The interaction of nucleosides in aqueous solution

Solie, T. N.; Schellman, John A.

doi:10.1016/0022-2836(68)90281-7

Cited by 149 publications

(120 citation statements)

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“…The parameters δ ij k for hydrogen bonding and stacking are estimated from a range of experimental and computational data in the literature. 30,35,36,[47][48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63] Since we eventually choose to match the experimental data for hairpin melting curves, 37 we only need to determine the relative strengths of each interaction. We first grouped all of the references by the type of measurement, often with several publications per group.…”

Section: Base-base Interactionsmentioning

confidence: 99%

Moving beyond Watson–Crick models of coarse grained DNA dynamics

Linak

Tourdot

Dorfman

2011

The Journal of Chemical Physics

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DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

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Section: Base-base Interactionsmentioning

confidence: 99%

Moving beyond Watson–Crick models of coarse grained DNA dynamics

Linak

Tourdot

Dorfman

2011

The Journal of Chemical Physics

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“…For example, below, for K = 0.1 M (for dissociation of free stacks), f = 0.5 (for the advantage of paired stacks), K 0 = 0.5 M (for dissociation of isolated, paired N from complementary polymer) and ΦU = 0.005 M (concentration of added polymer), are some results calculated for equilibrium in reactions with 0 to 0.2 M total added nucleotide (N 0 ). The dissociation constants used are guesses, but bear some resemblance to available measurements (e.g., Solie and Schellman 1968). We are particularly interested in free and polymer-bound nucleotide stacks (≥2 nucleotides), which are likely the productive precursors for NppN.…”

Section: Behavior Of a Paired Stacking Systemmentioning

confidence: 99%

Cross-backbone templating; ribodinucleotides made on poly(C)

Majerfeld

Puthenvedu

Yarus

2016

RNA

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′ G synthesis from pG and chemically activated 2MeImpG is accelerated by the addition of complementary poly(C), but affected only slightly by poly(G) and not at all by poly(U) and poly(A). This suggests that 3 ′ -5 ′ poly(C) is a template for uncatalyzed synthesis of 5 ′ -5 ′ GppG, as was poly(U) for AppA synthesis, previously. The reaction occurs at 50 mM monoand divalent ion concentrations, at moderate temperatures, and near pH 7. The reactive complex at the site of enhanced synthesis of 5 ′ -5 ′ GppG seems to contain a single pG, a single phosphate-activated nucleotide 2MeImpG, and a single strand of poly(C). Most likely this structure is base-paired, as the poly(C)-enhanced reaction is completely disrupted between 30 and 37°C, whereas slower, untemplated synthesis of GppG accelerates. More specifically, the reactive center acts as would be expected for short, isolated G nucleotide stacks expanded and ordered by added poly(C). For example, poly(C)-mediated GppG production is very nonlinear in overall nucleotide concentration. Uncatalyzed NppN synthesis is now known for two polymers and their complementary free nucleotides. These data suggest that varied, simple, primordial 3 ′ -5 ′ RNA sequences could express a specific chemical phenotype by encoding synthesis of complementary, reactive, coenzyme-like 5 ′ -5 ′ ribodinucleotides.

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“…qKaia&. However, it is generally (and reasonably) assumed [3] that the constants for successive associations are the same, so that the summation becomes unnecessary. It will be noted that the base concentration, and therefore that of the base-nucleotide complex, is 2-3 orders of magnitude lower than that of the total nucleotide.…”

Section: Methodsmentioning

confidence: 99%

“…Stacking interactions of considerable strength have been demonstrated in nucleosides and other derivatives in aqueous solution by thermodynamic [I -31, spectroscopic [4][5][6]3] and hydrodynamic [7,3] methods. These stacking interactions are absent in non-aqueous solvents [8], just as ordered structures in polynucleotides are destroyed under similar circumstances [9,10], and it therefore appears that there must be a considerable hydrophobic contribution to stacking interactions.…”

mentioning

confidence: 99%

“…So far however the results of such work have been confined almost entirely to self-association. Whereas in principle any physical method sensitive to associative processes can deliver data for two-component systems, in practice the precision which is called for in order to measure a weak association in the presence of a stronger one is largely beyond the scope of available methods, and complications of interpretation also exist [3]. A method is here described which is applicable to the study of heterologous associations.…”

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confidence: 99%

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Association of Nucleic-Acid Bases in Aqueous Solution: a Solvent Partition Study

Gratzer

2005

European Journal of Biochemistry

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A method is described for determining homologous and heterologous interactions between nucleic acid bases. Derivatives soluble in both water and an immiscible solvent, such as chloroform, are partitioned between the solvent and solutions of mononucleotides, a t pH corresponding to substantial ionization of the secondary phosphate, so that self-association of the nucleotide is minimised. The concentration of the base derivative is kept 2-3 orders of magnitude below that of the nucleotide, the partition ratio being determined spectrophotometrically by sampling the non-aqueous phase. Adenine and uracil, but not so far guanine and cytosine, derivatives with the requisite solubility characteristics have been found. 9-Ethyladenine and l-cyclohexyluracil were partitioned against a series of nucleotide solutions and association constants were determined and were found invariant with nucleotide concentration. Purine-purine associations are much the strongest, followed by purine-pyrimidine ; the pyrimidine-pyrimidine associations which have been investigated are vanishingly small. Published data, based on other methods, are largely confined to self-associations ; where comparison with results on uncharged derivatives, principally the nucleosides, is possible, agreement is satisfactory.It is now generally accepted that a factor of dominant importance in the stabilisation of polynucleotides in both the single and double-stranded forms is the tendency of the bases to stack one on the other. Stacking interactions of considerable strength have been demonstrated in nucleosides and other derivatives in aqueous solution by thermodynamic [I -31, spectroscopic [4-6,3] and hydrodynamic [7,3] methods. These stacking interactions are absent in non-aqueous solvents [8], just as ordered structures in polynucleotides are destroyed under similar circumstances [9,10], and it therefore appears that there must be a considerable hydrophobic contribution to stacking interactions.It is clear that studies on the association of nucleotides and their analogues in water provide the most basic information on the origins of stabilisation of polynucletide conformations. So far however the results of such work have been confined almost entirely to self-association. Whereas in principle any physical method sensitive to associative processes can deliver data for two-component systems, in practice the precision which is called for in order to measure a weak association in the presence of a stronger one is largely beyond the scope of available methods, and complications of interpretation also exist [3].

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The interaction of nucleosides in aqueous solution

Cited by 149 publications

References 25 publications

Moving beyond Watson–Crick models of coarse grained DNA dynamics

Moving beyond Watson–Crick models of coarse grained DNA dynamics

Cross-backbone templating; ribodinucleotides made on poly(C)

Association of Nucleic-Acid Bases in Aqueous Solution: a Solvent Partition Study

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