On the structural features of hairpin triloops in rRNA: From nucleotide to global conformational change upon ligand binding

Mitrasinovic, Petar M.

doi:10.1016/j.jsb.2005.12.001

Cited by 4 publications

(3 citation statements)

References 61 publications

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“…Six of the seven nucleotides that comprise the loop are absolutely conserved. The loop has features, suggesting that it may exist in something other than a single-stranded state ( 9 , 36 ) similar to previously published RNA triloop structures ( 57 ).…”

Section: Resultssupporting

confidence: 74%

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA

Yordanova

Andreev

et al. 2015

Journal of Biological Chemistry

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Background: Regulatory +1 frameshifting in antizyme mRNA is central for polyamine level homeostasis.Results: A nascent peptide stimulator of +1 frameshifting operates in Agaricomycete fungal antizyme mRNA.Conclusion: Frameshifting can be stimulated by nascent peptide interactions with the ribosome's peptide exit tunnel in a polyamine-dependent manner.Significance: Specific nascent peptide stimulators may be a more general and unappreciated feature of utilized ribosomal frameshifting.

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Section: Resultssupporting

confidence: 74%

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA

Yordanova

Andreev

et al. 2015

Journal of Biological Chemistry

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“…For instance, they are particularly prone for folding by induced-fit [see e.g. (54,55)] in presence of interacting partner or ligand. For example, the 11nt receptor (56), the T-loop (32), the UA_h 3WJ (57,58), the ATP-aptamer (37) and the UA_h minor junction of the TPP riboswitch (59,60) have all been observed to be rather flexible and meta-stable in absence of interacting partner while they can form stable tertiary interactions in their presence.…”

Section: Discussionmentioning

confidence: 99%

The UA_handle: a versatile submotif in stable RNA architectures†

Jaeger

Verzemnieks

Geary

2008

Nucleic Acids Research

121

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Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5′XU/ANnX3′). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.

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“…2 Nucleic acids are essentially dynamic structures that influence important biological functions. [3][4][5] Besides folding into canonical duplex structures, single-stranded DNA may form various noncanonical structures, such as hairpin, triplex, G-quadruplex (or G-tetraplex), and i-motif structures. G-tetrad structure, defined by four Hoogsteen G-G base pairs (Figure 1a), was firstly noticed in 1910 6 and identified about fifty years later.…”

Section: Introductionmentioning

confidence: 99%

G-Quadruplexes: Emerging Targets for the Structure-Based Design of Potential Anti-Cancer and Antiviral Therapies

Mitrasinovic¹

2020

ACSi

Self Cite

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G-quadruplexes (G4s) are noncanonical secondary structures that fold within guanine (G) rich strands of regulatory genomic regions. Recent evidences suggest their intimate involvement in important biological processes such as telomere maintenance, end-capping and protection, chromosome stability, gene expression, viral integration, and recombination. Mechanistic details of how and why G4 structures influence biological function indicate a rationale for treating G4s as emerging molecular targets for future therapeutics. In other words, the structural heterogeneity with well-defined binding sites, thermal stability and abundance of G4s in telomeres, oncogene promoter regions, and viral genomes make G4s attractive targets for small molecules, aimed to selectively recognize them over all other nucleic acids structures, particularly duplex forms that are most abundant in the genome. Herein, a critical survey of well-characterized G4-interactive ligands as potential tools in anti-cancer and antiviral therapies is presented. Effects that these ligands selectively exert in vitro and in vivo models are summarized. Unique ligands involved in specific G4 recognition are put forward.A key question, how to design and develop new G4 specific ligands that conform to the structural and physicochemical requirements for optimal biological activity, is discussed by considering both remarkable advances over the last few years and our recent contributions.

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On the structural features of hairpin triloops in rRNA: From nucleotide to global conformational change upon ligand binding

Cited by 4 publications

References 61 publications

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA

The UA_handle: a versatile submotif in stable RNA architectures†

G-Quadruplexes: Emerging Targets for the Structure-Based Design of Potential Anti-Cancer and Antiviral Therapies

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