Thermodynamic Parameters Based on a Nearest-Neighbor Model for DNA Sequences with a Single-Bulge Loop

Tomita, Fumiaki; Kameda, Atsushi; Yamamoto, Masahito; Ohuchi, Azuma

doi:10.1021/bi036188r

Cited by 36 publications

(29 citation statements)

References 44 publications

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“…Second, the thermodynamic influence of group II bulge loops on duplex formation (average value 3.8 kcal/mol) is very similar to that observed previously for group I bulge loops (4.0 kcal/mol) (Blose et al 2007). That the free energy increment for the insertion of a bulge loop into an RNA duplex is independent of both the identity of the bulge and its nearest neighbors is in marked contrast to the influence of bulge loops in a DNA helix, where both the bulge identity and nearest neighbors were shown to influence the stability of the insertion of a bulge (Tanaka et al 2004;Conceicao et al 2010). Also in contrast to our results where the insertion of a bulge always leads to destabilization of the duplex, the insertion of a bulge into a DNA duplex can result in helix stabilization.…”

Section: Nearest-neighbor Influences On the Thermodynamics Of Group Isupporting

confidence: 89%

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

McCann¹,

Lim²,

Manni³

et al. 2010

RNA

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Thirty-one RNA duplexes containing single-nucleotide bulge loops were optically melted in 1 M NaCl, and the thermodynamic parameters DH°, DS°, DG°3 7 , and T M for each sequence were determined. The bulge loops were of the group II variety, where the bulged nucleotide is identical to one of its nearest neighbors, leading to ambiguity as to the exact position of the bulge. The data were used to develop a model to predict the free energy of an RNA duplex containing a single-nucleotide bulge. The destabilization of the duplex by the bulge was primarily related to the stability of the stems adjacent to the bulge. Specifically, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. Since there is an ambiguity of the bulge position for group II bulges, several different stem combinations are possible. The destabilization of group II bulge loops is similar to the destabilization of group I bulge loops, if the second least stable stem is used to predict the influence of the group II bulge. In-line structure probing of the group II bulge loop embedded in a hairpin indicates that the bulged nucleotide is the one positioned farther from the hairpin loop.

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Section: Nearest-neighbor Influences On the Thermodynamics Of Group Isupporting

confidence: 89%

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

McCann¹,

Lim²,

Manni³

et al. 2010

RNA

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“…Single-base bulge loops have been extensively studied in DNA and RNA in 1 M NaCl (Tanaka et al 2004;Blose et al 2007;Minetti et al 2010). Temperature-gradient gel electrophoresis has been performed on DNA and RNA single bulge loop constructs in one study where adenine and guanine 1-nt bulge loops had similar mobility for RNA and DNA constructs, implying similar structural conformations form in these constructs (Zhu and Wartell 1999 loop of 3.8 kcal/mol, similar to our proposed value.…”

Section: Single-nucleotide Bulge Loopsmentioning

confidence: 99%

“…Single-nucleotide bulge loops have been studied in both RNA and DNA constructs (Zhu and Wartell 1999;Tanaka et al 2004;Blose et al 2007;Minetti et al 2010). A recent study examined the thermodynamic stability of the trinucleotide bulge loops in RNA (Murray et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs

Strom

Shiskova

Hahm

et al. 2015

RNA

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Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1-to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl 2 or 1 M KCl. The DG W 37 loop parameters for 1-to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔDG W values relative to 1 M KCl were 0.47-2.06 kcal/mol more favorable for the RNA bulge loops. The DG W 37 loop parameters for 1-to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4-and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1-to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1-to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride.

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“…Both Δ G min and Δ G gre are calculated based on the nearest-neighbor model, which calculates the total free energy as the summation of the contributions of various elementary structures (18,19). The elementary structures considered in this paper are stacking base pairs, bulge loops, internal loops, dangling ends and free ends.…”

Section: Algorithmmentioning

confidence: 99%

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

Tomita¹

2005

Nucleic Acids Research

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We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔGmin). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔGmin. This effectively excludes inappropriate sequences before ΔGmin is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔGexp) of 126 sequences correlated well with ΔGmin (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java.

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Thermodynamic Parameters Based on a Nearest-Neighbor Model for DNA Sequences with a Single-Bulge Loop

Cited by 36 publications

References 44 publications

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

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