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

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

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

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10-11-2017, 10:37 AM

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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]

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