The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution

Abstract

Sequence dependency of metal ion aggregation around RNA structures is known to be involved in critical functions ranging from processes of molecular recognition to enzymatic chemistry. Ion interactions with an HIV-1 TAR RNA core helix were examined with explicit solvent molecular dynamics simulations. The results have shown that there is a sequence-dependent cationic localization toward the purine-rich run within the TAR helix and other purine-rich duplexes. The behavior is independent of ionic species or a presence of a bulge. A region of high ion affinity agrees very well with the position of the X-ray determined divalent cations within a fragment from the HIV-1 TAR RNA. † Part of the "Barbara J. Garrison Festschrift".

Interactions of Cations with RNA Loop-Loop Complexes

“…Purine bases were the most preferred sites for cationic interactions in all KL complexes (Table 1). A similar effect was observed recently in RNA helices where monovalent ions associated with polypurine stretches of adenine and guanine (41). Also, purine-rich stretches in RNA aptamers are shown to be crucial for the binding of Co 2þ and are targets for 6-mer oligodeoxyribonucleotides (49).…”

Targeting structural features of viral genomes with a nano-sized supramolecular drug

“…12,13 UTRs have been mostly studied in RNA viruses, such as HIVs, 7,10,14,15 coronaviruses, [16][17][18] dengue, 11,12,19,20 zika 21 and other aviviruses 22 and, in every studied case, functional involvement of the UTR has been shown in either initiation of replication 16,19 (by recruiting proteins or by direct interaction with the ribosome) or regulation of the replication cycle. The most studied example is the retrovirus HIV-1 which contains a bulge in the rst stem loop of the 5 0 UTR of its RNA genome, [23][24][25][26][27][28][29][30] the structure and dynamics of which are crucial for initiation of viral replication. Similar bulges are found in UTRs of other RNA viruses including coronaviruses and SARS-COV-2.…”

The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study

“…A simulation setup described in details in previous studies was used [28]. Briefly, each fibril was first minimized in solvent for 10,000 steps, holding the molecule fixed during this time with a constraint of 20 kcal/mol.…”