1) and subcloning into this vector were by standard methods (Maniatis et al., 1982).Strain ANS ...
... al., 1987). Construction of the shuttle vector pGC2 (a hybrid of the S. aureus chloramphenicol-resistance plasmid pC194 opened at its HindIII site and inserted into the PvuII site of the E. coli vector pGEM1) and subcloning into this vector were by standard methods (Maniatis et al., 1982).Strain ANS ...
Recombinational Circularization of Salmonella Phage
... DNA in P22-infected cells destined for lysogeny. In the following experiment, we repeated their procedure and obtained similar results. A culture of strain 18 cells growing at 37” was infected with 32P-labeled c+ phage; the multiplicity of infection, 10 per cell, was sufficient to cause the lysogeni ...
... DNA in P22-infected cells destined for lysogeny. In the following experiment, we repeated their procedure and obtained similar results. A culture of strain 18 cells growing at 37” was infected with 32P-labeled c+ phage; the multiplicity of infection, 10 per cell, was sufficient to cause the lysogeni ...
Restriction Digestion of Lambda DNA
... Classification: Restriction enzymes, or restriction endonucleases, are proteins that recognize and cleave specific sequences of double stranded DNA (Mani et al., 2005a). Most, but not all of the 3000 discovered restriction enzymes found so far, come from bacteria, where they serve as a protection sy ...
... Classification: Restriction enzymes, or restriction endonucleases, are proteins that recognize and cleave specific sequences of double stranded DNA (Mani et al., 2005a). Most, but not all of the 3000 discovered restriction enzymes found so far, come from bacteria, where they serve as a protection sy ...
Article - School of Chemistry and Biochemistry
... To understand how nature has solved the problem of distinguishing the closely related DNA sites, we undertook the structure determination of BglII as a complement to our earlier work on BamHI4,5,16,17. BglII, a 223-amino acid protein, was originally isolated from B. globigii18 and its sequence shows ...
... To understand how nature has solved the problem of distinguishing the closely related DNA sites, we undertook the structure determination of BglII as a complement to our earlier work on BamHI4,5,16,17. BglII, a 223-amino acid protein, was originally isolated from B. globigii18 and its sequence shows ...
DNA purification and isolation of genomic DNA from bacterial
... overall versatility and consistency. This technique exploits the difference in denaturation and renaturation characteristics of covalently closed circular plasmid DNA and chromosomal DNA fragments. Under alkaline conditions (at pH 11), both plasmid and chromosomal DNA are efficiently denatured. Rapi ...
... overall versatility and consistency. This technique exploits the difference in denaturation and renaturation characteristics of covalently closed circular plasmid DNA and chromosomal DNA fragments. Under alkaline conditions (at pH 11), both plasmid and chromosomal DNA are efficiently denatured. Rapi ...
Genes: Structure, Replication, and Mutation
... 7. Most bacterial genes have at least four major parts, each with different functions: promoters, leaders, coding regions, and trailers. 8. Mutations are stable, heritable alterations in the gene sequence and usually, but not always, produce phenotypic changes. Nucleic acids are altered in several d ...
... 7. Most bacterial genes have at least four major parts, each with different functions: promoters, leaders, coding regions, and trailers. 8. Mutations are stable, heritable alterations in the gene sequence and usually, but not always, produce phenotypic changes. Nucleic acids are altered in several d ...
5. Harmful mutations
... chemotherapy to inhibit DNA replication in rapidly-growing cancer cells. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strand by unwinding of the double helix. These structural modifications inhibit transcription and replication processes, causin ...
... chemotherapy to inhibit DNA replication in rapidly-growing cancer cells. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strand by unwinding of the double helix. These structural modifications inhibit transcription and replication processes, causin ...
FluoCycle II™ SYBR® Master Mix
... stranded DNA. When SYBR® Green dye binds to double stranded DNA, the intensity of the fluorescent emissions increases. As more double stranded amplicons are produced, the SYBR® Green dye signal will increase. • Primers and probes should be designed within a region including a G/C content ranging fro ...
