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Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs.

Miller S, Jones LE, Giovannitti K, Piper D, Serra MJ - Nucleic Acids Res. (2008)

Bottom Line: The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3' single or double-nucleotide overhangs.Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3' double-nucleotide overhang.Thermodynamic parameters for the 5' single terminal overhangs adjacent to wobble closing base pairs are also presented.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Allegheny College, 520 N. Main St, Meadville, PA 16335, USA.

ABSTRACT
Thermodynamic parameters are reported for duplex formation of 40 self-complementary RNA duplexes containing wobble terminal base pairs with all possible 3' single and double-nucleotide overhangs, mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest neighbor analysis, the addition of a single 3' dangling nucleotide increases the stability of duplex formation up to 1 kcal/mol in a sequence-dependent manner. The addition of a second dangling nucleotide increases the stability of duplexes closed with wobble base pairs in an idiosyncratic manner. The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3' single or double-nucleotide overhangs. Phylogenetic analysis of naturally occurring miRNAs was performed. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3' double-nucleotide overhang. Thermodynamic parameters for the 5' single terminal overhangs adjacent to wobble closing base pairs are also presented.

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Stacking of bases on wobble GU base pairs. (A) View down the helix axis of  (B) View down helix axis of . (C) View down helix axis of . (D) View down helix axis of . The dangling bases are shown as the nearer base and are drawn in bold. Examples are taken from the NMR structure of the P1 helix of the group I intron (44).
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Figure 1: Stacking of bases on wobble GU base pairs. (A) View down the helix axis of (B) View down helix axis of . (C) View down helix axis of . (D) View down helix axis of . The dangling bases are shown as the nearer base and are drawn in bold. Examples are taken from the NMR structure of the P1 helix of the group I intron (44).

Mentions: These results are summarized in Table 2. We have assumed no interaction between the overhangs at the two ends of the helix, hence we have taken half of the free-energy increment for the two dangling ends as the contribution of a single dangling end. Nonneighbor interactions have not been observed with short helices with single nucleotide overhangs (13–15,18–20) and the thermodynamic stability of nonself-complementary oligomers had been shown to be predicted with the thermodynamic values derived from self-complementary oligomers (18–20). The stability provided by the 3′ dangling ends on wobble terminal base pairs is similar to the stability of the corresponding 3′ dangling end on a helix terminated by Watson–Crick base pairs. Similar results were observed for the stabilization of helices with 3′ dangling 2-aminopurine. The stabilization for helices by the addition of a 3′ dangling 2-aminopurine was nearly the same for duplexes with terminal Watson–Crick or wobble base pairs (42). There is very good agreement between the values measured here and the previously predicted values. For example, the average difference in free energy between measured and previously predicted is 0.1 kcal/mol; and, the largest difference is only 0.4 kcal/mol. There are no known structures for a 3′ dangling end on a duplex closed by a wobble base pair [the structure of a wobble pair that closes an RNA hairpin is known (43) but in this case, it appears that the wobble base pair is strained by the small 3-nt hairpin loop]; so, we chose to examine the stacking of a 3′ nucleotide (as part of an adjacent base pair) on an isolated interior wobble base pair (44). Figure 1A and B display the stacking of a 3′ nucleotide on a wobble base pair. In both the cases, and , the 3′ nucleotide is located directly above the wobble base pair. While this stacking was observed in the interior of a helix, where the 3′ nucleotide was part of a Watson–Crick base pair, the likelihood is that a 3′ dangling base at the end of a helix would have additional conformational plasticity and would be able to stack as well on a terminal wobble base pair. A 3′ dangling 2-aminopurine was shown to be primarily in the stacked orientation with both Watson–Crick and wobble terminal base pairs (42). The helix stabilization by 3′ dangling ends has been related to the strengthening of the hydrogen bonds in the terminal base pair provided by the shielding of the terminal base pair from the solvent by the dangling end (45).Table 2.


Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs.

Miller S, Jones LE, Giovannitti K, Piper D, Serra MJ - Nucleic Acids Res. (2008)

Stacking of bases on wobble GU base pairs. (A) View down the helix axis of  (B) View down helix axis of . (C) View down helix axis of . (D) View down helix axis of . The dangling bases are shown as the nearer base and are drawn in bold. Examples are taken from the NMR structure of the P1 helix of the group I intron (44).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553593&req=5

Figure 1: Stacking of bases on wobble GU base pairs. (A) View down the helix axis of (B) View down helix axis of . (C) View down helix axis of . (D) View down helix axis of . The dangling bases are shown as the nearer base and are drawn in bold. Examples are taken from the NMR structure of the P1 helix of the group I intron (44).
Mentions: These results are summarized in Table 2. We have assumed no interaction between the overhangs at the two ends of the helix, hence we have taken half of the free-energy increment for the two dangling ends as the contribution of a single dangling end. Nonneighbor interactions have not been observed with short helices with single nucleotide overhangs (13–15,18–20) and the thermodynamic stability of nonself-complementary oligomers had been shown to be predicted with the thermodynamic values derived from self-complementary oligomers (18–20). The stability provided by the 3′ dangling ends on wobble terminal base pairs is similar to the stability of the corresponding 3′ dangling end on a helix terminated by Watson–Crick base pairs. Similar results were observed for the stabilization of helices with 3′ dangling 2-aminopurine. The stabilization for helices by the addition of a 3′ dangling 2-aminopurine was nearly the same for duplexes with terminal Watson–Crick or wobble base pairs (42). There is very good agreement between the values measured here and the previously predicted values. For example, the average difference in free energy between measured and previously predicted is 0.1 kcal/mol; and, the largest difference is only 0.4 kcal/mol. There are no known structures for a 3′ dangling end on a duplex closed by a wobble base pair [the structure of a wobble pair that closes an RNA hairpin is known (43) but in this case, it appears that the wobble base pair is strained by the small 3-nt hairpin loop]; so, we chose to examine the stacking of a 3′ nucleotide (as part of an adjacent base pair) on an isolated interior wobble base pair (44). Figure 1A and B display the stacking of a 3′ nucleotide on a wobble base pair. In both the cases, and , the 3′ nucleotide is located directly above the wobble base pair. While this stacking was observed in the interior of a helix, where the 3′ nucleotide was part of a Watson–Crick base pair, the likelihood is that a 3′ dangling base at the end of a helix would have additional conformational plasticity and would be able to stack as well on a terminal wobble base pair. A 3′ dangling 2-aminopurine was shown to be primarily in the stacked orientation with both Watson–Crick and wobble terminal base pairs (42). The helix stabilization by 3′ dangling ends has been related to the strengthening of the hydrogen bonds in the terminal base pair provided by the shielding of the terminal base pair from the solvent by the dangling end (45).Table 2.

Bottom Line: The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3' single or double-nucleotide overhangs.Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3' double-nucleotide overhang.Thermodynamic parameters for the 5' single terminal overhangs adjacent to wobble closing base pairs are also presented.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Allegheny College, 520 N. Main St, Meadville, PA 16335, USA.

ABSTRACT
Thermodynamic parameters are reported for duplex formation of 40 self-complementary RNA duplexes containing wobble terminal base pairs with all possible 3' single and double-nucleotide overhangs, mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest neighbor analysis, the addition of a single 3' dangling nucleotide increases the stability of duplex formation up to 1 kcal/mol in a sequence-dependent manner. The addition of a second dangling nucleotide increases the stability of duplexes closed with wobble base pairs in an idiosyncratic manner. The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3' single or double-nucleotide overhangs. Phylogenetic analysis of naturally occurring miRNAs was performed. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3' double-nucleotide overhang. Thermodynamic parameters for the 5' single terminal overhangs adjacent to wobble closing base pairs are also presented.

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