A thermodynamic study on rA7U7

Ohms, J.; Ackermann, Th.

doi:10.1016/0301-4622(89)80051-1

Cited by 5 publications

(4 citation statements)

References 16 publications

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“…81-84, two-state conformity for a specific sequence was examined in two complementary ways: (i) by calculating the fraction (λ) of base pairs forming cooperatively, as obtained from the ratio of van't Hoff and calorimetric enthalpies and (ii) by calculating the fraction (F I,max ) of intermediates from the statistical deconvolution of differential scanning calorimetry curves. For oligoribonucleotides of the type (A n U n ) 2 , 81,82 with n = 5 or 7, λ was found to be larger than 1 (implying no intermediates), while F I,max was determined to be between 20% and 25% (implying intermediates). Other studies regarding the (A 7 U 7 ) 2 sequence found λ to be less than 1 and a single intermediate state having roughly 10 (∼70%) bases paired.…”

Section: A Population Distributions Of Denatured Intermediate and mentioning

confidence: 93%

“…Most likely the existence of such a process may help to elucidate conflicting experimental results involving the same type of sequences. [81][82][83][84] In the experiments of Refs. 81-84, two-state conformity for a specific sequence was examined in two complementary ways: (i) by calculating the fraction (λ) of base pairs forming cooperatively, as obtained from the ratio of van't Hoff and calorimetric enthalpies and (ii) by calculating the fraction (F I,max ) of intermediates from the statistical deconvolution of differential scanning calorimetry curves.…”

Section: A Population Distributions Of Denatured Intermediate and mentioning

confidence: 99%

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Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

Araque

Robert

2016

The Journal of Chemical Physics

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Because oligonucleotides are short sequences of nucleic acid bases, their association in solution with complementary strands (hybridization) is often seen to conform to a simple two-state model. However, experimental evidence suggests that, despite their short length, oligonucleotides may hybridize through multiple states involving intermediates. We investigate whether these apparently contradictory scenarios are possible by imposing different levels of sequence specificity on a lattice model of oligonucleotides in solution, which we introduced in Part I [J. C. Araque et al., J. Chem. Phys. 134, 165103 (2011)]. We find that both multiple-intermediate (weakly cooperative) and two-state (strongly cooperative) transitions are possible and that these are directly linked to the level of sequence specificity. Sequences with low specificity hybridize (base-by-base) by way of multiple stable intermediates with increasing number of paired bases. Such intermediate states are weakly cooperative because the energetic gain from adding an additional base pair is outweighed by the conformational entropy loss. Instead, sequences with high specificity hybridize through multiple metastable intermediates which easily bridge the configurational and energetic gaps between single- and double-stranded states. These metastable intermediates interconvert with minimal loss of conformational entropy leading to a strongly cooperative hybridization. The possibility of both scenarios, multiple- and two-states, is therefore encoded in the specificity of the sequence which in turn defines the level of cooperativity.

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Section: A Population Distributions Of Denatured Intermediate and mentioning

confidence: 93%

Section: A Population Distributions Of Denatured Intermediate and mentioning

confidence: 99%

Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

Araque

Robert

2016

The Journal of Chemical Physics

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“…Synthesis and Purification of Oligoribonucleotides. rA;L\ (y = 3-10) and rA-yU^( y = 5-11) have been synthesized and purified according to procedures described previously (Rockstroh et al, 1988;Ohms & Ackermann, 1989). Chain lengths were determined by means of relative band intensities in IR spectra of the random coil at 80 °C.…”

Section: Methodsmentioning

confidence: 99%

“…The deconvolution parameter F[max has been compared with the length of the cooperative unit A (Ohms & Ackermann, 1989). Additionally, for comparing our results with the former ones we present temperature-dependent UV melting data.…”

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confidence: 99%

Thermodynamics of double- and triple-helical aggregates formed by self-complementary oligoribonucleotides of the type rAxUy

Ohms¹,

Ackermann²

1990

Biochemistry

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The thermal denaturation of a series of oligoribonucleotides of the form rAxUy (x = 5 or 7 and y = 3-11) has been characterized by means of IR spectroscopy, UV spectroscopy, and DSC. IR spectra proved the occurrence of double- and triple-helical regions at various contents of uracil residues in the nucleotide. From DSC measurements transition enthalpies, entropies, and free enthalpies were derived. The effect of fraying in terminal base pairs of symmetrical nucleotides (x = y) was quantified. Thermodynamic excess parameters due to dangling ends (5'A and 3'U), terminal AU base pairs, and UAU base triplets were obtained by comparing DSC results from different nucleotides. Empirical values for contributions of base stacking and pairing to the stability of terminal AU base pairs have been estimated: for nucleotides under study with a high degree of fraying at the ends of the helix the major stabilization effect comes from base stacking. The size of the cooperative unit lambda in most nucleotides under study is larger than 1; i.e., in these cases intermolecular cooperation takes place. Through deconvolution of DSC data maximum populations of intermediate states FI,max were obtained. On the basis of these results all nucleotides under study were proved to melt in multistate manner. FI,max increases with the number of base pairs, decreases through dangling ends, and shows approximately constant values for triple-helical aggregates of the series rA5Uy as well as rA7Uy.

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Synthesis and Characterization of Novel Chiral Conjugated Materials

Rajca

Miyasaka

2006

Functional Organic Materials

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A thermodynamic study on rA7U7

Cited by 5 publications

References 16 publications

Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

Thermodynamics of double- and triple-helical aggregates formed by self-complementary oligoribonucleotides of the type rAxUy

Synthesis and Characterization of Novel Chiral Conjugated Materials

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