Minimal Models for the Structure and Dynamics of Nucleic Acids

2014 ◽  
pp. 162-185
Keyword(s):  
Nucleic Acids ◽  
Minimal Models ◽  
Structure And Dynamics

scholarly journals Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

2018 ◽  
Vol 14 ◽  
pp. 114-129 ◽  
Author(s):  
Mattias Bood ◽  
Sangamesh Sarangamath ◽  
Moa S Wranne ◽  
Morten Grøtli ◽  
L Marcus Wilhelmsson
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Orientation Factor ◽  
Design Synthesis ◽  
Structure And Dynamics ◽  
Donor And Acceptor ◽  
Structure Investigations ◽  
Fret Pair

Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base–base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ 2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base–base FRET and that are described here. Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications.

Impact of modified ribose sugars on nucleic acid conformation and function

2017 ◽  
Vol 23 (3) ◽  
pp. 155-165 ◽  
Author(s):  
Marina Evich ◽  
Alexander M. Spring-Connell ◽  
Markus W. Germann
Keyword(s):  
Nucleic Acids ◽  
Chemical Reactivity ◽  
Review Article ◽  
Global Structure ◽  
Sugar Moiety ◽  
Structure And Dynamics ◽  
Local Conformation ◽  
Conformational Properties ◽  
And Function ◽  
Nucleic Acid Conformation

AbstractThe modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.

scholarly journals A Novel Paramagnetic Relaxation Enhancement Tag for Nucleic Acids: A Tool to Study Structure and Dynamics of RNA

2013 ◽  
Vol 8 (12) ◽  
pp. 2697-2706 ◽  
Author(s):  
Christoph H. Wunderlich ◽  
Roland G. Huber ◽  
Romana Spitzer ◽  
Klaus R. Liedl ◽  
Karin Kloiber ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Structure And Dynamics

scholarly journals Interbase FRET in RNA: from A to Z

2019 ◽  
Vol 47 (19) ◽  
pp. 9990-9997 ◽  
Author(s):  
Anders F Füchtbauer ◽  
Moa S Wranne ◽  
Mattias Bood ◽  
Erik Weis ◽  
Pauline Pfeiffer ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Structural Changes ◽  
Average Structure ◽  
Structure And Dynamics ◽  
Rna Conformation ◽  
First Time ◽  
Existing Structure ◽  
Fret Pair

Abstract Interbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tCO and the non-emissive acceptor tCnitro. The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA structural changes is demonstrated by monitoring the transition from A- to Z-form RNA. Finally, the measured FRET data were compared with theoretical FRET patterns obtained from two previously reported Z-RNA PDB structures, to shed new light on this elusive RNA conformation.

Structure and Dynamics of Nucleic Acids

2011 ◽  
pp. 159-198 ◽  
Author(s):  
Ivan Krstić ◽  
Burkhard Endeward ◽  
Dominik Margraf ◽  
Andriy Marko ◽  
Thomas F. Prisner
Keyword(s):  
Nucleic Acids ◽  
Structure And Dynamics
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