Advances in the determination of nucleic acid conformational ensembles

L Salmon, S Yang, HM Al-Hashimi - Annual review of physical …, 2014 - annualreviews.org
Conformational changes in nucleic acids play a key role in the way genetic information is
stored, transferred, and processed in living cells. Here, we describe new approaches that …

Impact of modified ribose sugars on nucleic acid conformation and function

M Evich, AM Spring-Connell… - Heterocyclic …, 2017 - degruyter.com
The modification of the ribofuranose in nucleic acids is a widespread method of
manipulating the activity of nucleic acids. These alterations, however, impact the local …

Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics

MC Clay, LR Ganser, DK Merriman… - Nucleic acids …, 2017 - academic.oup.com
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-
abundance 'excited states' that form by reshuffling base pairs in and around non-canonical …

A symbolic regression-based modelling strategy of AC/DC rectifiers for RFID applications

V Ceperic, N Bako, A Baric - Expert Systems with Applications, 2014 - Elsevier
In this paper, we present the use of symbolic regression for the black-box modelling of non-
linear dynamic behaviour in the AC/DC rectifiers of radio-frequency identification (RFID) …

Solid-state NMR chemical shift analysis for determining the conformation of ATP bound to Na, K-ATPase in its native membrane

DA Middleton, J Griffin, M Esmann, NU Fedosova - RSC advances, 2023 - pubs.rsc.org
Structures of membrane proteins determined by X-ray crystallography and, increasingly, by
cryo-electron microscopy often fail to resolve the structural details of unstable or reactive …

Prediction of RNA 1H and 13C Chemical Shifts: A Structure Based Approach

AT Frank, SH Bae, AC Stelzer - The Journal of Physical Chemistry …, 2013 - ACS Publications
The use of NMR-derived chemical shifts in protein structure determination and prediction
has received much attention, and, as such, many methods have been developed to predict …

Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

A Victora, HM Möller, TE Exner - Nucleic acids research, 2014 - academic.oup.com
NMR chemical shift predictions based on empirical methods are nowadays indispensable
tools during resonance assignment and 3D structure calculation of proteins. However, owing …

A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

X Jin, T Zhu, JZH Zhang, X He - RSC advances, 2016 - pubs.rsc.org
1 H, 13C and 15N NMR chemical shift calculations on RNAs were performed using the
automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach …

Case study of 2-vinyloxypyridine: Quantitative assessment of the intramolecular CH⋯ N hydrogen bond energy and its contribution to the one-bond 13C1H coupling …

AV Afonin, DV Pavlov, AV Vashchenko - Journal of Molecular Structure, 2019 - Elsevier
DFT and MP2 calculations suggest that the intramolecular С‒Н··· N hydrogen bond between
the α-hydrogen of the vinyl group and pyridine nitrogen is formed in 2-vinyloxypyridine …

Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR

C Lawrence, A Grishaev - RNA, 2020 - rnajournal.cshlp.org
Determination of structure of RNA via NMR is complicated in large part by the lack of a
precise parameterization linking the observed chemical shifts to the underlying geometric …