Enzymatic Synthesis of Phosphoroselenoate DNA Using Thymidine 5‘-(α-P- seleno)triphosphate and DNA Polymerase for X-ray Crystallography via MAD

2004 ◽  
Vol 126 (2) ◽  
pp. 448-449 ◽  
Author(s):  
Nicolas Carrasco ◽  
Zhen Huang
Keyword(s):  
Dna Polymerase ◽  
Enzymatic Synthesis ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Revealing an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography

Biochemistry ◽  
2020 ◽  
Vol 59 (8) ◽  
pp. 955-963
Author(s):  
Vinod K. Batra ◽  
Khadijeh S. Alnajjar ◽  
Joann B. Sweasy ◽  
Charles E. McKenna ◽  
Myron F. Goodman ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Chemical Biology ◽  
Dna Polymerase Β ◽  
X Ray ◽  
X Ray Crystallography ◽  
Internal Stabilization ◽  
Combined Use

scholarly journals Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
Masaru Tsunoda ◽  
Takeshi Sakaue ◽  
Satoko Naito ◽  
Tomoko Sunami ◽  
Naoko Abe ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Dna Polymerase ◽  
Hydroxyl Radicals ◽  
Base Pair ◽  
Structural Basis ◽  
Dna Duplexes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Guanine Base ◽  
New Type

Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU), which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG) with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble) with G, the latter being a new type of base pair between ionized thymine base and guanine base.In silicostructural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

scholarly journals History of DNA polymerase β X-ray crystallography

DNA Repair ◽  
2020 ◽  
Vol 93 ◽  
pp. 102928 ◽  
Author(s):  
Amy M. Whitaker ◽  
Bret D. Freudenthal
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerase Β ◽  
X Ray ◽  
X Ray Crystallography ◽  
History Of

scholarly journals Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase

2017 ◽  
Vol 53 (94) ◽  
pp. 12704-12707 ◽  
Author(s):  
K. Betz ◽  
A. Nilforoushan ◽  
L. A. Wyss ◽  
K. Diederichs ◽  
S. J. Sturla ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Adduct ◽  
Structural Basis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Selective Incorporation

The structural basis for selective incorporation of BenziMP opposite O6-MeG by KlenTaq DNA polymerase is elucidated by X-ray crystallography.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Electron microscopy of rabbit FC crystals

1983 ◽  
Vol 41 ◽  
pp. 730-731
Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Resolution Electron Microscopy ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Replacement Technique ◽  
Hydrated Crystal ◽  
Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

Sign in / Sign up

Export Citation Format

Share Document