... stranded DNA. When SYBR® Green dye binds to double stranded DNA, the intensity of the fluorescent emissions increases. As more double stranded amplicons are produced, the SYBR® Green dye signal will increase. • Primers and probes should be designed within a region including a G/C content ranging fro ...
Specific inhibition of DNA polymerase (3 by its 14 kDa domain: role
... to require P-polymerase for filling short gaps in vitro (9,10) and it has been suggested that p-polymerase is involved in repair of the short gaps (i.e., base excision repair) induced by bleomycin and y-radiation (11). In addition, over-expression of P-polymerase has also been implicated in resistan ...
... to require P-polymerase for filling short gaps in vitro (9,10) and it has been suggested that p-polymerase is involved in repair of the short gaps (i.e., base excision repair) induced by bleomycin and y-radiation (11). In addition, over-expression of P-polymerase has also been implicated in resistan ...
Chapter 16: THE MOLECULAR BASIS OF INHERITANCE (DNA
... Meselson and Franklin Stahl in 1958. They showed that each daughter double helix contains an old strand and a new strand. Meselson and Stahl grew bacteria in heavy nitrogen (15N) medium to label the bases of DNA, making them more dense; and then transferred some of the cells to light nitrogen (14N, ...
... Meselson and Franklin Stahl in 1958. They showed that each daughter double helix contains an old strand and a new strand. Meselson and Stahl grew bacteria in heavy nitrogen (15N) medium to label the bases of DNA, making them more dense; and then transferred some of the cells to light nitrogen (14N, ...
Conformation of DNA in chromatin protein
... remains, for a certain histone/DNA ratio blocked in a B type conformation while for the DNA bound to hi stone HI or H5 the B -• A transition occurs with decreasing relative humidity (3,4). It has recently been shown that at least part of NHP is associated with the chromatin subunits, the nucleosomes ...
... remains, for a certain histone/DNA ratio blocked in a B type conformation while for the DNA bound to hi stone HI or H5 the B -• A transition occurs with decreasing relative humidity (3,4). It has recently been shown that at least part of NHP is associated with the chromatin subunits, the nucleosomes ...
Ch12_lecture - Dr. Brahmbhatt`s Class Handouts
... In a small test tube, DNA is mixed with primers, free nucleotides, and a special heat-resistant DNA polymerase. 1. The test tube is heated to 90°C, which breaks the hydrogen bonds between complementary bases, separating the DNA into single strands. 2. The temperature is lowered to about 50°C to al ...
... In a small test tube, DNA is mixed with primers, free nucleotides, and a special heat-resistant DNA polymerase. 1. The test tube is heated to 90°C, which breaks the hydrogen bonds between complementary bases, separating the DNA into single strands. 2. The temperature is lowered to about 50°C to al ...
Recombinant DNA Technology
... be synthesized by chemical means. In either case the DNA fragment must carry a unique marker (either a radioisotope or a chemical label), so that its incorporation into double-stranded molecules can be followed during the course of a hybridization reaction. A single-stranded DNA molecule used as an ...
... be synthesized by chemical means. In either case the DNA fragment must carry a unique marker (either a radioisotope or a chemical label), so that its incorporation into double-stranded molecules can be followed during the course of a hybridization reaction. A single-stranded DNA molecule used as an ...
The proteasomal deubiquitinating enzyme POH1 promotes the
... Received: 22 May 2012; accepted: 26 July 2012; published online: 21 August 2012 ...
... Received: 22 May 2012; accepted: 26 July 2012; published online: 21 August 2012 ...
A BB B BB - AIMS Press
... Various kinds of probes can be used in qPCR. TaqMan® probes can be used for both quantification and mutation detection, Molecular Beacons are probes that contain a stem-loop structure, with a fluorophore and a quencher at their 5’ and 3’ ends, respectively [10]; Scorpions® primers are suitable for b ...
