Allowance for Heterogeneous Stacking in the DNA Helix-Coil Transition Theory

Vologodskii, Alexander; Amirikyan, B. R.; Lyubchenko, Yu. L.; Frank‐Kamenetskii, Maxim D.

doi:10.1080/07391102.1984.10507552

Cited by 106 publications

(90 citation statements)

References 24 publications

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“…The values of a XY and γ XY are not uniquely defined in our approach and can be specified in different ways (27,28,(33)(34)(35). We used a method based on symmetry properties of DNA bases (34).…”

Section: Resultsmentioning

confidence: 99%

Sequence dependence of DNA bending rigidity

Geggier

Vologodskii

2010

Proc. Natl. Acad. Sci. U.S.A.

212

247

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For many aspects of DNA-protein interaction, it is vital to know how DNA bending rigidity (or persistence length, a) depends on its sequence. We addressed this problem using the method based on cyclization of short DNA fragments, which allows very accurate determination of a. Our approach was based on assigning specific values of a to each of 10 distinct dinucleotide steps. We prepared DNA fragments, each about 200 bp in length, with various quasiperiodic sequences, measured their cyclization efficiencies (j factors), and fitted the data by the theoretical equation to obtain the values of a for each fragment. From these data, we obtained a set of a for the dinucleotide steps. To test this set, we used it to design DNA sequences that should correspond to very low and very high values of a, prepared the corresponding fragments, and determined their values of a experimentally. The measured and calculated values of a were very close to one another, confirming that we have found the correct solution to this long-standing problem. The same experimental data also allowed us to determine the sequence dependence of DNA helical repeat.DNA elasticity | DNA persistence length T he value of DNA persistence length, a, closely related to the bending rigidity of the double helix, is very important for quantitative analysis of many aspects of DNA functioning. Many different methods were applied over the last decades to determine this value and its dependence on ionic conditions (1). These studies showed that under near physiological ionic conditions the value of a is close to 50 nm (1-3). They also showed that, in a good approximation, the value of a does not depend on DNA sequence, because many studies that use different DNA molecules gave very close values of a. However, the sequence dependence of DNA bending rigidity is vital for many aspects of DNAprotein interaction, and is particularly important for understanding how nucleosomes position along DNA molecules (4, 5). Despite its importance, the problem has formerly remained unsolved, although a few research groups have tried various approaches (6-8). The data that are generally considered most reliable were obtained from statistical analysis of DNA-protein crystal structures (9, 10). The large volume of available structural data allowed this group of researchers to present a very detailed picture of the sequence dependence of DNA conformational properties. This analysis, however, is based on the assumption that variations of the DNA bend angles in the crystals correspond to the amplitudes of thermal fluctuations of these angles in solution. It is hard to justify this assumption.The major obstacle in determining the sequence dependence of a is the necessity of highly accurate measurements of a for different sequences. The majority of methods applied for the measurements of a do not provide the necessary level of accuracy. The only known method that allows one to measure a with the required accuracy is based on cyclization of short DNA fragments by DNA ligase (2,3,11,12). It i...

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Section: Resultsmentioning

confidence: 99%

Sequence dependence of DNA bending rigidity

Geggier

Vologodskii

2010

Proc. Natl. Acad. Sci. U.S.A.

212

247

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“…Due to the high cooperativity of melting behavior, only the paired Watson-Crick neighbors appear in the constraint equations (86). In other words, if the cooperative unit is larger than the duplex (which is typically true for short oligonucleotide duplexes), there is no local melting and the population of intermediate states at any temperature is negligible.…”

Section: Discussionmentioning

confidence: 99%

Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs

et al. 1998

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Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of ∆G°3 7 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson-Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict ∆G°3 7 , ∆H°, ∆S°, and T M within 3.2%, 6.0%, 6.8%, and 1.3°C, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.The thermodynamics of secondary structure formation are important for unraveling structure-function relationships for RNA. For example, these thermodynamics provide a foundation for predicting secondary structure and stability, both of which can correlate with function. Moreover, predicting secondary structure is a crucial intermediate step toward predicting three-dimensional structure (1, 2). In addition, differences between the thermodynamics of secondary structure formation and of overall folding can provide insight into the thermodynamics of tertiary structure formation (3-7).Watson-Crick base pairs are one of the most important motifs in RNA secondary structures. The thermodynamics of Watson-Crick base pair formation have been studied in short RNA duplexes (8, 9). The results are well-represented by a nearest-neighbor model in which the thermodynamic stability of a base pair is dependent on the identity of the adjacent base pairs. This model has been termed an individual nearest-neighbor (INN) model (10, 11). The pioneering implementation by Borer et al. (8) employed 6 nearest-neighbor parameters and separate initiation parameters for duplexes with and without a GC base pair. Due to advances in oligoribonucleotide synthesis (12), Freier et al. (9) were able to determine all 10 nearest-neighbor parameters in the INN model and the initiation parameter for duplexes with at least one GC base pair. The initiation parameter for duplexes with only AU base pairs was not determined.It has been suggested that a nearest-neighbor model that treats terminal base pairs differently from internal base pairs (8) or treats terminal GC base pairs differently from terminal AU base pairs (10, 11, 13) may improve modeling of duplex stability. The model proposed by Gray (10) has been termed an independent short sequence (ISS) model because the 14 sequence-dependent parameters of the model must be combined into 12 "short sequence" p...

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“…Energetically favorable stacking interactions between bases play an important role in determining and stabilizing nucleic acid structures [117,118]. The physical fundamentals of nucleic acid bases stacking in water have been accurately defined and reviewed [119][120][121], the thermodynamic parameters for stacking have been determined [122,123].…”

Section: The 3 5 Cgmp Polymerization Reactionmentioning

confidence: 99%

Formamide and the origin of life

Saladino

Crestini

Pino

et al. 2012

Physics of Life Reviews

260

234

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The complexity of life boils down to the definition: "self-sustained chemical system capable of undergoing Darwinian evolution" (Joyce, 1994) [1]. The term "self-sustained" implies a set of chemical reactions capable of harnessing energy from the environment, using it to carry out programmed anabolic and catabolic functions. We briefly present our opinion on the general validity of this definition.Running anabolic and catabolic functions entails complex chemical information whose stability, reproducibility and evolution constitute the core of what is dubbed genetics.Life as-we-know-it is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, carbon). Other elements like phosphorus and sulphur play important but ancillary and potentially replaceable roles.The reproducible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information that we consider living entities. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, were embedded in physical-chemical conditions favourable for the onset of both.The most abundant three-atoms organic compound in interstellar environment is hydrogen cyanide HCN, the most abundant three-atoms inorganic compound is water H 2 O. The combination of the two results in the formation of formamide H 2 NCOH. We have explored the chemistry of formamide in conditions compatible with the synthesis and the stability of compounds of potential pre-genetic and pre-metabolic interest. We discuss evidence showing (i) that all the compounds necessary for the build-up of nucleic acids are easily obtained abiotically, (ii) that essentially all the steps leading to the spontaneous generation of RNA are abiotically possible, (iii) that the key compounds of extant metabolic cycles are obtained in the same chemical frame, often in the same test tube.How close are these observations to a plausible scenario for the origin of life?

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Allowance for Heterogeneous Stacking in the DNA Helix-Coil Transition Theory

Cited by 106 publications

References 24 publications

Sequence dependence of DNA bending rigidity

Sequence dependence of DNA bending rigidity

Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs

Formamide and the origin of life

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