DNA oligonucleotides with alternating GGG and GCG tracts adopt a tetrastrand fold stabilized by noncanonical base pairs

2014 ◽  
Author(s):  
Vojč Kocman ◽  
Janez Plavec
Keyword(s):  
Base Pairs ◽  
Dna Oligonucleotides ◽  
Noncanonical Base Pairs

scholarly journals Sequence-dependent structural changes in a self-assembling DNA oligonucleotide

2015 ◽  
Vol 71 (12) ◽  
pp. 2471-2478 ◽  
Author(s):  
Maithili Saoji ◽  
Paul J. Paukstelis
Keyword(s):  
Structural Changes ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Features ◽  
Base Pairing ◽  
Base Pairs ◽  
Dna Oligonucleotides ◽  
Self Assembling ◽  
Structure Relationship ◽  
Noncanonical Base Pairs

DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson–Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg2+through a combination of Watson–Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson–Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A–G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G–A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson–Crick duplex region. These results provide important new insights into the sequence–structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson–Crick and noncanonical base pairs that is responsible for crystallization fate.

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.

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.

Interaction of oligonucleotides with benzo[c]phenanthridine alkaloid sanguilutine

2013 ◽  
Vol 67 (5) ◽  
Author(s):  
Stanislava Rybáková ◽  
Michal Rájecký ◽  
Jana Urbanová ◽  
Kristýna Pěnčíková ◽  
Eva Táborská ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Luminescence Spectroscopy ◽  
Base Pairs ◽  
Dna Oligonucleotides ◽  
Sanguinaria Canadensis ◽  
Double Stranded Dna ◽  
Low Concentrations ◽  
Intensity Response ◽  
Heterogeneous Base ◽  
Positively Charged

AbstractBenzo[c]phenanthridine alkaloid sanguilutine was extracted and purified from the dried roots of Sanguinaria canadensis. The interaction of the positively charged iminium form of alkaloid with double-stranded DNA oligonucleotides was studied using luminescence spectroscopy. The results showed that the interaction with various double-stranded oligonucleotides was not specific to A-T or G-C base pairs; also, no preference was found for either homogeneous or heterogeneous base composition of strands. The association constants were calculated to be in the range of (1.31–14.36) × 105 M−1. The luminescence intensity response at 610 nm to low concentrations of double-stranded DNA was found to be linear and can potentially be used for the fluorometric quantification of DNA. The limit of detection was estimated to be 120 ng mL−1 of DNA (calculated by 3σ method).

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.

scholarly journals Deciphering the reading of the genetic code by near-cognate tRNA

2018 ◽  
Vol 115 (12) ◽  
pp. 3018-3023 ◽  
Author(s):  
Sandra Blanchet ◽  
David Cornu ◽  
Isabelle Hatin ◽  
Henri Grosjean ◽  
Pierre Bertin ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Code ◽  
Base Pairs ◽  
Stop Codons ◽  
The Third ◽  
Wobble Position ◽  
Cognate Trna ◽  
Noncanonical Base Pairs

Some codons of the genetic code can be read not only by cognate, but also by near-cognate tRNAs. This flexibility is thought to be conferred mainly by a mismatch between the third base of the codon and the first of the anticodon (the so-called “wobble” position). However, this simplistic explanation underestimates the importance of nucleotide modifications in the decoding process. Using a system in which only near-cognate tRNAs can decode a specific codon, we investigated the role of six modifications of the anticodon, or adjacent nucleotides, of the tRNAs specific for Tyr, Gln, Lys, Trp, Cys, and Arg inSaccharomyces cerevisiae.Modifications almost systematically rendered these tRNAs able to act as near-cognate tRNAs at stop codons, even though they involve noncanonical base pairs, without markedly affecting their ability to decode cognate or near-cognate sense codons. These findings reveal an important effect of modifications to tRNA decoding with implications for understanding the flexibility of the genetic code.

Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine·guanine base pairs

Cell ◽  
1987 ◽  
Vol 51 (6) ◽  
pp. 899-908 ◽  
Author(s):  
Eric Henderson ◽  
Charles C. Hardin ◽  
Steven K. Walk ◽  
Ignacio Tinoco ◽  
Elizabeth H. Blackburn
Keyword(s):  
Telomeric Dna ◽  
Base Pairs ◽  
Dna Oligonucleotides

Structure, Stability, and Dynamics of Canonical and Noncanonical Base Pairs:  Quantum Chemical Studies

2008 ◽  
Vol 112 (12) ◽  
pp. 3786-3796 ◽  
Author(s):  
Ashim Roy ◽  
Swati Panigrahi ◽  
Malyasri Bhattacharyya ◽  
Dhananjay Bhattacharyya
Keyword(s):  
Quantum Chemical ◽  
Structure Stability ◽  
Base Pairs ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Noncanonical Base Pairs

scholarly journals RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Rhiju Das ◽  
Andrew M Watkins
Keyword(s):  
Ribosomal Proteins ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Base Pairs ◽  
Beet Western Yellows Virus ◽  
Rna Tertiary Structure ◽  
Functional Features ◽  
Matlab Package ◽  
Noncanonical Base Pairs

Abstract Publishing, discussing, envisioning, modeling, designing and experimentally determining RNA three-dimensional (3D) structures involve preparation of two-dimensional (2D) drawings that depict critical functional features of the subject molecules, such as noncanonical base pairs and protein contacts. Here, we describe RiboDraw, new software for crafting these drawings. We illustrate the features of RiboDraw by applying it to several RNAs, including the Escherichia coli tRNA-Phe, the P4–P6 domain of Tetrahymena ribozyme, a −1 ribosomal frameshift stimulation element from beet western yellows virus and the 5′ untranslated region of SARS-CoV-2. We show secondary structure diagrams of the 23S and 16S subunits of the E. coli ribosome that reflect noncanonical base pairs, ribosomal proteins and structural motifs, and that convey the relative positions of these critical features in 3D space. This software is a MATLAB package freely available at https://github.com/DasLab/RiboDraw.

Sign in / Sign up

Export Citation Format

Share Document