single molecule studies of viral dna packaging

... Equilibrium HMGB protein –DNA interactions Analysis of DNA force–extension measurements Experimental data curves for extension and release of a single double-stranded DNA (dsDNA) molecule are displayed ... persistencelength of the DNA by a factor of two, the concentration ofdouble box versus single box differs by one order of magni-tude When the DNA is exposed to HMGB proteins, the effec-tive DNA contour ... forDNA compared to single box proteins To gain more insightinto the mechanical properties of the HMGB–DNA complexes,the elastic response of the dsDNA polymer in the absence and in the presence of

Ngày tải lên: 04/12/2022, 16:21

... understanding the DNA unwinding mechanism of WRN, we comprehensively characterized the DNA unwinding properties of chicken WRN helicase core in details, by taking advantages of single-molecule fluorescence ... CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China 4School of Physical Sciences, University of Chinese Academy of Sciences, Beijing ... Trang 1Single-molecule studies reveal reciprocating of WRN helicase core along ssDNA during DNA unwinding Wen-Qiang Wu1, Xi-Miao Hou1, Bo Zhang1,

Ngày tải lên: 04/12/2022, 16:08

... on DNA of various oligomerization states and mutants of GR andestrogen receptor- (ER), which permitted us to resolve different modes of DNA binding of GR Wedemonstrated two-color single molecule ... previousestimates for the DNA bound fraction of nuclear STAT1 and p53 On a single molecule basis, thesepercentages correspond to the fractions of time a GR is bound to DNA DNA residence times of transcription ... concentrations of single intracellular fluorescent molecules can be visualized using wide-fieldillumination, distinguishing higher concentrations of single molecules requires a reduction of the excitationvolume

Ngày tải lên: 18/10/2022, 10:46

... begin by writing the total energy of a viral DNA molecule as the sum of the energy of DNA segments ejected outside the capsid with length L oand the energy of DNA segments remaining inside the ... verify the strongly correlated physics of DNA–DNA interaction in the presence of divalent counterions inside viral capsids, we perform simulation of a system of DNA ... Unlike free DNA molecules in solution, DNA packaged inside capsid are strongly bent and the thermal fluctuations of DNA molecule is strongly suppressed It is due to this unique setup of the bacteriophage

Ngày tải lên: 16/12/2017, 17:51

... spectroscopy of QDs and 5) optical trapping and excitation of single QDs In all of these applications, the focus is on the single particle sensitivity level of QDs The high applicability of QDs in ... sensitivity 3.1 Single Particle Tracking (SPT) The foremost single molecule application where QDs have been used is single particle tracking (SPT) [48] In SPT, single molecules of interests (MOIs) ... extended to track single fluorescent dyes and proteins (sometimes called single molecule fluorescent tracking, SMFT) [50] By studying the motion of single molecules, different modes of motion can

Ngày tải lên: 04/12/2022, 16:21

... maturation, or viral glycoprotein packaging Additional experiments indicated that deletion of this motif reduced viral RNA packaging 6–8 fold and affected the transient association of Gag with nuclear ... dur-ing the early stages of the viral life cycle where they may help facilitate uncoating, reverse transcription and nuclear entry of the viral DNA The regions and modifications of Pr78 required for ... inability of the mutant particles to incorporate the viral glycopro-teins Genome packaging Having demonstrated that the deletion of the KR box did not affect the packaging or processing of the gag-,

Ngày tải lên: 13/08/2014, 09:21

... pattern of the rate of DNA replication along a strand of DNA?" would be "the rate of DNA replication is con-stant." Even without any experimental measurements, our knowledge of the ... cell cycle are single-cell studies, where growth during the cell cycle of a single cell is measured, and cell-culture studies, where growth during the cell cycle of a large number of cells as an ... increase in DNA content with growth rate [25-27], and the DNA contents gave the first accurate measurement of the size of the E. coli genome [25] This model of DNA replication, with bilinear DNA (not

