Bridging the gap between in vitro and in vivo RNA folding
Deciphering the folding pathways and predicting the structures of complex three-
dimensional biomolecules is central to elucidating biological function. RNA is single …
dimensional biomolecules is central to elucidating biological function. RNA is single …
RNA structure through multidimensional chemical mapping
The discoveries of myriad non-coding RNA molecules, each transiting through multiple
flexible states in cells or virions, present major challenges for structure determination …
flexible states in cells or virions, present major challenges for structure determination …
In vivo mutation rates and the landscape of fitness costs of HIV-1
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but
essential for a quantitative understanding of evolution. Using whole genome deep …
essential for a quantitative understanding of evolution. Using whole genome deep …
RNA structure inference through chemical mapping after accidental or intentional mutations
CY Cheng, W Kladwang… - Proceedings of the …, 2017 - National Acad Sciences
Despite the critical roles RNA structures play in regulating gene expression, sequencing-
based methods for experimentally determining RNA base pairs have remained inaccurate …
based methods for experimentally determining RNA base pairs have remained inaccurate …
Stability and conformation of the dimeric HIV-1 genomic RNA 5′ UTR
RJ Blakemore, C Burnett, C Swanson, S Kharytonchyk… - Biophysical journal, 2021 - cell.com
During HIV-1 assembly, the viral Gag polyprotein specifically selects the dimeric RNA
genome for packaging into new virions. The 5′ untranslated region (5′ UTR) of the …
genome for packaging into new virions. The 5′ untranslated region (5′ UTR) of the …
Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage
F van Hemert, AC van der Kuyl… - Journal of General …, 2016 - microbiologyresearch.org
We are interested in the influence of nucleotide composition on the fundamental
characteristics of the virus RNA genome. Most RNA viruses have genomes with a distinct …
characteristics of the virus RNA genome. Most RNA viruses have genomes with a distinct …
Carbon ink-based electrodes modified with nanocomposite as a platform for electrochemical detection of HIV RNA
ACR Moco, JAS Neto, DD de Moraes, PH Guedes… - Microchemical …, 2021 - Elsevier
This work reports a new and easy-to-use methodology for construction of screen-printed
electrodes (SPE) based on carbon ink and its modification with 4-aminothiophenol (4-ATP) …
electrodes (SPE) based on carbon ink and its modification with 4-aminothiophenol (4-ATP) …
Stability of HIV frameshift site RNA correlates with frameshift efficiency and decreased virus infectivity
P Garcia-Miranda, JT Becker, BE Benner… - Journal of …, 2016 - Am Soc Microbiol
Human immunodeficiency virus (HIV) replication is strongly dependent upon a programmed
ribosomal frameshift. Here we investigate the relationships between the thermodynamic …
ribosomal frameshift. Here we investigate the relationships between the thermodynamic …
Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells
RNA represents a potential target for new antiviral therapies, which are urgently needed to
address public health threats such as the human immunodeficiency virus (HIV). We showed …
address public health threats such as the human immunodeficiency virus (HIV). We showed …
Solution structure of the HIV-1 intron splicing silencer and its interactions with the UP1 domain of heterogeneous nuclear ribonucleoprotein (hnRNP) A1
Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through
cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of …
cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of …