ChemInform Abstract: Nucleic Acid X-Ray Crystallography via Direct Selenium Derivatization

ChemInform ◽  
2011 ◽  
Vol 42 (49) ◽  
pp. no-no
Author(s):  
Lina Lin ◽  
Jia Sheng ◽  
Zhen Huang
Keyword(s):  
Nucleic Acid ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe

2019 ◽  
Vol 47 (12) ◽  
pp. 6059-6072 ◽  
Author(s):  
Ashok Nuthanakanti ◽  
Ishtiyaq Ahmed ◽  
Saddam Y Khatik ◽  
Kayarat Saikrishnan ◽  
Seergazhi G Srivatsan
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Real Time ◽  
Telomeric Dna ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Class ◽  
Loop Region ◽  
Dna Repeat ◽  
G Quadruplex

Abstract Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2′-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.

Nucleic Acid Related Compounds. 136. Synthesis of 2-Amino- and 2,6-Diaminopurine Derivatives via Inverse-Electron-Demand Diels-Alder Reactions

2006 ◽  
Vol 71 (7) ◽  
pp. 1029-1041 ◽  
Author(s):  
Xiaoyu Lin ◽  
Morris J. Robins
Keyword(s):  
Nucleic Acid ◽  
Diels Alder ◽  
Curtius Rearrangement ◽  
X Ray ◽  
Inverse Electron Demand ◽  
X Ray Crystallography ◽  
Acid Catalyzed ◽  
Hydrolysis Of ◽  
Related Compounds ◽  
Electron Demand

Thermal inverse-electron-demand Diels-Alder reactions of 5-aminoimidazoles and 2,4,6-tris(ethoxycarbonyl)-1,3,5-triazine (2) with spontaneous retro-Diels-Alder loss of ethyl cyanoformate and elimination of ammonia give 2,6-bis(ethoxycarbonyl)purines. A report that selective alkaline hydrolysis followed by acid-catalyzed decarboxylation gave 6-(ethoxycarbonyl)purine products was not in harmony with known reactions in purine chemistry. Our reinvestigation has shown that the 6-(ethoxycarbonyl) group undergoes preferential base-promoted hydrolysis, as expected, but regioselectivity for attack of hydroxide at the carbonyl group at C6 is not high (relative to hydrolysis of both C2 and C6 esters). The structure of 9-benzyl-2-(ethoxycarbonyl)purine was determined by X-ray crystallography and confirmed by Curtius rearrangement of the azidocarbonyl analogue to give 2-amino-6-benzylpurine. Acid-catalyzed decarboxylation of the 2,6-dicarboxylate formed during hydrolysis gave 9-benzylpurine, and Curtius rearrangement of 2,6-bis(azidocarbonyl)-9-benzylpurine gave 2,6-diamino-9-benzylpurine. Attempted applications of inverse-electron-demand Diels-Alder reactions of 2 with nucleoside derivatives were problematic.

Address of the President Professor A. L. Hodgkin at the Anniversary Meeting, 30 November 1971

1972 ◽  
Vol 180 (1058) ◽  
Keyword(s):  
Chemical Composition ◽  
Nucleic Acid ◽  
Liquid Crystalline ◽  
Accurate Information ◽  
X Ray ◽  
Virus Particles ◽  
X Ray Crystallography ◽  
Crystalline Forms ◽  
Outstanding Work

Award of Medals 1971 The Copley Medal is awarded to Mr N. W. Pirie, F.R.S. for his outstanding work on the nature of viruses. Pirie discovered the chemical composition of viruses and his work transformed ideas about their morphology and method of multiplication. He was the first to show that nucleic acid is a necessary component of a virus and, at a time when tobacco mosaic virus was thought to be a crystalline globulin, he made liquid crystalline preparations of several strains which he correctly identified as nucleoproteins containing 5 % ribose nucleic acid. He then generalized his discovery by isolating several other viruses, with widely different stabilities and other properties, in crystalline or liquid crystalline forms, and by showing th at all contained nucleic acid, but in amounts and held in ways that differed characteristically in different viruses. His work was the first to show that different viruses differed greatly in shape and that those with anisometric particles could change their length in vitro . X-ray crystallography applied to his preparations provided the first accurate information about the sizes of virus particles and first showed them to be composed of uniform subunits regularly arranged. Pirie also showed that nucleic acids could be much larger than generally thought, and the methods he used to prepare them were among those used by later workers who showed that nucleic acid alone could be infective.

Nucleic acid X-ray crystallography via direct selenium derivatization

2011 ◽  
Vol 40 (9) ◽  
pp. 4591 ◽  
Author(s):  
Lina Lin ◽  
Jia Sheng ◽  
Zhen Huang
Keyword(s):  
Nucleic Acid ◽  
X Ray ◽  
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).

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