Ngày tải lên: 13/08/2014, 23:20

... SPECTROSCOPIC STUDIES OF METAL CARBONYL COMPLEXES FOR SMALL MOLECULE ACTIVATION KEE JUN WEI NATIONAL UNIVERSITY OF SINGAPORE 2013 SPECTROSCOPIC STUDIES OF METAL CARBONYL COMPLEXES FOR SMALL MOLECULE ... of Contents Acknowledgement i Table of Contents ii viii Summary List of Tables x List of Figures xii List of Schemes xvi Abbreviations xix List of Symbols xxi CHAPTER Introduction 1.1 Small Molecule ... determination of H2 and CO2 100 4.2.3 Photolysis of Mn2(CO)10 in cyclohexane/water mixture 101 4.2.4 Photolysis of Mn2(CO)10 under a variety of conditions 102 4.2.5 Deuteration studies 103 4.2.6 Time Profile

Ngày tải lên: 08/09/2015, 19:33

... the impact of influenza infection and inflammation on DNA damage and DNA damage responses By studying chromatin phosphorylation as a measure of DNA damage, we show that the level of DNA damage ... consistent with DNA damage in lung epithelium after the phase of active viral infection Given that influenza infection in vitro causes single- and double-stranded lesions in the DNA of cultured MDCK ... respond by eliciting DNA damage responses (DDR), which include activation of cell cycle arrest, DNA repair, senescence or cell death, depending on the cell type and severity of DNA damage [11, 12]

Ngày tải lên: 09/09/2015, 08:16

... APPLICATION OF NEW APPROACHES FOR STUDIES OF INFLUENZA-INDUCED INFLAMMATION AND DNA DAMAGE Li Na B.Sc (Hons), NUS A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN SCIENCE DEPARTMENT OF ... INDUCES DNA DAMAGE AND ROBUST DNA DAMAGE RESPONSES IN VIVO 66 3.1 Introduction 66 3.1.1 Investigation of DNA damage as a potential mechanism of influenza pathogenesis 66 3.1.2 Phosphorylation of ... 120 3.5 Future studies 121 3.5.1 Verification of forms of DNA damage 121 3.5.2 DNA repair deficiencies on cell fate and disease outcome 122 CHAPTER 4 FLUORESCENT DETECTION OF HOMOLOGOUS RECOMBINATION

Ngày tải lên: 30/09/2015, 06:20

... time being Trang 152 Single-Molecule Biophysics and Tools Single-molecule biophysics/mechanics studies life processes at the molecular level Some of these studies, regardless of the scientific questions, ... Trang 1Possible Use of DNAs in single molecule force spectroscopy to probe single protein unfolding signatures DEPARTMENT OF PHYSICS NATIONAL UNIVERSITY OF SINGAPORE Trang 2Saw Thuan ... One-DNA and 6 kbp for Two-DNA Figure 19: (A) Pipetting fluid induces shear flow on DNA but it is verified that DNA-bead stays intact after normal pipetting (B) Example of cantilever pulling DNA

Ngày tải lên: 01/10/2015, 17:27

... STUDIES OF NEW PROPERTIES AND APPLICATIONS OF G-QUADRUPLEX DNA NG TAO TAO MAGDELINE B.Sc. (Hons.), NUS A THESIS SUBMITTED FOR THE DEGREE OF THE MASTER OF SCIENCE DEPARTMENT OF CHEMISTRY NATIONAL ... Information of DNA Deoxyribonucleic acid (DNA) is a type of biomacromolecule that contains genetic information used for the functioning of living organisms and certain viruses [1]. DNA is a long ... through a backbone made of sugars and phosphate groups [1-3]. A single strand form of DNA is a long chain composed of different nucleotides. Each nucleotide in DNA consists of three parts: (1) a

Ngày tải lên: 16/10/2015, 12:00

... design-ing of distorted cubane Mn4+Mn33+single molecule magnets The essential idea of the method is a process consisting of sparse regressions and cross-validation for analyzing calculated data of the ... geometry of the core of Mn4+Mn33+ molecules and the formal charges of Mn ions, ligands substituted for the core μ3-O ligand should satisfy the following conditions: (i) To have the valence of 2; ... (1) electron negativity of X (χ X), (2) electron negativity of L1 (χ L1 ), (3) electron negativity of Z1 (χ Z1),35 , 36 (4) electron affinity of L (E EA L ).37The selection of these fea-tures comes

