Faculty Opinions recommendation of The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.

2006 ◽  
Author(s):  
Scott Silverman
Keyword(s):  
Long Range ◽  
Structural Element ◽  
Internal Loop ◽  
Tertiary Interactions

scholarly journals 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

2021 ◽  
Author(s):  
Christian Richter ◽  
Katharina F. Hohmann ◽  
Sabrina Toews ◽  
Daniel Mathieu ◽  
Nadide Altincekic ◽  
...  
Keyword(s):  
Life Cycle ◽  
Chemical Shift ◽  
Base Pair ◽  
Chemical Shift Assignment ◽  
Potential Functions ◽  
Regulatory Rna ◽  
Structural Element ◽  
Stem Loop ◽  
Internal Loop ◽  
Shift Assignment

AbstractThe stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

scholarly journals Secondary and tertiary structural foldings in tRNA. A diagonal plot analysis using the blocked nucleotide scheme

1982 ◽  
Vol 205 (2) ◽  
pp. 457-460 ◽  
Author(s):  
R Malathi ◽  
N Yathindra
Keyword(s):  
Long Range ◽  
Structural Domains ◽  
Variable Loop ◽  
Helix Loop Helix ◽  
Plot Analysis ◽  
Long Range Interactions ◽  
D Loop ◽  
Tertiary Interactions

A distance plot obtained using the blocked nucleotide concept, which regards the repeating nucleotide moieties to be made up of two blocks of nearly equal magnitude, has permitted us to visualize the polynucleotide backbone folding in yeast tRNAPhe. The plot clearly manifests medium- and long-range tertiary interactions involving various structural domains. Apart from the well known T psi-D loop interactions, other long-range interactions associated with the variable loop as well as the D loop are explicitly seen. Most importantly, the plot reveals an approximate two-fold symmetry in the molecule between the domains related to the tertiary interactions in addition to the symmetry between long helical domains. The different patterns on the plot are interpreted in terms of helix-helix, loop-helix and loop-loop interactions.

scholarly journals Author response: Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer

2015 ◽  
Author(s):  
Van K Duesterberg ◽  
Irena T Fischer-Hwang ◽  
Christian F Perez ◽  
Daniel W Hogan ◽  
Steven M Block
Keyword(s):  
Ligand Binding ◽  
Long Range ◽  
Author Response ◽  
Tertiary Interactions

scholarly journals Roles of Long-Range Tertiary Interactions in Limiting Dynamics of the Tetrahymena Group I Ribozyme

2014 ◽  
Vol 136 (18) ◽  
pp. 6643-6648 ◽  
Author(s):  
Xuesong Shi ◽  
Namita Bisaria ◽  
Tara L. Benz-Moy ◽  
Steve Bonilla ◽  
Dmitri S. Pavlichin ◽  
...  
Keyword(s):  
Long Range ◽  
Group I ◽  
Tertiary Interactions

scholarly journals From The Cover: Release of long-range tertiary interactions potentiates aggregation of natively unstructured  -synuclein

2005 ◽  
Vol 102 (5) ◽  
pp. 1430-1435 ◽  
Author(s):  
C. W. Bertoncini ◽  
Y.-S. Jung ◽  
C. O. Fernandez ◽  
W. Hoyer ◽  
C. Griesinger ◽  
...  
Keyword(s):  
Long Range ◽  
Tertiary Interactions

scholarly journals Time-resolved, single-molecule, correlated chemical probing of RNA

2020 ◽  
Author(s):  
Jeffrey E. Ehrhardt ◽  
Kevin M. Weeks
Keyword(s):  
Long Range ◽  
Single Molecule ◽  
Rna Folding ◽  
Dimethyl Sulfate ◽  
Space Structure ◽  
Time Resolved ◽  
Chemical Probing ◽  
Structure Probing ◽  
Wide Range ◽  
Tertiary Interactions

AbstractMethods for capturing the folding dynamics of functionally important RNAs, especially large RNAs, have relied primarily on global measurements of structure or on per-nucleotide chemical probing. These approaches infer, but do not directly measure, through-space tertiary interactions. Here we introduce trimethyloxonium (TMO) as a chemical probe for RNA. TMO enables time-resolved, single-molecule, through-space structure probing of RNA folding using a correlated chemical probing framework. TMO methylates RNA about 90 times faster than the widely used dimethyl sulfate probe, allowing structure interrogation on the second time scale. We used TMO to monitor folding of the RNase P RNA – a functional RNA with extensive long-range and noncanonical interactions – by direct measurement of through-space tertiary interactions in a time-resolved way. Time-dependent correlation changes directly revealed the central role of a long-range tertiary loop-loop interaction that guides native RNA folding. Single-molecule, time-resolved RNA structure probing with TMO is poised to reveal a wide range of dynamic RNA folding processes and principles of RNA folding.

scholarly journals Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Van K Duesterberg ◽  
Irena T Fischer-Hwang ◽  
Christian F Perez ◽  
Daniel W Hogan ◽  
Steven M Block
Keyword(s):  
Ligand Binding ◽  
Long Range ◽  
Single Molecule ◽  
Conformational Changes ◽  
Structural Changes ◽  
Regulatory Element ◽  
Optical Trap ◽  
Resonance Energy ◽  
Thiamine Pyrophosphate ◽  
Tertiary Interactions

The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The ‘Force-FRET’ approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.

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