Physics of protein–DNA interaction
... Not every combination of bases is permitted: in particular only B–B∗ pairs of purines and pyrimidines are possible. The Watson–Crick base pairing consists of combining A with T and G with C. An A–T pair is connected by two hydrogen bonds and a G–C pair by three hydrogen bonds, so they have a higher ...
... Not every combination of bases is permitted: in particular only B–B∗ pairs of purines and pyrimidines are possible. The Watson–Crick base pairing consists of combining A with T and G with C. An A–T pair is connected by two hydrogen bonds and a G–C pair by three hydrogen bonds, so they have a higher ...
Conformation and Rigidity of DNA Microcircles Containing waf1
... microscopy; APM, atomic probe microscope; APTES or AP, 3-aminopropyltriethoxysilane. E-mail address of the corresponding author: [email protected] ...
... microscopy; APM, atomic probe microscope; APTES or AP, 3-aminopropyltriethoxysilane. E-mail address of the corresponding author: [email protected] ...
Nonenzymatic Sequence-Specific Cleavage of Single
... of nucleic acid strands with bifunctional reagents.’ Using (2chloroethy1)amine derivatives attached to the 5’-terminal phosphate of an oligonucleotide,Vlassov et al. observed alkylation and cleavage of three adjacent G residues on a single-stranded DNA target.2 A second synthetic approach has been d ...
... of nucleic acid strands with bifunctional reagents.’ Using (2chloroethy1)amine derivatives attached to the 5’-terminal phosphate of an oligonucleotide,Vlassov et al. observed alkylation and cleavage of three adjacent G residues on a single-stranded DNA target.2 A second synthetic approach has been d ...
View
... H2AX organization around the tss in the replicating genome is noteworthy. The canonical nucleosome and the H2AZ variant typically display the arrangement of −1 nucleosome and nucleosome-free region (NFR) upstream of the tss, and +1 nucleosome stably residing just downstream of the tss (17,25) (Suppl ...
... H2AX organization around the tss in the replicating genome is noteworthy. The canonical nucleosome and the H2AZ variant typically display the arrangement of −1 nucleosome and nucleosome-free region (NFR) upstream of the tss, and +1 nucleosome stably residing just downstream of the tss (17,25) (Suppl ...
Characterization of a novel DNA polymerase activity assay enabling
... has the potential to be used as a rapid and sensitive diagnostic tool, capable of detecting virtually any organism harboring active DNA polymerase within a given environmental or biological matrix where sterility is expected. The most common method used to measure DNA polymerase activity in vitro de ...
... has the potential to be used as a rapid and sensitive diagnostic tool, capable of detecting virtually any organism harboring active DNA polymerase within a given environmental or biological matrix where sterility is expected. The most common method used to measure DNA polymerase activity in vitro de ...
The Role of DNA Methylation in Transposable Element Silencing
... genome (120 Mb) of Arabidopsis, TE fragments constitute approximately 17 % of the genome [4]. In contrast, maize, with a 20-fold larger genome, 2.3 Gb, has TE fragments represent 85 % of the genome [5]. TE activities can potentially change the expression and function of genes near their insertion si ...
... genome (120 Mb) of Arabidopsis, TE fragments constitute approximately 17 % of the genome [4]. In contrast, maize, with a 20-fold larger genome, 2.3 Gb, has TE fragments represent 85 % of the genome [5]. TE activities can potentially change the expression and function of genes near their insertion si ...
Forensic DNA Fundamentals for the Prosecutor
... cific determinations that have significant forensic value to the prosecution of a case. First, they can determine the genetic profile drawn from biological evidence found at a crime scene and match it to the genetic profile from a defendant, which would tie this defendant to this charged crime. Then ...
... cific determinations that have significant forensic value to the prosecution of a case. First, they can determine the genetic profile drawn from biological evidence found at a crime scene and match it to the genetic profile from a defendant, which would tie this defendant to this charged crime. Then ...
Chapter 7
... cytosine nucleotide. The phosphodiester bond will always link the 5-carbon of one deoxyribose (or ribose in RNA) to the 3-carbon of the next sugar. This also means that on one end of a chain of linked nucleotides, there will be a free 5’ phosphate (-PO4) group, and on the other end, a free 3’ hydro ...
... cytosine nucleotide. The phosphodiester bond will always link the 5-carbon of one deoxyribose (or ribose in RNA) to the 3-carbon of the next sugar. This also means that on one end of a chain of linked nucleotides, there will be a free 5’ phosphate (-PO4) group, and on the other end, a free 3’ hydro ...