Ngày tải lên: 16/12/2017, 10:33

... ions, of a few Mn4 molecules, a description of the mechanism of exchange couplings between manganese ions of Mn4 molecules is still missing Recently, many synthetic efforts aim at combining molecules ... study of the influence of ligand substitutions on the geometric structure, electronic structure, and magnetic properties of Mn4 single-molecule magnets (SMMs), in order to investigate the role of ... LS state of Mn2+ ions is more favorable than the IS state of Mn2+ ions in Types II and II* of Mn4+Mn2+3 molecules, while the IS state of Mn2+ ions is more favorable than the LS state of Mn2+ ions

Ngày tải lên: 16/12/2017, 17:21

... different methods of stretching and immobilizing DNA molecules for studying single- molecule DNA protein interactions Single- molecule experiments overcome the problem of ensemble-averaging of molecular ... rate of a single DNA polymerase (DNAP) on a single- stranded DNA (ssDNA) stretched by a magnetic trap as shown in Fig 5A Similarly to RNAP, DNAP reads the Fig (A) Schematic representation of experimental ... destabilizing the DNA (B) Comparison of the elasticity of a charomid and pXD II ssDNA and the WLC model curve for dsDNA The difference in G + C content in ssDNA molecules influences the stability of secondary...

Ngày tải lên: 22/06/2014, 18:20

... are capable to probe the DNA binding properties of these important proteins at the singlemolecule level Single- molecule manipulation using magnetic tweezers and single- molecule imaging using atomic ... presence of MvaT and MvaU mixture 67 71 73 75 76 79 81 Single- molecule stretching experiments on Ler -DNA complexes 92 Persistence length and DNA occupancy measurement of LerDNA complexes and H-NS -DNA ... to this thesis Single molecule manipulation method using transverse magnetic tweezers enables us to stretch single DNA molecule and probe the e↵ects of DNA- binding proteins on DNA mechanical...

Ngày tải lên: 09/09/2015, 11:26

... absence of this molecule results in Page of 14 (page number not for citation purposes) Virology Journal 2005, 2:55 delayed onset of viral DNA synthesis as well as inefficient replication of the viral ... onset and expansion of viral DNA synthesis suggest that it functions as part of the DNA replication machinery We propose a model in which pUL114 functions as part of the viral DNA polymerase complex ... subsequent expansion phase of viral DNA synthesis and suggests that this gene product functions as part of the viral DNA replication machinery Discussion Figure in Defects DNA synthesis associated...

Ngày tải lên: 19/06/2014, 08:20

... objective of finding the characteristics of protein binding to single DNA molecules needs the aid of singlemolecule manipulation During the last twenty years, single molecule manipulations have brought ... the position of the magnets relative to the bead Such a magnetic tweezers setup allows the probing of the mechanical properties of a single DNA molecule For that, DNA molecules of interest are ... by the DNA bending rigidity DNA conformations are controlled by the interplay between thermal energy and the bending stiffness of DNA backbone In DNA polymer models, the bending energy of DNA with...

Ngày tải lên: 09/09/2015, 11:25

... micromanipulation of single DNA molecules In brief, the two ends of a DNA molecule (normally the 48.5kb -DNA) is first labeled with biotin- and digoxygenin-labeled oligonucleotides, respectively [2] One end of ... most of the Escherichia coli cells are about µm long and 0.5µm wide, but their chromosomal DNA molecules have a contour length of approximately mm In absence of restriction, such a long DNA molecule ... DNA According to their effects on DNA, these proteins can be roughly divided into classes: DNA wrapper, DNA bender and DNA bridger This classification is based mostly on the topographies of DNA- protein...

Ngày tải lên: 14/09/2015, 08:39