Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer

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Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer

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NMR processing:

MDD

NMR assignment:

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NOEs:

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Rosetta-NMR (Robetta)

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GeNMR

I-TASSER

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Amber

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Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

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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

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NOEs, other restraints:

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Methyl S2

B-factor

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Shiftx2

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ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

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Shifty

Camcoil

Poulsen_rc_CS

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05-06-2017, 03:44 PM

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Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer

Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer

Abstract

Using NMR magnetization transfer experiments, the hydrogen exchange rate constants (k ex ) of the DNA imino protons in the cocaine-binding aptamer have been determined for the free, cocaine-bound, and quinine-bound states. The secondary structure of the cocaine-binding aptamer is composed of three stems built around a three-way junction. In the free aptamer the slowest exchanging imino protons are located in the middle of the stems. The highest k ex values were found for a nucleotide in the GAA loop of stem 3 and for nucleotides at the end of the stems that form the three-way junction structure and in the tandem GA mismatch. Upon ligand binding, the k ex values of nucleotides at the ligand binding site are reduced, indicating that these base pairs become more stable or less solvent accessible in the bound state. The imino proton k ex values of nucleotides located away from the binding site are only minimally affected by ligand binding.

Source: Journal of Biomolecular NMR

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