A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination

Y Koldobskaya, EM Duguid, DM Shechner… - Nature structural & …, 2011 - nature.com
RNA crystallization and phasing represent major bottlenecks in RNA structure
determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we …

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif

SA Shelke, Y Shao, A Laski, D Koirala… - Nature …, 2018 - nature.com
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole
red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB) …

Exploring RNA structure by integrative molecular modelling

B Masquida, B Beckert, F Jossinet - New biotechnology, 2010 - Elsevier
RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With
new structured RNAs constituting a central class of cellular regulators discovered every …

The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study

J Sgrignani, A Magistrato - The Journal of Physical Chemistry B, 2012 - ACS Publications
According to the RNA world hypothesis, self-replicating ribozymes, storing the genetic
information and being able to perform catalysis, were the constituents of the first living …

The structural basis of RNA-catalyzed RNA polymerization

DM Shechner, DP Bartel - Nature structural & molecular biology, 2011 - nature.com
Early life presumably required polymerase ribozymes capable of replicating RNA. Known
polymerase ribozymes best approximating such replicases use as their catalytic engine an …

Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment

JA Piccirilli, Y Koldobskaya - … Transactions of the Royal …, 2011 - royalsocietypublishing.org
All models of the RNA world era invoke the presence of ribozymes that can catalyse RNA
polymerization. The class I ligase ribozyme selected in vitro 15 years ago from a pool of …

Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core

DM Truong, DJ Sidote, R Russell… - Proceedings of the …, 2013 - National Acad Sciences
Mobile group II introns are bacterial retrotransposons thought to be evolutionary ancestors of
spliceosomal introns and retroelements in eukaryotes. They consist of a catalytically active …

Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube

C Díaz Arenas, N Lehman - BMC evolutionary biology, 2010 - Springer
Abstract Background During the RNA World, molecular populations were probably very
small and highly susceptible to the force of strong random drift. In conjunction with Muller's …

Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles

S Lee, H Kim, S Tian, T Lee, S Yoon, R Das - Bioinformatics, 2015 - academic.oup.com
Motivation: Capillary electrophoresis (CE) is a powerful approach for structural analysis of
nucleic acids, with recent high-throughput variants enabling three-dimensional RNA …

The chemical origins of life and its early evolution: an introduction

DMJ Lilley, J Sutherland - Philosophical Transactions of …, 2011 - royalsocietypublishing.org
Can we look at contemporary biology and couple this with chemical insight to propose some
plausible mechanisms for the origin of life on the planet? In what follows, we examine some …