[Jmol-users] Unable to display electron density mapping

Sat, 19 Mar 2016 20:43:34 -0700

Hey Guys, 

I have been having some problems displaying an electron density mapping on an html page I am making for a class. I have been using the following script: 

<p> <script language="_javascript_">
  jmolButton("<p> <script language="_javascript_">
  jmolButton("zap;load 5c7w2.pdb; backbone off; cartoon off;spacefill off; wireframe 75; isosurface id ~mesh color purple within 2.0 {18 or 78} "5c7w.ccp4.gz" mesh nofill; restrict [50N or 50L]; centre [50N] or [50L];","Button 3");;","Button 3”);

What is weird is that when I type the red text into the java console that you can access from the webpage directly, this works perfectly. This also works in the Jmol.jar application I have. But the button does not appear whenever I open the html. If someone could help me with this, I would really appreciate it. I have attached my html script. Thanks,

Sarabjeet Seehra

Title: RNA Riboswitch containing unnatural nucleobase pair

RNA Riboswitch containing unnatural nucleobase pair

Sarabjeet Seehra '16

A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair; Hernandez, A. R.; Shao, Y.; Hoshika, S.; Yang, Z.; Shelke, S. A.; Herrou, J.; Kim, H. J.; Kim, M. J.; Piccirilli, J. A.; Benner, S. A.. Angew. Chemie - Int. Ed. 2015, 54 (34), 9853–9856

Contents:

I. Introduction

The idea of increasing the number of replicable nucleotides in DNA and RNA has been a topic of interest in synthetic biological/chemical research for over two decades. In particular, modification of nucleotide base pairs on RNA are structurally more important due to the increase in conformational freedom as a result of the 2'-hydroxyl group. One strategy used to increase the nucleobase library, called "artificially expanded genetic information system (AEGIS)"involves designing nucleotide base pairs with specific size, geometry and hydrogen bond specifications that resemble Watson-Crick base pairing geometry.

An unnatural base pair between 6- amino-5-nitro-3-(1'-b-d-ribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-b-d-ribo-furanosyl)-imidazo-[1,2-a]-1,3,5-tria-zin-4-(8H)-one (called a Z and P base pair)is being shown in a spacefill model of with the atoms colored according to cpk convention with the hydrogens omitted. The carbons are grey, the nitrogens blue, oxygen red, phosphorus yellow.The unnatural base pairs are displayed in purple.In this tutorial, the effect of replacing a C:G base pair with a Z and P base pairing interaction to the function of a 67 nucleotide xpt-pbuX riboswitch aptamer domain in binding a hypoxanthine ligand.

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Z:P unnatural base pairing and base stacking interactions

As further clarification, AEGIS involves attempting to fit a base pair to Watson-Crick base pair geometry, as well as incorporate a other pairing specifications. First, you have size complementarity, in which a large purine interacts with a small pyrimidine. Below are some examples of artificial base pairs created using the AEGIS method (denoted in purple), compared to the standard Watson Crick Base Pairs (in green).

Depiction of the Z and P base pairing interaction in riboswitch aptamer. Notice that both the Z and P unnatural bases adopts a c3'-endo conformation, which conforms to characteristics of A-DNA. Also notice that the G:C hydrogen bonding interactions is retained in the Z:P interactions, rather than pairing via hydrophobic interactions.

Base stacking interaction between Z and adjacent A base. Notice that the nitro group (labeled in yellow) of the Z base lies in the plane of the adenine base, suggesting it might play a role in base stacking interactions.

Electron Density Map of Z:P base pair. The 2mFo-DFc maps, are contoured at 1.0 and shown in green. Notice that

Locations of bound water molecules in pink.

Locations of bound water molecules on solvent accessible surface in pink.

Location of phosphate oxygens shown in red, phosphorus in yellow.

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Base pairing and stacking

DNA adopts the c2'-endo conformation that results in the longest possible phosphate phosphate distance so that the phosphates point out and can be well hydrated.

Base pair in DNA showing 2'-endo sugar conformation on G, but C1'-exo conformation on the C

Base pair stacking at Purine Pyrimidine step showing intrastrand base stacking showing propellar twist and major groove purine purine clash.

Base pair stacking at Pyrimidine Purine step showing interstrand base stacking and minor groove purine purine clash.

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IV. Conformational analysis of backbone

The major conformations of the DNA phosphodiester backbone are generally typified by low energy anti butane conformations except for the O5'-C5'-C4'-C3' conformation which is gauche+ and the phosphodiester bonds which are governed by the anomeric effect and are gauche-

This is the alpha torsion bond which you can see is gauche- because of the anomeric effect

This is the beta torsion bond which you can see is anti which minimizes the energy based on sterics

This is the gamma torsion bond which you can see is gauche+ so as to allow DNA double helix to form

This is the delta torsion bond which you can see is trying to be anti and is governed by the 5-membered ring

This is the epsilon torsion bond which you can see is anti to minimize steric effects

This is the zeta torsion bond which you can see is gauche- because of the anomeric effect

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V. TOPIC 5

Your text here

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VI. References

PDB Reference

PubMed Ref

Reference 3

Reference 4

Reference 5

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