RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Nucleic acid based molecular devices

Y Krishnan, FC Simmel - Angewandte Chemie International …, 2011 - Wiley Online Library
In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores
and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a …

Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds

T Bose, G Fridkin, C Davidovich, M Krupkin… - Nucleic acids …, 2022 - academic.oup.com
Although the mode of action of the ribosomes, the multi-component universal effective
protein-synthesis organelles, has been thoroughly explored, their mere appearance …

[HTML][HTML] Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

DH Mathews, J Sabina, M Zuker, DH Turner - Journal of molecular biology, 1999 - Elsevier
An improved dynamic programming algorithm is reported for RNA secondary structure
prediction by free energy minimization. Thermodynamic parameters for the stabilities of …

Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage

S Riesenberg, N Helmbrecht, P Kanis, T Maricic… - Nature …, 2022 - nature.com
The first step in CRISPR-Cas9-mediated genome editing is the cleavage of target DNA
sequences that are complementary to so-called spacer sequences in CRISPR guide RNAs …

Bacteriophage T4 genome

ES Miller, E Kutter, G Mosig, F Arisaka… - Microbiology and …, 2003 - Am Soc Microbiol
Phage T4 has provided countless contributions to the paradigms of genetics and
biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene …

An RNA motif that binds ATP

M Sassanfar, JW Szostak - Nature, 1993 - nature.com
RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized
on a solid support are present at a frequency of roughly one in 1010-1011 in pools of …

Hierarchy and dynamics of RNA folding

P Brion, E Westhof - Annual review of biophysics and …, 1997 - annualreviews.org
▪ Abstract The evidence showing that the self-assembly of complex RNAs occurs in discrete
transitions, each relating to the folding of sub-systems of increasing size and complexity …

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

P Nissen, JA Ippolito, N Ban… - Proceedings of the …, 2001 - National Acad Sciences
Analysis of the 2.4-Å resolution crystal structure of the large ribosomal subunit from
Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif …

[22] absorbance melting curves of RNA

JD Puglisi, I Tinoco Jr - Methods in enzymology, 1989 - Elsevier
Publisher Summary This chapter discusses the experimental methods needed to acquire a
melting curve and the analysis and interpretation of the data. Any standard commercial UV …