scholarly journals Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

2017 ◽  
Author(s):  
Abhinav Mittal ◽  
Antarip Halder ◽  
Sohini Bhattacharya ◽  
Dhananjay Bhattacharyya ◽  
Abhijit Mitra
Keyword(s):  
Structural Alignment ◽  
Bimodal Distribution ◽  
Base Pairs ◽  
Purine Base ◽  
Functional Roles ◽  
Nmr Structures ◽  
Sharp Turn ◽  
Interesting Class ◽  
Functional Rnas ◽  
Noncanonical Base Pairs

AbstractIdentification of static and/or dynamic roles of different noncanonical base pairs is essential for a comprehensive understanding of the sequence-structure-function space of RNA. In this context, reverse Watson-Crick purine-purine base pairs (A:A, G:G&A:GW:W Trans) constitute an interesting class of noncanonical base pairs in RNA due to their characteristic C1′–C1′ distance (highest among all base pairing geometries) and parallel local strand orientation. Structural alignment of the RNA stretches containing these W:W Trans base pairs with their corresponding homologous sites in a non-redundant set of RNA crystal structures show that, as expected, these base pairs are associated with specific structural folds or functional roles. Detailed analysis of these contexts further revealed a bimodal distribution in the local backbone geometry parameters associated with these base pairs. One mode, populated by both A:A and G:G W:W Trans pairs, manifests itself as a characteristic backbone fold. We call this fold a ‘Sharp-turn’ motif. The other mode is exclusively associated with A:A W:W Trans pairs involved in mediating higher order interactions. The same trend is also observed in available solution NMR structures. We have also characterized the importance of recurrent hydrogen bonding interactions between adenine and guanine in W:W Trans geometry. Quantum chemical calculations performed at M05-2X/6-31++(2d,2p) level explain how the characteristic electronic properties of these W:W Trans base pairs facilitate their occurrence in such exclusive structural folds that are important for RNA functionalities.

scholarly journals Structural landscape of base pairs containing post-transcriptional modifications in RNA

2017 ◽  
Author(s):  
Preethi S. P. ◽  
Purshotam Sharma ◽  
Abhijit Mitra
Keyword(s):  
Binding Energies ◽  
Rna Structures ◽  
Base Pairs ◽  
Functional Roles ◽  
Naturally Occurring ◽  
Quantum Chemical Methods ◽  
Geometrical Features ◽  
Modified Nucleobases ◽  
Functional Rnas

ABSTRACTBase pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts towards understanding the structural and functional role of naturally occurring modified base pairs by analyzing their distribution in different RNA classes, with the help of crystal structure and sequence database analyses. In addition, we quantify the variation in geometrical features of modified base pairs within RNA structures, and characterize their optimum geometries and binding energies using advanced quantum chemical methods. Further comparison of modified base pairs with their unmodified counterparts illustrates the effect of steric and electronic structure alterations due to base modifications. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding site and the three-way junctions within tRNA, which when analyzed in context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with the specific functional roles they play in context of RNA macromolecules.

Purine-purine base pairs and the origin of transversion-type mutation

2009 ◽  
Vol 12 (S4) ◽  
pp. 197-204
Author(s):  
Ramon Gardun̄to ◽  
Robert Rein ◽  
John T. Egan ◽  
Yves Coeckelenbergh ◽  
Robert D. Macelroy
Keyword(s):  
Base Pairs ◽  
Purine Base

NMR Structures of r(GCAGGCGUGC)2and Determinants of Stability for Single Guanosine−Guanosine Base Pairs†,‡

Biochemistry ◽  
2000 ◽  
Vol 39 (38) ◽  
pp. 11748-11762 ◽  
Author(s):  
Mark E. Burkard ◽  
Douglas H. Turner
Keyword(s):  
Base Pairs ◽  
Nmr Structures

Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site

1998 ◽  
Vol 5 (1) ◽  
pp. 60-66 ◽  
Author(s):  
Scott A. Strobel ◽  
Lori Ortoleva-Donnelly ◽  
Sean P. Ryder ◽  
Jamie H. Cate ◽  
Eileen Moncoeur
Keyword(s):  
Active Site ◽  
Group I Intron ◽  
Base Pairs ◽  
Group I ◽  
Helix Packing ◽  
Noncanonical Base Pairs

scholarly journals Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity

2019 ◽  
Vol 48 (3) ◽  
pp. 1451-1465 ◽  
Author(s):  
Zhe Zhang ◽  
Peng Xiong ◽  
Tongchuan Zhang ◽  
Junfeng Wang ◽  
Jian Zhan ◽  
...  
Keyword(s):  
3D Structure ◽  
Noncoding Rnas ◽  
Unsupervised Classification ◽  
Base Pairing ◽  
Base Pairs ◽  
False Negatives ◽  
Epistasis Analysis ◽  
Direct Coupling Analysis ◽  
3D Structure Determination ◽  
Noncanonical Base Pairs