... Various kinds of probes can be used in qPCR. TaqMan® probes can be used for both quantification and mutation detection, Molecular Beacons are probes that contain a stem-loop structure, with a fluorophore and a quencher at their 5’ and 3’ ends, respectively [10]; Scorpions® primers are suitable for b ...
in vivo chromatin structures
... (12, 24) was prepared from pJW270 (12). DNA fragments were end-labeled with 32P as described (25). Restriction Endonuclease Digestions. When up to 0.1% NaDodSO4 was present in the sample to be digested, 10% Triton X-100 was added to a final concentration of 1%. Most of the endonucleases tested were ...
... (12, 24) was prepared from pJW270 (12). DNA fragments were end-labeled with 32P as described (25). Restriction Endonuclease Digestions. When up to 0.1% NaDodSO4 was present in the sample to be digested, 10% Triton X-100 was added to a final concentration of 1%. Most of the endonucleases tested were ...
"Dot and Slot Blotting of DNA". In: Current Protocols in Molecular
... Dot and Slot Blotting of DNA Dot and slot blotting are simple techniques for immobilizing bulk unfractionated DNA on a nitrocellulose or nylon membrane. Hybridization analysis (UNIT 2.10) can then be carried out to determine the relative abundance of target sequences in the blotted DNA preparations. ...
... Dot and Slot Blotting of DNA Dot and slot blotting are simple techniques for immobilizing bulk unfractionated DNA on a nitrocellulose or nylon membrane. Hybridization analysis (UNIT 2.10) can then be carried out to determine the relative abundance of target sequences in the blotted DNA preparations. ...
Influence of the environment and probes on rapid DNA sequencing
... bandwidth of the electrical probes reduces these overlapping distributions into sharply peaked and disjoint distributions, rather than just limiting the sampling rate. Therefore, assuming that no external sources of noise are present other than shot, thermal and structural fluctuation noise, a singl ...
... bandwidth of the electrical probes reduces these overlapping distributions into sharply peaked and disjoint distributions, rather than just limiting the sampling rate. Therefore, assuming that no external sources of noise are present other than shot, thermal and structural fluctuation noise, a singl ...
Physical and Topological Properties of Circular DNA
... weakly bonded duplex rings containing an interruption in one or both strands. Single rings are exemplified by the viral DNA from X174 bacteriophage. Duplex rings appear to exist in a twisted configuration in neutral salt solutions at room temperature. Examples of such molecules are the DNA's from th ...
... weakly bonded duplex rings containing an interruption in one or both strands. Single rings are exemplified by the viral DNA from X174 bacteriophage. Duplex rings appear to exist in a twisted configuration in neutral salt solutions at room temperature. Examples of such molecules are the DNA's from th ...
RECOMBINANT-DNA METHODOLOGY
... Most useful restriction enzymes cut DNA at specific recognition sites, usually four to six nucleotides in length. There can be multiple restriction sites for a single endonuclease within a given piece of DNA, there can be only one (a unique restriction site), or there can be none. It all depends on ...
... Most useful restriction enzymes cut DNA at specific recognition sites, usually four to six nucleotides in length. There can be multiple restriction sites for a single endonuclease within a given piece of DNA, there can be only one (a unique restriction site), or there can be none. It all depends on ...
DNA repair
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and DNA crosslinkages (interstrand crosslinks or ICLs).The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment. A cell that has accumulated a large amount of DNA damage, or one that no longer effectively repairs damage incurred to its DNA, can enter one of three possible states: an irreversible state of dormancy, known as senescence cell suicide, also known as apoptosis or programmed cell death unregulated cell division, which can lead to the formation of a tumor that is cancerousThe DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal functionality of that organism. Many genes that were initially shown to influence life span have turned out to be involved in DNA damage repair and protection.