Electrokinetic Stretching of Tethered DNA
... Shaqfeh, 2003). The observation of single molecules of DNA using fluorescence microscopy has also provided new information on biological processes. For example, several groups have investigated the structure of chromatin fibers, a packaging structure in eukaryotes made up of DNA wound tightly around ...
... Shaqfeh, 2003). The observation of single molecules of DNA using fluorescence microscopy has also provided new information on biological processes. For example, several groups have investigated the structure of chromatin fibers, a packaging structure in eukaryotes made up of DNA wound tightly around ...
DNA Binding Properties of Novel Platinum and Palladium
... Figure 1. Structures of cisplatin (left) and Pt(dione)Cl4 (right). ...
... Figure 1. Structures of cisplatin (left) and Pt(dione)Cl4 (right). ...
Mechanisms of fast and stringent search in homologous pairing of
... targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a k ...
... targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a k ...
Analyzing the Changes in DNA Flexibility Due to Base Modifications
... issues. To strip water, we will first make a psf and pdb without water. We will then make an index file and feed the dcd and the index file into catdcd, which will produce a new dcd without water that takes up much less space. The vmd script, strip.tcl, accomplishes these tasks and takes as input a ...
... issues. To strip water, we will first make a psf and pdb without water. We will then make an index file and feed the dcd and the index file into catdcd, which will produce a new dcd without water that takes up much less space. The vmd script, strip.tcl, accomplishes these tasks and takes as input a ...
LAB 1: Scientific Method/Tools of Scientific Inquiry
... *Exercise 2A – Building a double-stranded DNA molecule To build your DNA molecule use the model kit and key to the parts at your table. Acquire a single-strand DNA sequence from your instructor and then follow the instructions below: 1. on your worksheet, write the single-strand DNA sequence you’ve ...
... *Exercise 2A – Building a double-stranded DNA molecule To build your DNA molecule use the model kit and key to the parts at your table. Acquire a single-strand DNA sequence from your instructor and then follow the instructions below: 1. on your worksheet, write the single-strand DNA sequence you’ve ...
Protocol for RiboShredder™ RNase Blend
... unwanted DNase activities prior to use. RiboShredder RNase Blend is useful in a number of applications. When used for DNA purification, all unwanted RNA can be removed using a simple 10-minute procedure. After the reaction is complete, RiboShredder RNase Blend can be removed using a phenol-chlorofor ...
... unwanted DNase activities prior to use. RiboShredder RNase Blend is useful in a number of applications. When used for DNA purification, all unwanted RNA can be removed using a simple 10-minute procedure. After the reaction is complete, RiboShredder RNase Blend can be removed using a phenol-chlorofor ...
Aging is No Longer an Unsolved Problem in Biology
... fact that the senescent phenotype of different species was quite similar, even though the longevity of these species varied by about 30-fold. Thus, similar chemical or biochemical changes, such as the cross-linking of collagen, were occurring at very different rates. Then, at the end of the 20th cen ...
... fact that the senescent phenotype of different species was quite similar, even though the longevity of these species varied by about 30-fold. Thus, similar chemical or biochemical changes, such as the cross-linking of collagen, were occurring at very different rates. Then, at the end of the 20th cen ...
light - Microbiology
... the effect is exclusively due to an increase in the fertility of the donor (F+ male) population ; irradiation of the recipient (F- female) parental bacteria decreases the number of recombinants in proportion to the survivors. Subsequent analysis showed that U.V. irradiation fails to increase the fer ...
... the effect is exclusively due to an increase in the fertility of the donor (F+ male) population ; irradiation of the recipient (F- female) parental bacteria decreases the number of recombinants in proportion to the survivors. Subsequent analysis showed that U.V. irradiation fails to increase the fer ...
Processivity of DNA polymerases: two mechanisms, one goal
... each Okazaki fragment. Ten times more Okazaki fragments are formed during replication than the number of sliding clamps present within the cell, therefore, clamps must also be recycled. In prokaryotes and eukaryotes the clamp loader has a dual function: besides its role as a clamp loader it also fun ...
... each Okazaki fragment. Ten times more Okazaki fragments are formed during replication than the number of sliding clamps present within the cell, therefore, clamps must also be recycled. In prokaryotes and eukaryotes the clamp loader has a dual function: besides its role as a clamp loader it also fun ...