Abstract Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained only from costly and time-consuming 3D structure determination. Here, we performed deep mutational scanning of self-cleaving CPEB3 ribozyme by error-prone PCR and showed that a library of <5 × 104 single-to-triple mutants is sufficient to infer 25 of 26 base pairs including non-nested, nonhelical, and noncanonical base pairs with both sensitivity and precision at 96%. Such accurate inference was further confirmed by a twister ribozyme at 100% precision with only noncanonical base pairs as false negatives. The performance was resulted from analyzing covariation-induced deviation of activity by utilizing both functional and nonfunctional variants for unsupervised classification, followed by Monte Carlo (MC) simulated annealing with mutation-derived scores. Highly accurate inference can also be obtained by combining MC with evolution/direct coupling analysis, R-scape or epistasis analysis. The results highlight the usefulness of deep mutational scanning for high-accuracy structural inference of self-cleaving ribozymes with implications for other structured RNAs that permit high-throughput functional selections.

Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs

Biochemistry ◽  
1994 ◽  
Vol 33 (10) ◽  
pp. 2741-2747 ◽  
Author(s):  
John L. Battiste ◽  
Ruoying Tan ◽  
Alan D. Frankel ◽  
James R. Williamson
Keyword(s):  
Base Pairs ◽  
Purine Base ◽  
Responsive Element

The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences

2015 ◽  
Vol 71 (10) ◽  
pp. 2119-2126 ◽  
Author(s):  
Arunachalam Thirugnanasambandam ◽  
Selvam Karthik ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Hydrogen Bonds ◽  
Dna Sequences ◽  
Single Strand ◽  
Triplet Repeat ◽  
The Novel ◽  
Base Pairs ◽  
Purine Base ◽  
Ion Interactions ◽  
Folded Structure ◽  
Triplet Repeat Sequences

The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson–Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.

IMPORTANCE OF CHARGE TRANSFER EXCITATIONS IN DNA ELECTRON SPECTRUM: A ZINDO SEMIEMPIRICAL QUANTUM-CHEMICAL STUDY

2004 ◽  
Vol 18 (16) ◽  
pp. 825-831 ◽  
Author(s):  
E. B. STARIKOV
Keyword(s):  
Charge Transfer ◽  
Quantum Chemical ◽  
Spectral Band ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Molecular Orbitals ◽  
Base Pairs ◽  
Purine Base ◽  
Dna Conformations

Electron spectra of DNA model compounds, adenosine-thymidine and guanosine-cytidine nucleoside base pairs, as well as the relevant homogeneous stacked base pair steps in A-DNA and B-DNA conformations, were investigated using ZINDO semiempirical quantum-chemical method. This work confirms that, in DNA with intact Watson–Crick hydrogen bonding and base stacking, the highest occupied molecular orbitals (HOMO) are residing on purine base residues, whereas the lowest unoccupied molecular orbitals (LUMO) — on pyrimidine base residues. In general, the present results are satisfactorily comparable with the available experimental data. The role of charge transfer excitations in the polymer DNA 260 nm spectral band is discussed.

scholarly journals 7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization

2020 ◽  
Vol 76 (5) ◽  
pp. 513-523
Author(s):  
Dasharath Kondhare ◽  
Simone Budow-Busse ◽  
Constantin Daniliuc ◽  
Frank Seela
Keyword(s):  
Base Pair ◽  
Crystal Packing ◽  
Donor Site ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Acceptor Site ◽  
Base Pairs ◽  
Purine Base ◽  
Value Differences ◽  
Ribose Moiety

The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′-endo) for the ribose moiety, with an antiperiplanar orientation of the 5′-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2′ of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H...O and N—H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.

scholarly journals Blind prediction of noncanonical RNA structure at atomic accuracy

2017 ◽  
Author(s):  
Andrew Watkins ◽  
Caleb Geniesse ◽  
Wipapat Kladwang ◽  
Paul Zakrevsky ◽  
Luc Jaeger ◽  
...  
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
Grand Challenge ◽  
Chemical Mapping ◽  
Base Pairs ◽  
General Ability ◽  
Rna Structural Motifs ◽  
Nucleotide Resolution ◽  
Noncanonical Base Pairs

AbstractPrediction of RNA structure from nucleotide sequence remains an unsolved grand challenge of biochemistry and requires distinct concepts from protein structure prediction. Despite extensive algorithmic development in recent years, modeling of noncanonical base pairs of new RNA structural motifs has not been achieved in blind challenges. We report herein a stepwise Monte Carlo (SWM) method with a unique add-and-delete move set that enables predictions of noncanonical base pairs of complex RNA structures. A benchmark of 82 diverse motifs establishes the method’s general ability to recover noncanonical pairs ab initio, including multistrand motifs that have been refractory to prior approaches. In a blind challenge, SWM models predicted nucleotide-resolution chemical mapping and compensatory mutagenesis experiments for three in vitro selected tetraloop/receptors with previously unsolved structures (C7.2, C7.10, and R1). As a final test, SWM blindly and correctly predicted all noncanonical pairs of a Zika virus double pseudoknot during a recent community-wide RNA-puzzle. Stepwise structure formation, as encoded in the SWM method, enables modeling of noncanonical RNA structure in a variety of previously intractable problems.

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