BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 10-11-2017, 10:37 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-protein Interactions by 19F NMR Spectroscopy.

Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-protein Interactions by 19F NMR Spectroscopy.

Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-protein Interactions by 19F NMR Spectroscopy.

J Org Chem. 2017 Oct 09;:

Authors: Olszewska A, Pohl R, Hocek M

Abstract
A series of 7-[4-(trifluoroacetyl)phenyl]-7-deazaadenine and -7-deazaguanine as well as 5-substituted uracil and cytosine 2'-deoxyribonucleosides and mono- and triphosphates through aqueous Suzuki-Miyaura crosscoupling of halogenated nucleosides or nucleotides with 4-(trifluoroacetyl)phenylboronic acid were synthesized. The modified nucleoside triphosphates were good sub-strates for DNA polymerases applicable in primer extension or PCR synthesis of modified oligonucleotides or DNA. Attempted cross-linking with a serine-containing protein did not proceed, however the trifluoroacetophenone group was a sensitive probe for the study of DNA-protein interactions by 19F NMR.


PMID: 28991457 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
High pressure 31 P NMR spectroscopy on guanine nucleotides
High pressure 31 P NMR spectroscopy on guanine nucleotides Abstract The 31P NMR pressure response of guanine nucleotides bound to proteins has been studied in the past for characterizing the pressure perturbation of conformational equilibria. The pressure response of the 31P NMR chemical shifts of the phosphate groups of GMP, GDP, and GTP as well as the commonly used GTP analogs GppNHp, GppCH2p and GTPĪ³S was measured in the absence and presence of Mg2+-ions within a pressure range up to 200Ā*MPa. The pressure dependence of chemical shifts is clearly...
nmrlearner Journal club 0 12-24-2016 08:34 AM
[NMR paper] Recent Progresses in Studying Helix-helix Interactions in Proteins by Incorporating the Wenxiang Diagram into the NMR Spectroscopy.
Recent Progresses in Studying Helix-helix Interactions in Proteins by Incorporating the Wenxiang Diagram into the NMR Spectroscopy. Related Articles Recent Progresses in Studying Helix-helix Interactions in Proteins by Incorporating the Wenxiang Diagram into the NMR Spectroscopy. Curr Top Med Chem. 2015 Aug 18; Authors: Zhou GP, Chen D, Liao S, Sun L, Huang RB Abstract All residues in an alpha helix can be characterized and dispositioned on a 2D the wenxiang diagram, which possesses the following features: (1) the relative...
nmrlearner Journal club 0 08-20-2015 07:36 PM
[NMR paper] Smaller*Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR.
Smaller*Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR. Related Articles Smaller*Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR. Protein J. 2015 May 17; Authors: Wang X, Mu Z, Li Y, Bi Y, Wang Y Abstract Phospholipid bilayer nanodiscs, a newly developed model membrane system, provides "native-like" membrane environment for membrane protein studies. Nanodiscs assembled by membrane scaffold protein and phospholipid bilayer, with defined sizes that can be accurately...
nmrlearner Journal club 0 05-20-2015 10:27 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy Abstract Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as proteinā??protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron...
nmrlearner Journal club 0 01-31-2011 06:03 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy. Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy. J Biomol NMR. 2011 Jan 28; Authors: Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of...
nmrlearner Journal club 0 01-29-2011 12:35 PM
[NMR paper] Bead-linked proteoliposomes: a reconstitution method for nmr analyses of membrane protein-ligand interactions.
Bead-linked proteoliposomes: a reconstitution method for nmr analyses of membrane protein-ligand interactions. Related Articles Bead-linked proteoliposomes: a reconstitution method for nmr analyses of membrane protein-ligand interactions. J Am Chem Soc. 2005 Aug 31;127(34):12021-7 Authors: Yokogawa M, Takeuchi K, Shimada I Structural information about the interactions between membrane proteins and their ligands provides insights into the membrane protein functions. A variety of surfactants have been used for structural analyses of membrane...
nmrlearner Journal club 0 12-01-2010 06:56 PM
The STINT-NMR Method for Studying In-cell Protein-Protein Interactions.
The STINT-NMR Method for Studying In-cell Protein-Protein Interactions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles The STINT-NMR Method for Studying In-cell Protein-Protein Interactions. Curr Protoc Protein Sci. 2010 Aug;Chapter 17:Unit17.11 Authors: Burz DS, Shekhtman A This unit describes critical components and considerations required to study protein-protein structural interactions inside a living cell by using NMR...
nmrlearner Journal club 0 09-05-2010 05:53 AM
[NMR paper] Studying DNA-protein interactions using NMR.
Studying DNA-protein interactions using NMR. Related Articles Studying DNA-protein interactions using NMR. Trends Biotechnol. 1991 Mar;9(3):96-104 Authors: Russu IM NMR spectroscopy is emerging as a powerful tool in molecular biology and biotechnology; one aspect of which is the use of one- and two-dimensional NMR methodologies to investigate the interactions of proteins with DNA. The dynamic and structural information which NMR can provide, on the changes in conformation and molecular flexibility, complements X-ray crystallography data and...
nmrlearner Journal club 0 08-21-2010 11:16 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 12:06 PM.


Map