N6-methyl-adenine: an epigenetic signal for DNA - HAL
... significance was the Dam enzyme of E. coli4,6,7. Dam transfers a methyl group from Sadenosyl-methionine to the amino group of the adenine moiety embedded in 5'-GATC-3' sites4. Methylation occurs shortly (but not immediately) after DNA replication; hence, passage of the replication fork leaves GATC s ...
... significance was the Dam enzyme of E. coli4,6,7. Dam transfers a methyl group from Sadenosyl-methionine to the amino group of the adenine moiety embedded in 5'-GATC-3' sites4. Methylation occurs shortly (but not immediately) after DNA replication; hence, passage of the replication fork leaves GATC s ...
13 Interplay Between H2AX and 53BP1 Pathways in DNA Double
... passed to the progeny cells. If not properly repaired, DSBs can cause alterations in the DNA sequence, chromosomal translocations, genomic instability, and eventually neoplastic transformation. Thus, it is not surprising that the DSB damage response is a highly sophisticated set of reactions that ch ...
... passed to the progeny cells. If not properly repaired, DSBs can cause alterations in the DNA sequence, chromosomal translocations, genomic instability, and eventually neoplastic transformation. Thus, it is not surprising that the DSB damage response is a highly sophisticated set of reactions that ch ...
Paper I- Discussion Points
... To establish the experimental set up that we need, let us move the green locus to the other side of the origin so that the distance between the origin and the red locus is the same as the distance between the red and the green loci. Or, the green locus is now twice as far away from the origin as the ...
... To establish the experimental set up that we need, let us move the green locus to the other side of the origin so that the distance between the origin and the red locus is the same as the distance between the red and the green loci. Or, the green locus is now twice as far away from the origin as the ...
The effect of human serum DNAases on the ability to detect
... In¯uence of human DNAases on the detection rate of puri®ed E. coli DNA by PCR Twenty samples of serum (0.1 ml) from a healthy individual were each inoculated with 30 pg of puri®ed E. coli DNA (Amersham Pharmacia Biotech, Freiburg, Germany). Native human serum was prepared from venous blood as descri ...
... In¯uence of human DNAases on the detection rate of puri®ed E. coli DNA by PCR Twenty samples of serum (0.1 ml) from a healthy individual were each inoculated with 30 pg of puri®ed E. coli DNA (Amersham Pharmacia Biotech, Freiburg, Germany). Native human serum was prepared from venous blood as descri ...
MHF1 plays Fanconi anaemia complementation group M protein
... under standard conditions, the plantlets were incubated for 2 weeks in different concentrations of the genotoxin, followed by the determination of the fresh weight. To evaluate the results, we compared the fresh weights of the mutant lines with the fresh weights of WT plants that had been treated si ...
... under standard conditions, the plantlets were incubated for 2 weeks in different concentrations of the genotoxin, followed by the determination of the fresh weight. To evaluate the results, we compared the fresh weights of the mutant lines with the fresh weights of WT plants that had been treated si ...
STRUCTURE AND DIAGNOSTIC APPLICATIONS OF DNA
... • Nucleotide sequence of each DNA strand is the same when each is read in 5’ to 3’ direction; • Restriction enzymes can cut the Phosphodiester bonds on each DNA strand in three different ways; • Several Restriction Enzymes have been isolated from bacteria; they are named according to the bacterial s ...
... • Nucleotide sequence of each DNA strand is the same when each is read in 5’ to 3’ direction; • Restriction enzymes can cut the Phosphodiester bonds on each DNA strand in three different ways; • Several Restriction Enzymes have been isolated from bacteria; they are named according to the bacterial s ...
Non-Enzymatic, Low Temperature Fluorescence in situ
... couples), alternative mechanisms for ISH may exist. For example, small amounts of single-stranded target DNA present either naturally, or as the result of the fixation process alone, might in some cases be sufficient to allow visualization of probetarget binding sites using low temperature protocols ...
... couples), alternative mechanisms for ISH may exist. For example, small amounts of single-stranded target DNA present either naturally, or as the result of the fixation process alone, might in some cases be sufficient to allow visualization of probetarget binding sites using low temperature protocols ...
DNA Structure Changes Coupled to Protein Binding
... preferred direction of bending. Induced DNA bending is usually associated with protein binding, but can also be caused by binding of other ligands. It has been shown using various experimental techniques that both intrinsic and protein-induced DNA bending depend on the sequence of nucleotide base pa ...
