Sequence Analysis of the DNA Encoding the Eco RI Endonuclease
... the Eco RI enzymes. In spite of this problem, we were able to obtain high quality templatefor sequence analysis. The cloning experiments, analysis of therecombinant phage, andtemplatepreparationare described in the miniprint. Primers wereisolated from restriction endonucleasedigests of pMBl and pPG3 ...
... the Eco RI enzymes. In spite of this problem, we were able to obtain high quality templatefor sequence analysis. The cloning experiments, analysis of therecombinant phage, andtemplatepreparationare described in the miniprint. Primers wereisolated from restriction endonucleasedigests of pMBl and pPG3 ...
The energetic basis of the DNA double helix: a
... on temperature, i.e. the assumption that DNA melting proceeds without heat capacity increment is incorrect; (ii) the duplex formed at 30◦ C is not completely folded; (iii) the separated strands have residual structure, so that in order to associate they must first unfold and the heat of their unfold ...
... on temperature, i.e. the assumption that DNA melting proceeds without heat capacity increment is incorrect; (ii) the duplex formed at 30◦ C is not completely folded; (iii) the separated strands have residual structure, so that in order to associate they must first unfold and the heat of their unfold ...
Identification of a Preinitiation Step in DNA Replication That Is
... Interphase extract was incubated with 2,000 sperm/ml for 30 min. Cyclin A (100 nM) was added and incubated for another 30 min. After this, membrane was added together with 0.5 mM bromodeoxyuridine (BrdU), 0.5 mM MgCl2, and 10 mCi of [a-32P]dATP, and then the reaction was incubated a further 90 min. ...
... Interphase extract was incubated with 2,000 sperm/ml for 30 min. Cyclin A (100 nM) was added and incubated for another 30 min. After this, membrane was added together with 0.5 mM bromodeoxyuridine (BrdU), 0.5 mM MgCl2, and 10 mCi of [a-32P]dATP, and then the reaction was incubated a further 90 min. ...
The DpnI/DpnII pneumococcal system, defense against foreign
... the 7 acidic carboxy terminal amino acids of SsbB (ssbB∆7 mutant).12 Neither the lack of SsbB nor the absence of its acidic tail altered chromosomal transformation of plasticity islands (Fig. 3A), suggesting that the ssDNA-binding protein neither competes with or recruits DpnA to internalized ssDNA ...
... the 7 acidic carboxy terminal amino acids of SsbB (ssbB∆7 mutant).12 Neither the lack of SsbB nor the absence of its acidic tail altered chromosomal transformation of plasticity islands (Fig. 3A), suggesting that the ssDNA-binding protein neither competes with or recruits DpnA to internalized ssDNA ...
The Functions of Introns: From Junk DNA to Designed DNA
... yet known. This raises the question, “If introns produce a major selection advantage and consequently are characteristic of higher, more developed organisms, what could explain their loss in lower organisms?” Variety is critical for species survival, and producing variety is especially difficult in ...
... yet known. This raises the question, “If introns produce a major selection advantage and consequently are characteristic of higher, more developed organisms, what could explain their loss in lower organisms?” Variety is critical for species survival, and producing variety is especially difficult in ...
structure and mechanism of dna polymerases
... abasic sites (Matsumoto and Kim, 1995). The enzyme has a modular organization with an 8‐kDa amino‐terminal domain connected to the carboxy‐terminal domain (31 kDa) by a protease‐hypersensitive hinge region. The 8‐kDa domain contains a 5’‐deoxyribose phosphate (dRP) lyase activity that is needed for ...
... abasic sites (Matsumoto and Kim, 1995). The enzyme has a modular organization with an 8‐kDa amino‐terminal domain connected to the carboxy‐terminal domain (31 kDa) by a protease‐hypersensitive hinge region. The 8‐kDa domain contains a 5’‐deoxyribose phosphate (dRP) lyase activity that is needed for ...
Mechanisms of fast and stringent search in homologous pairing of
... PH, and shear force, suggesting that it may serve as the ‘default’ mode of chromosome pairing in vivo [2]. Various models have been proposed to explain the homology-dependent attraction between dsDNA molecules [9–11], many of which attribute this interaction to hydrophobic forces or electrostatics. ...
... PH, and shear force, suggesting that it may serve as the ‘default’ mode of chromosome pairing in vivo [2]. Various models have been proposed to explain the homology-dependent attraction between dsDNA molecules [9–11], many of which attribute this interaction to hydrophobic forces or electrostatics. ...
... Choice B: Briefly describe one way by which metabolic pathways can be regulated. Illustrate your answer using either glucose storage/release from glycogen, as regulated by hormones, or glycolysis or the TCA cycle, as regulated by energy sensing. Choice C: Briefly describe how corn starch or cane sug ...
A type III-like restriction endonuclease functions as a major barrier to
... and HsdM. Alignment of the HsdS protein sequences from NCTC 8325 (parent of RN4220, clonal complex CC8) with those of the CC30 strain UAMS-1 (24) and CC5 strain SA564 (25) reveals important differences in their respective target recognition domains (TRDs) (Fig. S1). Each TRD binds to part of the rec ...