Recombination
... past. Without recombination, in a strictly asexual population, every gene shares the same ancestor. In sexually reproducing populations, however, gene genealogies will differ, as they are being shuffled by recombination. This can be well illustrated with parts of the human genome differing in their ...
... past. Without recombination, in a strictly asexual population, every gene shares the same ancestor. In sexually reproducing populations, however, gene genealogies will differ, as they are being shuffled by recombination. This can be well illustrated with parts of the human genome differing in their ...
Ultraviolet Induction of Chromosome Transfer by
... the effect is exclusively due to an increase in the fertility of the donor (F+ male) population ; irradiation of the recipient (F- female) parental bacteria decreases the number of recombinants in proportion to the survivors. Subsequent analysis showed that U.V. irradiation fails to increase the fer ...
... the effect is exclusively due to an increase in the fertility of the donor (F+ male) population ; irradiation of the recipient (F- female) parental bacteria decreases the number of recombinants in proportion to the survivors. Subsequent analysis showed that U.V. irradiation fails to increase the fer ...
DNA-dependent protein kinase in nonhomologous end joining: a
... also for a functional immune system in higher organisms (for review see Weterings and van Gent, 2004). As a result, two highly efficient DSB repair pathways have evolved in eukaryotic cells: homologous recombination (HR) and nonhomologous end joining (NHEJ). The HR process mediates DSB repair by usi ...
... also for a functional immune system in higher organisms (for review see Weterings and van Gent, 2004). As a result, two highly efficient DSB repair pathways have evolved in eukaryotic cells: homologous recombination (HR) and nonhomologous end joining (NHEJ). The HR process mediates DSB repair by usi ...
From Genetics to DNA
... pull apart. In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two ent ...
... pull apart. In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two ent ...
Genetic dissection of Helicobacter pylori AddAB role in homologous
... of the damage, they could partially complement each other. Unlike what was shown for E. coli (Lloyd et al., 1988), the inactivation of RecOR in H. pylori has a more dramatic effect on UV survival than the inactivation of AddAB (RecBCD in E. coli). A different picture emerges from the analysis of the ...
... of the damage, they could partially complement each other. Unlike what was shown for E. coli (Lloyd et al., 1988), the inactivation of RecOR in H. pylori has a more dramatic effect on UV survival than the inactivation of AddAB (RecBCD in E. coli). A different picture emerges from the analysis of the ...
Molecular Machines
... asymmetric, sawtooth-shaped teeth only allow rotation in one direction. In other words, symmetric motion is made directional by an asymmetric geometry. Ten years ago, Ben Feringa at Groningen University in the Netherlands realised that the rotation of molecular groups entailed by cis–trans isomerisa ...
... asymmetric, sawtooth-shaped teeth only allow rotation in one direction. In other words, symmetric motion is made directional by an asymmetric geometry. Ten years ago, Ben Feringa at Groningen University in the Netherlands realised that the rotation of molecular groups entailed by cis–trans isomerisa ...
Chapter 13 Mutation, DNA Repair, and Recombination
... In eukaryotes, crossing over is associated with the formation of the synaptonemal complex during prophase of meiosis I (Chiasmata). Crossing over involves the breakage of parental chromosomes and rejoining of the parts in new combinations. The Holliday model and the double-strand break model a ...
... In eukaryotes, crossing over is associated with the formation of the synaptonemal complex during prophase of meiosis I (Chiasmata). Crossing over involves the breakage of parental chromosomes and rejoining of the parts in new combinations. The Holliday model and the double-strand break model a ...
Document
... -How can a mixture of molecules, too small to be seen with even a high-powered microscope, be separated from one another? Such was the dilemma facing scientists until the development of a process that has now become standard in many laboratories worldwide- gel electrophoresis. -Laboratories rely hea ...
... -How can a mixture of molecules, too small to be seen with even a high-powered microscope, be separated from one another? Such was the dilemma facing scientists until the development of a process that has now become standard in many laboratories worldwide- gel electrophoresis. -Laboratories rely hea ...
Multiple Barriers to Nonhomologous DNA End Joining
... through the two rounds of meiotic divisions and, while the second division is much like mitosis, it is the unique first division that separates the two homologous chromosomes. Prior to the first division, each pair of homologous chromosomes is linked by a chiasma, which forms once a crossover has occu ...
... through the two rounds of meiotic divisions and, while the second division is much like mitosis, it is the unique first division that separates the two homologous chromosomes. Prior to the first division, each pair of homologous chromosomes is linked by a chiasma, which forms once a crossover has occu ...