... preferred direction of bending. Induced DNA bending is usually associated with protein binding, but can also be caused by binding of other ligands. It has been shown using various experimental techniques that both intrinsic and protein-induced DNA bending depend on the sequence of nucleotide base pa ...
the roles of apoptotic nucleases in cell death and animal development
... has been found in C. elegans. However, a human nuclease, DFF40 [40-kd DNA fragmentation factor (DFF)] or CAD (caspase-activated deoxyribonuclease), appears to be a good candidate for such an activity. DFF40/CAD was first identified biochemically as a component of a DFF complex, which also contained ...
... has been found in C. elegans. However, a human nuclease, DFF40 [40-kd DNA fragmentation factor (DFF)] or CAD (caspase-activated deoxyribonuclease), appears to be a good candidate for such an activity. DFF40/CAD was first identified biochemically as a component of a DFF complex, which also contained ...
Restriction Digest of pAMP and pKAN
... Hind III and BamH I have digested the original plasmids and that we have the correct restriction fragments. Gel electrophoresis is a procedure commonly used to separate fragments of DNA according to molecular size or number of base pairs. DNA fragments will migrate through the agarose maze. DNA, bec ...
... Hind III and BamH I have digested the original plasmids and that we have the correct restriction fragments. Gel electrophoresis is a procedure commonly used to separate fragments of DNA according to molecular size or number of base pairs. DNA fragments will migrate through the agarose maze. DNA, bec ...
Genetic Technology - McGraw Hill Higher Education
... manufacture short pieces of DNA of any sequence it is programmed to produce. The DNA synthesizer cannot easily make entire genes, but it can make small fragments that can act as primers to DNA replication. If one primer is made for each end of the region of interest, they act to bracket the region t ...
... manufacture short pieces of DNA of any sequence it is programmed to produce. The DNA synthesizer cannot easily make entire genes, but it can make small fragments that can act as primers to DNA replication. If one primer is made for each end of the region of interest, they act to bracket the region t ...
Comparative studies on molecular techniques for detecting
... other hand, the purity of DNA for PCR is not very important. Therefore, the quick extraction method has been recommended by some researchers (Daryl et al. 1994). Because of the presence of inhibitors of Taq polymerase in chiggers after engorgement, it was necessary to remove them when employed for P ...
... other hand, the purity of DNA for PCR is not very important. Therefore, the quick extraction method has been recommended by some researchers (Daryl et al. 1994). Because of the presence of inhibitors of Taq polymerase in chiggers after engorgement, it was necessary to remove them when employed for P ...
Crystal structure of the nucleosome core particle at 2.8 Å
... constructed from three α-helices connected by two loops, L1 and L2, denoted as α1-L1-α2-L2-α3 (Fig. 1c). These regions form crescent-shaped heterodimers in the pairings H3-H4 (Fig. 2a) and H2A-H2B (Fig. 2b) and bind 2.5 turns of DNA double helix, which arcs around them along their long axes to gener ...
... constructed from three α-helices connected by two loops, L1 and L2, denoted as α1-L1-α2-L2-α3 (Fig. 1c). These regions form crescent-shaped heterodimers in the pairings H3-H4 (Fig. 2a) and H2A-H2B (Fig. 2b) and bind 2.5 turns of DNA double helix, which arcs around them along their long axes to gener ...
GeneMorph II EZClone Domain Mutagenesis Kit
... denatured and annealed to the original donor plasmid and extended with a specialized enzyme mix containing a high fidelity DNA polymerase. Using a high-fidelity polymerase minimizes unwanted secondary mutations during the cloning process, which can affect downstream results. The EZClone reaction is ...
... denatured and annealed to the original donor plasmid and extended with a specialized enzyme mix containing a high fidelity DNA polymerase. Using a high-fidelity polymerase minimizes unwanted secondary mutations during the cloning process, which can affect downstream results. The EZClone reaction is ...
DNA Methyltransferases and Structural–Functional Specificity of
... But there is a pronounced gap in structural–functional studies on the enzymatic methylation of eukaryotic DNAs, because only the CpG-type of this modification has been investigated. At present, the association of other site-specific types of eukaryotic DNA methylation with various genetic functions ...
... But there is a pronounced gap in structural–functional studies on the enzymatic methylation of eukaryotic DNAs, because only the CpG-type of this modification has been investigated. At present, the association of other site-specific types of eukaryotic DNA methylation with various genetic functions ...
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.