... and HsdM. Alignment of the HsdS protein sequences from NCTC 8325 (parent of RN4220, clonal complex CC8) with those of the CC30 strain UAMS-1 (24) and CC5 strain SA564 (25) reveals important differences in their respective target recognition domains (TRDs) (Fig. S1). Each TRD binds to part of the rec ...
DpnII - Inv. PCR of miniMos for distribution
... 1. Isolate genomic DNA ......................................................................................................................... 3 2. Digest 150 ng of genomic DNA in 25 ul volume for 3 hours. ............................................ 3 3. Ligate the digested DNA for 2 hours at roo ...
... 1. Isolate genomic DNA ......................................................................................................................... 3 2. Digest 150 ng of genomic DNA in 25 ul volume for 3 hours. ............................................ 3 3. Ligate the digested DNA for 2 hours at roo ...
Chapter 8
... Genetic information is used within a cell to produce the proteins needed for the cell to function. ...
... Genetic information is used within a cell to produce the proteins needed for the cell to function. ...
Mechanistic Comparison of High-Fidelity and Error
... (kpol/Kd,app)inc]/(kpol/Kd,app)inc, where the subscripts “cor” and “inc” indicate the correct and incorrect nucleotide incorporation, respectively. Note that many researchers use a slightly different, “direct ratio” definition of fidelity: (kpol/Kd,app)cor/ (kpol/Kd,app)inc. The latter definition wi ...
... (kpol/Kd,app)inc]/(kpol/Kd,app)inc, where the subscripts “cor” and “inc” indicate the correct and incorrect nucleotide incorporation, respectively. Note that many researchers use a slightly different, “direct ratio” definition of fidelity: (kpol/Kd,app)cor/ (kpol/Kd,app)inc. The latter definition wi ...
Lack of biological significance in the `linguistic features` of
... ‘steeper’ than those of the (mostly) coding ones. This result supports qualitatively the finding (2) that the Zipf exponent is larger, by ∼50%, for the noncoding sequences. In order to quantify this finding we applied the chi-square test to the sequences comparing them with the mean of five highly c ...
... ‘steeper’ than those of the (mostly) coding ones. This result supports qualitatively the finding (2) that the Zipf exponent is larger, by ∼50%, for the noncoding sequences. In order to quantify this finding we applied the chi-square test to the sequences comparing them with the mean of five highly c ...
A Tn 10-lacZ-kanR-URA3 Gene Fusion Transposon for Insertion Mutagenesis and Fusion Analysis of Yeast and Bacterial Genes.
... We describe here a new variant of transposon TnlO especially adapted for transposon analysis of cloned yeast genes; it can equally well be used for analysis of prokaryotic genes. We have applied this element to analysis of the LEU2, RADSO, and CDC48 genes of Saccharomyces cerevisiae. This transposon ...
... We describe here a new variant of transposon TnlO especially adapted for transposon analysis of cloned yeast genes; it can equally well be used for analysis of prokaryotic genes. We have applied this element to analysis of the LEU2, RADSO, and CDC48 genes of Saccharomyces cerevisiae. This transposon ...
Two Waves of Nuclear Factor κB Recruitment to Target Promoters
... modifications of N-terminal histone tails. ATP-dependent chromatin remodeling complexes act by modifying the spatial relationship between nucleosomes and DNA, either through changing the position of specific nucleosomes (sliding) or through altering their three-dimensional structure (for recent revi ...
... modifications of N-terminal histone tails. ATP-dependent chromatin remodeling complexes act by modifying the spatial relationship between nucleosomes and DNA, either through changing the position of specific nucleosomes (sliding) or through altering their three-dimensional structure (for recent revi ...
Using an Alu Insertion Polymorphism to Study Human
... Alu is a member of the family of short interspersed elements (SINEs) and is approximately 300 nucleotides in length. Alu owes its name to a recognition site for the endonuclease AluI in its middle. Although Alu is sometimes called a “jumping gene,” it is not properly a gene, because it does not prod ...
... Alu is a member of the family of short interspersed elements (SINEs) and is approximately 300 nucleotides in length. Alu owes its name to a recognition site for the endonuclease AluI in its middle. Although Alu is sometimes called a “jumping gene,” it is not properly a gene, because it does not prod ...
Physical mapping shows that the unstable oxytetracycline gene
... fragments of 415 kb and 300 kb hybridized. The 415 kb fragment is the fragment that carries the OTC-cluster (Gravius et al., 1993). This fragment was isolated from a PFGE gel, labelled with digoxigenin and used as a probe for colony hybridizations of the S. rimosus gene bank (S. Pandza and others, u ...
... fragments of 415 kb and 300 kb hybridized. The 415 kb fragment is the fragment that carries the OTC-cluster (Gravius et al., 1993). This fragment was isolated from a PFGE gel, labelled with digoxigenin and used as a probe for colony hybridizations of the S. rimosus gene bank (S. Pandza and others, u ...
