Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2’-O-Methyl RNA and RNA Oligonucleotides

Szabat, Marta; Pędziński, Tomasz; Czapik, Tomasz; Kierzek, Elżbieta; Kierzek, Ryszard

doi:10.1371/journal.pone.0143354

Cited by 11 publications

(18 citation statements)

References 41 publications

(48 reference statements)

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“…The increase in thermodynamic stability of these structures correlates with the frequency of LNAs. These results are supported by the findings of Kierzek's group . The same trend was observed in reverse transcription experiments, where the inhibition of the process by parallel triplexes with LNA moieties was more efficient than unmodified structures .…”

Section: Parallel Dna and Rna Duplexessupporting

confidence: 86%

“…DNA duplexes were more stable under acidic conditions, whereas RNA and 2′‐ O ‐methyl‐RNA duplexes were less stable. These results correlated with the different geometry of these structures, hydrogen bonds and base stacking interactions . Furthermore, there are a number of studies that revealed the effects of LNA on the structure and stability of parallel‐stranded DNA or RNA duplexes.…”

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 84%

“…Scheme for the chemical structure of the Watson–Crick (A), reverse Watson–Crick and Hoogsteen base pairs (B) .…”

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 99%

“…These sequences were selected due to their propensity to form stable parallel‐stranded duplexes according to the study of Szabat et al . . blastn (Bethesda, MD, USA) programs were used to search a nucleotide ‘query’ sequence to scan a nucleotide database, Human RefSeqGene (RefSeq_Gene).…”

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 99%

“…Interestingly, the sequences 5 0 -AGAAAGAGAAGA and 5 0 -TCTTTCTCTTCT were utilized for comparative genome analysis based on the Basic Local Alignment Search Tool (BLAST) [26]. These sequences were selected due to their propensity to form stable parallelstranded duplexes according to the study of Szabat et al [27]. BLASTN (Bethesda, MD, USA) programs were used to search a nucleotide 'query' sequence to scan a nucleotide database, Human RefSeqGene (RefSeq_Gene).…”

Section: Parallel Oriented Strands In Natural Dna and Rnamentioning

confidence: 99%

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Parallel‐stranded DNA and RNA duplexes – structural features and potential applications

Szabat

Kierzek

2017

The FEBS Journal

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Nowadays, decades after the discovery of the right-handed B form of DNA, it is well known that nucleic acids have great conformational flexibility, exhibiting a large degree of variation in their structure. In nature, DNA and RNA exist in an antiparallel orientation, stabilized by WatsonCrick base pairs. However, in some cases, nucleic acid fragments with specific nucleotide sequences can adopt a parallel orientation involving non-canonical base pairing. Interestingly, parallel-stranded duplexes have been found in specific chromosome regions. Furthermore, parallel oriented regions have also been found in bacterial (Escherichia coli, Listeria innocua) and insect genomes (Drosophila melanogaster). These unusual structures could have a remarkable evolutionary role, as well as significant impact on biological processes. For example, parallel stretches were shown to be involved in processing the 3 0 ends of mRNAs and in specific gene silencing. Moreover, certain types of parallel-stranded duplexes may be useful tools, with several practical applications. They can constitute excellent templates for the formation of other structures and for the development of antigene and antisense approaches.

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Section: Parallel Dna and Rna Duplexessupporting

confidence: 86%

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 84%

“…Scheme for the chemical structure of the Watson–Crick (A), reverse Watson–Crick and Hoogsteen base pairs (B) .…”

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 99%

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 99%

Section: Parallel Oriented Strands In Natural Dna and Rnamentioning

confidence: 99%

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Parallel‐stranded DNA and RNA duplexes – structural features and potential applications

Szabat

Kierzek

2017

The FEBS Journal

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Combinatorial Design of a Nanobody that Specifically Targets Structured RNAs

Cawez

Duray

et al. 2018

Journal of Molecular Biology

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Recent advances in transcriptome sequencing and analysis have revealed the complexity of the human genome. The majority (≈ 98%) of cellular transcripts is not translated into proteins and represents a vast, unchartered world of functional non-coding RNAs. Most of them adopt a well-defined three-dimensional structure to achieve their biological functions. However, only very few RNA structures are currently available which reflects the challenges associated with RNA crystallization. Nevertheless, these structures would represent a critical step in understanding functions of non-coding RNAs and their molecular mechanisms in the cell. The overall goal of this study is to develop an innovative and versatile tool to facilitate the functional study and crystallization of structured RNAs (stRNAs). In this work, we have engineered an antibody fragment from camelid heavy-chain antibody (nanobody) able to specifically bind with low nanomolar affinity to stRNA, while no binding could be detected for single-stranded DNA/RNA, double-stranded DNA/RNA or a negatively charged protein. However, this nanobody recognizes different and non-related stRNAs, this observation suggests that it binds to an epitope shared by these stRNAs. Finally, our data also show that the binding of the nanobody does not alter the secondary structure content of the stRNA as well as its unfolding/refolding processes during heat treatment. This work constitutes a successful proof of concept demonstrating that nanobodies can be engineered to recognize RNA-related epitopes.

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