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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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Normalized fluorescence intensity of D1-D18 duplexes at pH 7.0 (blue line) and pH 5.0 (red line).Black line indicates fluorescence of control probe S1 for D1-D6 duplexes, control probe S2 for D7-D12 duplexes as well as control probe S3 for D13-D18 duplexes.
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pone.0143354.g005: Normalized fluorescence intensity of D1-D18 duplexes at pH 7.0 (blue line) and pH 5.0 (red line).Black line indicates fluorescence of control probe S1 for D1-D6 duplexes, control probe S2 for D7-D12 duplexes as well as control probe S3 for D13-D18 duplexes.

Mentions: In order to confirm that the model duplexes adopt a parallel orientation the efficiency of fluorescence resonance energy transfer (FRET) between 5,6-carboxyfluorescein (FAM) and 5-carboxytetramethylrhodamine (TAMRA) terminally attached to the 5’-end of the homopurine and homopyrimidine oligonucleotides, respectively, was studied. Common fluorophores pair, FAM as the donor (excitation at 494 nm and emission at 520 nm) and TAMRA as the acceptor (excitation at 565 nm and emission at 580 nm), also called the quencher was used [36]. In this system, changes of distance between FAM and TAMRA are due to the alteration of orientation from parallel to antiparallel by increasing the pH from 5.0 to 7.0 and they will correlate with efficiency of the energy transfer. The fluorescence intensity of FAM should decrease when the parallel duplex is formed and increase when the antiparallel structure is formed. That sequence/structure dependent energy transfer was observed for duplexes D1-D18 (Figs 3–5).


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)

Normalized fluorescence intensity of D1-D18 duplexes at pH 7.0 (blue line) and pH 5.0 (red line).Black line indicates fluorescence of control probe S1 for D1-D6 duplexes, control probe S2 for D7-D12 duplexes as well as control probe S3 for D13-D18 duplexes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143354.g005: Normalized fluorescence intensity of D1-D18 duplexes at pH 7.0 (blue line) and pH 5.0 (red line).Black line indicates fluorescence of control probe S1 for D1-D6 duplexes, control probe S2 for D7-D12 duplexes as well as control probe S3 for D13-D18 duplexes.
Mentions: In order to confirm that the model duplexes adopt a parallel orientation the efficiency of fluorescence resonance energy transfer (FRET) between 5,6-carboxyfluorescein (FAM) and 5-carboxytetramethylrhodamine (TAMRA) terminally attached to the 5’-end of the homopurine and homopyrimidine oligonucleotides, respectively, was studied. Common fluorophores pair, FAM as the donor (excitation at 494 nm and emission at 520 nm) and TAMRA as the acceptor (excitation at 565 nm and emission at 580 nm), also called the quencher was used [36]. In this system, changes of distance between FAM and TAMRA are due to the alteration of orientation from parallel to antiparallel by increasing the pH from 5.0 to 7.0 and they will correlate with efficiency of the energy transfer. The fluorescence intensity of FAM should decrease when the parallel duplex is formed and increase when the antiparallel structure is formed. That sequence/structure dependent energy transfer was observed for duplexes D1-D18 (Figs 3–5).

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