scholarly journals Higher-order structure of nucleic acids in the gas phase: Top-down analysis of base-pairing interactions

2012 ◽  
Vol 312 ◽  
pp. 155-162 ◽  
Author(s):  
D. Fabris ◽  
K.A. Kellersberger ◽  
J.A. Wilhide
Keyword(s):  
Nucleic Acids ◽  
Gas Phase ◽  
Higher Order ◽  
Order Structure ◽  
Base Pairing ◽  
Top Down ◽  
Pairing Interactions

Higher Order Structure in the Gas Phase Reflects Solution Structure

1998 ◽  
Vol 120 (18) ◽  
pp. 4542-4543 ◽  
Author(s):  
Joseph A. Loo ◽  
John X. He ◽  
Wayne L. Cody
Keyword(s):  
Gas Phase ◽  
Solution Structure ◽  
Higher Order ◽  
Order Structure

Characterization of nucleic acid higher order structure by gas-phase H/D exchange in a quadrupole-FT-ICR mass spectrometer

Biopolymers ◽  
2009 ◽  
Vol 91 (4) ◽  
pp. 256-264 ◽  
Author(s):  
Jingjie Mo ◽  
Gabrielle C. Todd ◽  
Kristina Håkansson
Keyword(s):  
Nucleic Acid ◽  
Gas Phase ◽  
Mass Spectrometer ◽  
Higher Order ◽  
Order Structure ◽  
Ft Icr

scholarly journals A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥ 20 Mb genomic length scales

Nucleus ◽  
2011 ◽  
Vol 2 (5) ◽  
pp. 465-477 ◽  
Author(s):  
Kathrin Teller ◽  
Doris Illner ◽  
Stefanie Thamm ◽  
Corella S. Casas-Delucchi ◽  
Rogier Versteeg ◽  
...  
Keyword(s):  
Higher Order ◽  
Order Structure ◽  
Top Down ◽  
Length Scales ◽  
Genomic Length

Macrocycles of Higher Ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Macrocycles of Higher ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

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