Hoogsteen-Paired Homopurine [RP-PS]-DNA and Homopyrimidine RNA Strands Form a Thermally Stable Parallel Duplex

Guga, Piotr; Janicka, Magdalena; Maciaszek, Anna; Rębowska, Beata; Nowak, Genowefa

doi:10.1529/biophysj.107.108183

Cited by 13 publications

(11 citation statements)

References 40 publications

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“…Unlike in DNA ( 59 ) where experimental evidence has been provided for the isolated existence of such a ps duplex, more detailed data indicating formation of an isolated ps Hoogsteen-paired RNA duplex appear to be lacking to our knowledge. On the other hand, formation of a ps Hoogsteen-paired duplex between a homo-pyrimidine RNA strand and a homo-purine all- R p-phosphorothioate DNA strand has recently been demonstrated ( 61 ).…”

Section: Resultsmentioning

confidence: 99%

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

Pallan

Lubini

Bolli

et al. 2007

Nucleic Acids Research

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The crystal structure of the duplex formed by oligo(2′,3′-dideoxy-β-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847–10856]. This inclination is easily perceived because homo-DNA exhibits only a modest helical twist. Conversely, the tight coiling of strands conceals that the backbone-base inclinations for A- (DNA and RNA) and B-form (DNA) duplexes differ considerably. We have defined a parameter ηB that corresponds to the local inclination between sugar-phosphate backbone and base plane in nucleic acid strands. Here, we show its biological significance as a predictive measure for the relative strand polarities (antiparallel, aps, or parallel, ps) in duplexes of DNA, RNA and artificial nucleic acid pairing systems. The potential of formation of ps duplexes between complementary 16-mers with eight A and U(T) residues each was investigated with DNA, RNA, 2′-O-methylated RNA, homo-DNA and p-RNA, the ribopyranosyl isomer of RNA. The thermodynamic stabilities of the corresponding aps duplexes were also measured. As shown previously, DNA is capable of forming both ps and aps duplexes. However, all other tested systems are unable to form stable ps duplexes with reverse Watson–Crick (rWC) base pairs. This observation illustrates the handicap encountered by nucleic acid systems with inclinations ηB that differ significantly from 0° to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of −30°, pairs strictly in an aps fashion. On the other hand, the more or less perpendicular orientation of backbone and bases in DNA allows it to adopt a ps rWC paired duplex. In addition to providing a rationalization of relative strand polarity with nucleic acids, the backbone-base inclination parameter is also a determinant of cross-pairing. Thus, systems with strongly deviating ηB angles will not pair with each other. Nucleic acid pairing systems with significant backbone-base inclinations can also be expected to display different stabilities depending on which terminus carries unpaired nucleotides. The negative inclination of RNA is consistent with the higher stability of duplexes with 3′- compared to those with 5′-dangling ends.

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Section: Resultsmentioning

confidence: 99%

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

Pallan

Lubini

Bolli

et al. 2007

Nucleic Acids Research

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“…For unmodified oligonucleotides, the thermal stability of parallel duplexes is significantly lower compared to antiparallel WatsonÀCrick duplexes. However, Guga et al found that homopurine PS-Oligos possessing all internucleotide linkages of (R P )-configuration form parallel duplexes with an RNA or 2'-MeO-RNA strand with Hoogsteen complementarity [162]. The parallel orientation of strands was confirmed by fluorescence quenching experiments.…”

Section: For Example the Duplex [All-(s P )-Ps]-da 12 /T 12 Is More mentioning

confidence: 97%

Phosphorothioate Nucleotides and Oligonucleotides – Recent Progress in Synthesis and Application

Guga

Koziołkiewicz

2011

Chemistry & Biodiversity

Self Cite

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We dedicate this work to Prof. Fritz Eckstein (MPI, Gçttingen) and Prof. Wojciech J. Stec (CMMS PAS, Łó dź ), who invented the phosphorothioate modification of nucleic acids, envisioned its many important applications, carefully elucidated its biochemical and stereochemical aspects, and fostered PS-Oligos over decades. We are very grateful to have had the honor and pleasure to develop our understanding of PS-Oligos through guidance by their papers and lectures, and through stimulating scientific discussions with these two great scientists.

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“…Furthermore, Guga's group reported that homopurine DNA phosphorothioates possessing all internucleotide linkages of the R P configuration form stable parallel duplexes. Remarkably, the structures formed with 2′‐ O ‐methyl‐RNA are thermally more stable than unmodified duplexes with antiparallel orientation and the modified forms were also stable under neutral conditions .…”

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 99%

“…Because DNA and RNA with parallel strands could be promising tools in molecular genetics, researchers have shown an interest in improving their physicochemical properties . As a result, various chemical modifications of oligonucleotides have been developed.…”

Section: Parallel Dna and Rna Duplexesmentioning

confidence: 99%

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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Hoogsteen-Paired Homopurine [RP-PS]-DNA and Homopyrimidine RNA Strands Form a Thermally Stable Parallel Duplex

Cited by 13 publications

References 40 publications

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

Phosphorothioate Nucleotides and Oligonucleotides – Recent Progress in Synthesis and Application

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

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