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

Szabat M, Pedzinski T, Czapik T, Kierzek E, Kierzek R - PLoS ONE (2015)

Bottom Line: Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes.However, at pH 5.0, parallel duplexes were more favorable.Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

ABSTRACT
This study investigated the influence of the nature of oligonucleotides on the abilities to form antiparallel and parallel duplexes. Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes. UV melting, circular dichroism and fluorescence studies revealed the influence of nucleotide composition on duplex structure and thermal stability depending on the buffer pH value. Most duplexes simultaneously adopted both orientations. However, at pH 5.0, parallel duplexes were more favorable. Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

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Parallel and antiparallel-stranded DNA duplexes depending on pH value (A) and chemical structure of the Watson-Crick and reverse Watson-Crick as well as Hoogsteen base pairs (B).
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pone.0143354.g001: Parallel and antiparallel-stranded DNA duplexes depending on pH value (A) and chemical structure of the Watson-Crick and reverse Watson-Crick as well as Hoogsteen base pairs (B).

Mentions: This study presents the thermodynamic and structural details of a series of unmodified and modified DNA, 2’-O-MeRNA and RNA homo- and heteroduplexes. A homoduplex is a duplex that is formed by the same type of strands (e.g., DNA or RNA), whereas a heteroduplex is a duplex formed by various types of strands (e.g., one strand is DNA and the second strand is RNA). The model duplexes were designed accordingly to previously published paper [29]. The parallel duplex was arranged to form fully matched base pairs and for the formation of this duplex it is necessary protonation of cytosine bases at acidic pH. Parallel DNA duplex is stabilized by Hoogsteen hydrogen bonds, whereas at neutral pH, the antiparallel duplex is formed with Watson-Crick base pairings and two bulges (A and T) (Fig 1). To confirm parallel and antiparallel orientations of model duplexes, many biophysical studies, including steady-state fluorescence, time-resolved fluorescence, UV melting and circular dichroism (CD) spectroscopy, were performed. The data, particularly fluorescence resonance energy transfer (FRET) measurements, suggested that 2’-O-MeRNA and RNA duplexes form parallel duplexes at pH 5.0 and 7.0. Furthermore, incorporation of LNA moieties favored parallel duplex formation at pH 7.0.


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

Szabat M, Pedzinski T, Czapik T, Kierzek E, Kierzek R - PLoS ONE (2015)

Parallel and antiparallel-stranded DNA duplexes depending on pH value (A) and chemical structure of the Watson-Crick and reverse Watson-Crick as well as Hoogsteen base pairs (B).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4666348&req=5

pone.0143354.g001: Parallel and antiparallel-stranded DNA duplexes depending on pH value (A) and chemical structure of the Watson-Crick and reverse Watson-Crick as well as Hoogsteen base pairs (B).
Mentions: This study presents the thermodynamic and structural details of a series of unmodified and modified DNA, 2’-O-MeRNA and RNA homo- and heteroduplexes. A homoduplex is a duplex that is formed by the same type of strands (e.g., DNA or RNA), whereas a heteroduplex is a duplex formed by various types of strands (e.g., one strand is DNA and the second strand is RNA). The model duplexes were designed accordingly to previously published paper [29]. The parallel duplex was arranged to form fully matched base pairs and for the formation of this duplex it is necessary protonation of cytosine bases at acidic pH. Parallel DNA duplex is stabilized by Hoogsteen hydrogen bonds, whereas at neutral pH, the antiparallel duplex is formed with Watson-Crick base pairings and two bulges (A and T) (Fig 1). To confirm parallel and antiparallel orientations of model duplexes, many biophysical studies, including steady-state fluorescence, time-resolved fluorescence, UV melting and circular dichroism (CD) spectroscopy, were performed. The data, particularly fluorescence resonance energy transfer (FRET) measurements, suggested that 2’-O-MeRNA and RNA duplexes form parallel duplexes at pH 5.0 and 7.0. Furthermore, incorporation of LNA moieties favored parallel duplex formation at pH 7.0.

Bottom Line: Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes.However, at pH 5.0, parallel duplexes were more favorable.Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

ABSTRACT
This study investigated the influence of the nature of oligonucleotides on the abilities to form antiparallel and parallel duplexes. Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes. UV melting, circular dichroism and fluorescence studies revealed the influence of nucleotide composition on duplex structure and thermal stability depending on the buffer pH value. Most duplexes simultaneously adopted both orientations. However, at pH 5.0, parallel duplexes were more favorable. Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

Show MeSH