Supplementary Figures (doc 9746K)
... FGFR2 are shown. From right to left, they are exon 7, exon 8, exon 9, and exon 10. Exon 8 is the IIIb-specific exon, whereas exon 9 is IIIc-specific. The blue exon peaks are the alignment results of normal RNA-Seq reads, while the yellow ones are from tumor reads. The arcs with numbers in them show ...
... FGFR2 are shown. From right to left, they are exon 7, exon 8, exon 9, and exon 10. Exon 8 is the IIIb-specific exon, whereas exon 9 is IIIc-specific. The blue exon peaks are the alignment results of normal RNA-Seq reads, while the yellow ones are from tumor reads. The arcs with numbers in them show ...
DNA How the Molecule of Heredity Carries, Replicates, and
... exact register; not a single base pair is lost or gained. Two strands do not break and rejoin at the same location; often they are hundreds of base pairs apart. Region between break points is called heteroduplex. Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display ...
... exact register; not a single base pair is lost or gained. Two strands do not break and rejoin at the same location; often they are hundreds of base pairs apart. Region between break points is called heteroduplex. Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display ...
The Structure and Function of the DNA from Bacteriophage Lambda
... sites at each end of the open form consist of a small number of unpaired bases resulting from the protrusion of one strand over the other; the closed form would result from the pairing of the bases in one protrusion with those in the ...
... sites at each end of the open form consist of a small number of unpaired bases resulting from the protrusion of one strand over the other; the closed form would result from the pairing of the bases in one protrusion with those in the ...
Enzyme Mechanisms - Illinois Institute of Technology
... Cross-shaped structures arise from palindromic structures, including interrupted palindromes like this example These are less stable than regular duplexes but they are common, and they do create recognition sites for DNA-binding proteins, including restriction enzymes ...
... Cross-shaped structures arise from palindromic structures, including interrupted palindromes like this example These are less stable than regular duplexes but they are common, and they do create recognition sites for DNA-binding proteins, including restriction enzymes ...
A small organic compound enhances the religation reaction of
... Top1–DNA complex slowing down the religation of the cleaved DNA strand, thus inducing cell death [5]. Two water-soluble CPT derivatives, topotecan and irinotecan have been approved by the FDA (Food and Drug Administration) for clinical use. The 3D structure of the topotecan–enzyme–DNA ternary comple ...
... Top1–DNA complex slowing down the religation of the cleaved DNA strand, thus inducing cell death [5]. Two water-soluble CPT derivatives, topotecan and irinotecan have been approved by the FDA (Food and Drug Administration) for clinical use. The 3D structure of the topotecan–enzyme–DNA ternary comple ...
Section Title – One Line Preferred, Two Line Maximum
... Many PCR parameters might need to be optimized to increase yield, sensitivity of detection or amplification specificity. These parameters include: • Magnesium concentration • Primer annealing temperature • PCR primer design • DNA quality • DNA quantity ...
... Many PCR parameters might need to be optimized to increase yield, sensitivity of detection or amplification specificity. These parameters include: • Magnesium concentration • Primer annealing temperature • PCR primer design • DNA quality • DNA quantity ...
Document
... DNA contains the information needed to make proteins. However, DNA is too large to leave the nucleus. RNA acts as a set of working instructions for ribosomes to make proteins. This process is also known as gene expression. Gene expression is a regulated process. ...
... DNA contains the information needed to make proteins. However, DNA is too large to leave the nucleus. RNA acts as a set of working instructions for ribosomes to make proteins. This process is also known as gene expression. Gene expression is a regulated process. ...
Holliday junction
A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined together. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after the molecular biologist Robin Holliday, who proposed its existence in 1964.In biology, Holliday junctions are a key intermediate in many types of genetic recombination, as well as in double-strand break repair. These junctions usually have a symmetrical sequence and are thus mobile, meaning that the four individual arms may slide though the junction in a specific pattern that largely preserves base pairing. Additionally, four-arm junctions similar to Holliday junctions appear in some functional RNA molecules.Immobile Holliday junctions, with asymmetrical sequences that lock the strands in a specific position, were artificially created by scientists to study their structure as a model for natural Holliday junctions. These junctions also later found use as basic structural building blocks in DNA nanotechnology, where multiple Holliday junctions can be combined into specific designed geometries that provide molecules with a high degree of structural rigidity.