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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 07-21-2022, 04:02 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
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 Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy

Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy

The majority of base pairs in double-stranded DNA exist in the canonical Watson-Crick geometry. However, they can also adopt alternate Hoogsteen conformations in various complexes of DNA with proteins and small molecules, which are key for biological function and mechanism. While detection of Hoogsteen base pairs in large DNA complexes and assemblies poses considerable challenges for traditional structural biology techniques, we show here that multidimensional dynamic nuclear...

More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy.
Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy. Related Articles Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy. Biochem Soc Trans. 2020 May 07;: Authors: Chakraborty A, Deligey F, Quach J, Mentink-Vigier F, Wang P, Wang T Abstract Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing...
nmrlearner Journal club 0 05-08-2020 06:11 PM
[ASAP] Characterizing Watson–Crick versus Hoogsteen Base Pairing in a DNA–Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA
Characterizing Watson–Crick versus Hoogsteen Base Pairing in a DNA–Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.9b00027/20190405/images/medium/bi-2019-00027k_0007.gif Biochemistry DOI: 10.1021/acs.biochem.9b00027 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/cxEpU-ZUkcg More...
nmrlearner Journal club 0 04-06-2019 06:58 PM
Probing the surface of ?-Al2O3 by oxygen-17 dynamic nuclear polarization enhanced solid-state NMR spectroscopy #DNPNMR
From The DNP-NMR Blog: Probing the surface of ?-Al2O3 by oxygen-17 dynamic nuclear polarization enhanced solid-state NMR spectroscopy #DNPNMR Li, Wenzheng, Qiang Wang, Jun Xu, Fabien Aussenac, Guodong Qi, Xingling Zhao, Pan Gao, Chao Wang, and Feng Deng. “Probing the Surface of ?-Al2O3 by Oxygen-17 Dynamic Nuclear Polarization Enhanced Solid-State NMR Spectroscopy.” Physical Chemistry Chemical Physics 20, no. 25 (June 27, 2018): 17218–25. https://doi.org/10.1039/C8CP03132K.
nmrlearner News from NMR blogs 0 11-25-2018 06:02 AM
Atomic structures of excited state Aâ??T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations
Atomic structures of excited state Aâ??T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations Abstract NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watsonâ??Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1Aâ??T Hoogsteen...
nmrlearner Journal club 0 04-19-2018 01:52 PM
DirectNMR Evidence that Transient Tautomeric andAnionic States in dG·dT Form Watson–Crick-like Base Pairs
DirectNMR Evidence that Transient Tautomeric andAnionic States in dG·dT Form Watson–Crick-like Base Pairs Eric S. Szymanski, Isaac J. Kimsey and Hashim M. Al-Hashimi http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.7b01156/20170320/images/medium/ja-2017-01156m_0004.gif Journal of the American Chemical Society DOI: 10.1021/jacs.7b01156 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/sMXmx3Kniac
nmrlearner Journal club 0 03-21-2017 08:29 AM
Dynamic Nuclear Polarization as an Enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy
From The DNP-NMR Blog: Dynamic Nuclear Polarization as an Enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy Smith, A.N. and J.R. Long, Dynamic Nuclear Polarization as an Enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy. Analytical Chemistry, 2016. 88(1): p. 122-132. http://dx.doi.org/10.1021/acs.analchem.5b04376
nmrlearner News from NMR blogs 0 02-01-2016 05:12 PM
[NMR paper] NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by
NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Related Articles NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14147-51 Authors: Pervushin K, Ono A, Fernández C, Szyperski T, Kainosho M, Wüthrich K This paper describes the NMR observation of 15N---15N and 1H---15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs...
nmrlearner Journal club 0 11-17-2010 11:15 PM
Dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of GNNQQNY nanocry
Dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of GNNQQNY nanocrystals and amyloid fibrils. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of GNNQQNY nanocrystals and amyloid fibrils. Phys Chem Chem Phys. 2010 Jun 14;12(22):5911-9 Authors: Debelouchina GT, Bayro MJ, van der Wel PC, Caporini MA, Barnes AB, Rosay M, Maas WE, Griffin RG Dynamic nuclear polarization (DNP) utilizes the...
nmrlearner Journal club 0 08-26-2010 04:41 PM



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 02:56 PM.


Map