Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy

2010 ◽  
Vol 87 (7) ◽  
pp. 732-734 ◽  
Author(s):  
Rasha A. Ruhayel ◽  
Susan J. Berners-Price
Keyword(s):  
Nmr Spectroscopy ◽  
Dna Sequence ◽  
Solution Structure ◽  
Double Stranded Dna

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

Solution Structure of [Me-L-Leu7]Didemnin B Determined by NMR Spectroscopy and Refined by MD Calculation

1990 ◽  
Vol 73 (1) ◽  
pp. 25-47 ◽  
Author(s):  
Horst Kessler ◽  
Siggi Mronga ◽  
Martin Will ◽  
Ulrich Schmidt
Keyword(s):  
Nmr Spectroscopy ◽  
Solution Structure ◽  
Didemnin B

Solution Structure of a GA Mismatch DNA Sequence, d(CCATGAATGG)2, Determined by 2D NMR and Structural Refinement Methods

Biochemistry ◽  
1994 ◽  
Vol 33 (5) ◽  
pp. 1053-1062 ◽  
Author(s):  
Karen L. Greene ◽  
Robert L. Jones ◽  
Ying Li ◽  
Howard Robinson ◽  
Andrew H.-J. Wang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Solution Structure ◽  
2D Nmr ◽  
Structural Refinement

Solution structure of branched U3′p5′A2′p5′G3′p5′C and its comparison with A2′p5′G3′p5′U by 500 MHz NMR spectroscopy

Tetrahedron ◽  
1991 ◽  
Vol 47 (20-21) ◽  
pp. 3417-3430 ◽  
Author(s):  
C. Glemarec ◽  
M. Jaseja ◽  
A. Sandström ◽  
L. Koole ◽  
P. Agback ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Solution Structure

Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Determined by NMR Spectroscopy

Biochemistry ◽  
1995 ◽  
Vol 34 (27) ◽  
pp. 8542-8553 ◽  
Author(s):  
H. Peter Spielmann ◽  
David E. Wemmer ◽  
Jens Peter Jacobsen
Keyword(s):  
Nmr Spectroscopy ◽  
Solution Structure ◽  
Dna Complex

Selective dismantling of closo-1,2-C2B10H12 to lower-cage dicarbaborane systems

1991 ◽  
Vol 56 (8) ◽  
pp. 1618-1635 ◽  
Author(s):  
Jaromír Plešek ◽  
Bohumil Štíbr ◽  
Xavier L. R. Fontaine ◽  
John D. Kennedy ◽  
Stanislav Heřmánek ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Solution Structure ◽  
High Yield ◽  
Two Dimensional ◽  
Oxidizing Agents ◽  
Elimination Reactions

A modified, high-yield synthesis of the two isomeric nido twelve-vertex [C2B10H13]- anions, "reactive" [nido-7,9-C2B10H13]- and "unreactive" [nido-7,12-C2B10H13]-, has been developed. A solution structure for the reactive [nido-7,9-C2H10B13]- isomer is proposed on the basis of the result of two-dimensional 11B and 1H correlation NMR spectroscopy. It is concluded that there is a marked similarity between this species and the eleven-vertex congener [nido-7,8-C2B9H12]-. In accord with this parallel, the "reactive" twelve-vertex species is found to undergo selective boron-vertex elimination reactions in the presence of oxidizing agents. These reactions give excellent yields of smaller-cage nido dicarbaborane compounds, namely [nido-7,8-C2B9H12]-, [9-(SMe2)-nido-7,8-C2B9H11], and nido-5,6-C2B8H12. NMR spectroscopy assigns cluster 11B and 1H resonances for all the compounds isolated, and thence permits comparison with the equivalent shielding patterns of structurally related analogues such as [nido-7-CB10H13]- and [nido-7,9-C2B9H12]-.

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