B.2 Specific Aims. The term `epigenetics` literally means `above the
... modifications of gene expression potential[1]. DNA methylation is one molecular mechanism mediating epigenetic phenomena, and indicates the covalent transfer of a methyl group to the carbon at position 5 of cytosine residues,[2] usually within regions of DNA in which cytosine occurs next to a guanin ...
... modifications of gene expression potential[1]. DNA methylation is one molecular mechanism mediating epigenetic phenomena, and indicates the covalent transfer of a methyl group to the carbon at position 5 of cytosine residues,[2] usually within regions of DNA in which cytosine occurs next to a guanin ...
Nucleolar caspase-2: Protecting us from DNA damage
... show that, in response to DNA damage, caspase-2 forms a complex with the PIDDosome and NPM1 within the nucleolus. Caspase-2 is a critical component of the cellular machinery designed to remove damaged cells, preventing disease. Consistent with a function in the apoptosis pathway, caspase-2, like cas ...
... show that, in response to DNA damage, caspase-2 forms a complex with the PIDDosome and NPM1 within the nucleolus. Caspase-2 is a critical component of the cellular machinery designed to remove damaged cells, preventing disease. Consistent with a function in the apoptosis pathway, caspase-2, like cas ...
Construction of plant BAC libraries This document
... 9. Run the gel using the following parameters: 5.0 v/cm, included angle = 120°, initial switch time = 3.0 sec, final switch time = 4.5 sec, run time = 13 hours, ramping = linear. 10. Using a ruler as a “straight-edge”, cut the gel with a scalpel as shown in FIGURE 2b. There will be seven gel pieces ...
... 9. Run the gel using the following parameters: 5.0 v/cm, included angle = 120°, initial switch time = 3.0 sec, final switch time = 4.5 sec, run time = 13 hours, ramping = linear. 10. Using a ruler as a “straight-edge”, cut the gel with a scalpel as shown in FIGURE 2b. There will be seven gel pieces ...
CHARACTERlZATION OF THE ~ 0 CHONDRIA . L DNA MOLECULE
... genomes are compared between insects, sea urchins and nematodes (Clary and Wolstenholme, 1985; Crozier and Crozier, 1993; Jacobs et al., 1988; Cantatore et al., 1989; Okiomoto et al., 1992). Furthemore, among insects, the location and orientation of pmtein and rRNA genes and the putative control reg ...
... genomes are compared between insects, sea urchins and nematodes (Clary and Wolstenholme, 1985; Crozier and Crozier, 1993; Jacobs et al., 1988; Cantatore et al., 1989; Okiomoto et al., 1992). Furthemore, among insects, the location and orientation of pmtein and rRNA genes and the putative control reg ...
CSE 181 Project guidelines
... • Codon: The sequence of 3 nucleotides in DNA/RNA that encodes for a specific amino acid. • mRNA (messenger RNA): A ribonucleic acid whose sequence is complementary to that of a protein-coding gene in DNA. • Ribosome: The organelle that synthesizes polypeptides under the direction of mRNA • rRNA (ri ...
... • Codon: The sequence of 3 nucleotides in DNA/RNA that encodes for a specific amino acid. • mRNA (messenger RNA): A ribonucleic acid whose sequence is complementary to that of a protein-coding gene in DNA. • Ribosome: The organelle that synthesizes polypeptides under the direction of mRNA • rRNA (ri ...
RECOMBINEERING: A POWERFUL NEW TOOL FOR MOUSE
... strains is that the recombination pathway is constitutively active in them, causing rearrangements and deletions between the repeat sequences that are found in most BAC and PAC clones. Chi-stimulated recombination. Chi-stimulated recombination provides a way to modify genomes with linear dsDNA in wi ...
... strains is that the recombination pathway is constitutively active in them, causing rearrangements and deletions between the repeat sequences that are found in most BAC and PAC clones. Chi-stimulated recombination. Chi-stimulated recombination provides a way to modify genomes with linear dsDNA in wi ...
Nucleosome
A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is often compared to thread wrapped around a spool.Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control, which ensures correct gene expression. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones.Nucleosomes were observed as particles in the electron microscope by Don and Ada Olins and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg. The role of the nucleosome as a general gene repressor was demonstrated by Lorch et al. in vitro and by Han and Grunstein in vivo.The nucleosome core particle consists of approximately 147 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of 2 copies each of the core histones H2A, H2B, H3, and H4. Core particles are connected by stretches of ""linker DNA"", which can be up to about 80 bp long. Technically, a nucleosome is defined as the core particle plus one of these linker regions; however the word is often synonymous with the core particle. Genome-wide nucleosome positioning maps are now available for many model organisms including mouse liver and brain.Linker histones such as H1 and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. Non-condensed nucleosomes without the linker histone resemble ""beads on a string of DNA"" under an electron microscope.In contrast to most eukaryotic cells, mature sperm cells largely use protamines to package their genomic DNA, most likely to achieve an even higher packaging ratio. Histone equivalents and a simplified chromatin structure have also been found in Archea, suggesting that eukaryotes are not the only organisms that use nucleosomes.