Dataset Information

Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.

ABSTRACT: The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in (GGiCGAiGCCA)2. The structures contrast with the formation of tandem imino and sheared GA pairs flanked by GC pairs in the RNA self-complementary duplexes (GCGGACGC)2 and (GGCGAGCC)2, respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC substitutions result in less favorable loop stability. The results provide benchmarks for testing computations of molecular interactions that shape RNA three-dimensional structure.

SUBMITTER: Chen G

PROVIDER: S-EPMC3738747 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature

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Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.

Chen Gang G Kierzek Ryszard R Yildirim Ilyas I Krugh Thomas R TR Turner Douglas H DH Kennedy Scott D SD

The journal of physical chemistry. B 20070406 24

The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in (GGiCG ...[more]

PMID: 17411085

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Project description:Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5'-GCGGACGC-3')(2), (5'-GCiGGAiCGC-3')(2), (5'-GGCGAGCC-3')(2), and (5'-GGiCGAiGCC-3')(2). Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave DeltaG degrees values 2-4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.

Project description:The construction of the Suez Canal connected the Red Sea and the Mediterranean Sea, which allowed rapid marine bio-invasion. Over the last century, several bivalve species have invaded the Levantine basin, yet their distribution and impact on the benthic community have not been thoroughly studied. Large-scale benthic surveys along the rocky substrate of the Israeli Mediterranean coastline indicate that invading bivalves, such as Spondylus spinosus, Brachidontes pharaonis, and Pinctada radiata, now dominate the rocky environment, with densities of tens to hundreds of individuals per m2. No native bivalve specimens were found in any of the transects surveyed. The small-scale ecological effects of the established invading populations on the benthic community were examined over a year using an in-situ exclusion experiment where all invading bivalves were either physically removed or poisoned and kept in place to maintain the physical effect of the shells. Surprisingly, the experimental exclusion showed a little measurable effect of bivalve presence on the invertebrate community in close vicinity (~ 1 m). Bivalve presence had a small, but statistically significant, effect only on the community composition of macroalgae, increasing the abundance of some filamentous macroalgae and reducing the cover of turf. The generally low impact of bivalves removal could be due to (1) wave activity and local currents dispersing the bivalve excreta, (2) high grazing pressure, possibly by invading herbivorous fish, reducing the bottom-up effect of increased nutrient input by the bivalves, or (3) the natural complexity of the rocky habitat masking the contribution of the increased complexity associated with the bivalve's shell. We found that established invading bivalves have replaced native bivalve species, yet their exclusion has a negligible small-scale effect on the local benthic community.Supplementary informationThe online version contains supplementary material available at 10.1007/s10530-022-02986-1.

Dataset Information

Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.

Publications

Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.

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