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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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CD spectra of D1-D18 duplexes at pH 5.0 (black line) and 7.0 (red line).
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pone.0143354.g002: CD spectra of D1-D18 duplexes at pH 5.0 (black line) and 7.0 (red line).

Mentions: The use of CD spectroscopy to study the geometry of DNA and RNA molecules is well established [21, 35]. CD spectra were performed at pH 5.0 and 7.0 in RB buffer containing 100 mM NaCl at 4°C (Table 1, Fig 2). In general, a positive long wavelength band at about 260–280 nm suggests the formation of right-handed helices. It is also a postulate that for DNA duplexes transition from positive to negative peak in the 210–220 nm range is a consequence of changing strand orientation from antiparallel to parallel [29]. For selected homopurine and homopyrimidine oligonucleotides the inversion of both strands was observed due to changing buffer pH value from 7.0 to 5.0. Moreover, LNA introduction into homopyrimidine oligonucleotide can facilitate reorientation of interacting strands and parallel duplex can form at neutral pH more efficiently due to their higher stability.


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)

CD spectra of D1-D18 duplexes at pH 5.0 (black line) and 7.0 (red line).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143354.g002: CD spectra of D1-D18 duplexes at pH 5.0 (black line) and 7.0 (red line).
Mentions: The use of CD spectroscopy to study the geometry of DNA and RNA molecules is well established [21, 35]. CD spectra were performed at pH 5.0 and 7.0 in RB buffer containing 100 mM NaCl at 4°C (Table 1, Fig 2). In general, a positive long wavelength band at about 260–280 nm suggests the formation of right-handed helices. It is also a postulate that for DNA duplexes transition from positive to negative peak in the 210–220 nm range is a consequence of changing strand orientation from antiparallel to parallel [29]. For selected homopurine and homopyrimidine oligonucleotides the inversion of both strands was observed due to changing buffer pH value from 7.0 to 5.0. Moreover, LNA introduction into homopyrimidine oligonucleotide can facilitate reorientation of interacting strands and parallel duplex can form at neutral pH more efficiently due to their higher stability.

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