The Thermodynamics of DNA Structural Motifs

SantaLucia, John; Hicks, Donald A.

doi:10.1146/annurev.biophys.32.110601.141800

Cited by 1,160 publications

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References 97 publications

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“…It is previously described that terminal mismatches are more stable than internal mismatches 23 . As could be observed from our data, the intensities of oligos 10 and 12 indeed systematically deviated from the expected thermodynamical behaviour.…”

Section: Data Presented Inmentioning

confidence: 98%

“…These experiments have validated a simple model known as the nearest-neighbor (NN) model, where the ∆G is calculated as the sum of ∆G values for each couple of two neighboring bases in a sequence 21 . The free energy for mismatching bases in DNA sequences has been investigated too, and ∆G values are described that can be used to calculate the overall ∆G of a mismatch-containing DNA sequence [22][23] .…”

Section: Introductionmentioning

confidence: 99%

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Thermodynamic Behavior of Short Oligonucleotides in Microarray Hybridizations Can Be Described Using Gibbs Free Energy in a Nearest-Neighbor Model

et al. 2007

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While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb concerning oligo length, overall similarity, and continuous stretches, the final behavior is difficult to predict. The aim of this study was to investigate the effect of well-defined mismatches on hybridization specificity using CodeLink Activated Slides, and to study quantitatively the relation between hybridization intensity and Gibbs free energy (∆G), taking the mismatches into account. Our data clearly showed a correlation between the hybridization intensity and ∆G of the oligos over three orders of magnitude for the hybridization intensity, which could be described by the Langmuir model. As ∆G was calculated according to the nearest-neighbor model, using values related to DNA hybridizations in solution, this study clearly shows that target-probe hybridizations on microarrays with a three-dimensional coating are in quantitative agreement with the corresponding reaction in solution. These results can be interesting for some practical applications. The correlation between intensity and ∆G can be used in quality control of microarray hybridizations by designing probes and corresponding RNA spikes with a range of ∆G values. Furthermore, this correlation might be of use to fine-tune oligonucleotide design algorithms in a way to improve the prediction of the influence of mismatching targets on microarray hybridizations. KEYWORDSMicroarray oligonucleotide design, nearest-neighbor model, Langmuir model, microarray quality control 3

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Section: Data Presented Inmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Thermodynamic Behavior of Short Oligonucleotides in Microarray Hybridizations Can Be Described Using Gibbs Free Energy in a Nearest-Neighbor Model

et al. 2007

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“…Similarly, the structures of pseudoknots (10) are stabilized by a complicated interplay between single-stranded and double-stranded motifs. A multitude of literature on the stabilizing interactions of native single-stranded oligonucleotides is available (9,(11)(12)(13)(14).Accurate prediction of nucleic acid secondary structure and stability from its primary sequence is a key interest for probe binding optimization in biotechnological applications such as microarrays (15) and molecular beacons (16). To develop an accurate algorithm (14,(17)(18)(19)(20)(21)(22)(23)(24) for predicting the thermodynamics of hybridization and folding of long nucleic acid sequences, the free energy contributions from all natural Watson-Crick basepairs including the nearestneighbor effects as well as all possible alternative basepairing modes, mismatches, and higher ordered structural motifs such as bulges, loops, and dangling ends must be known.…”

mentioning

confidence: 99%

“…To develop an accurate algorithm (14,(17)(18)(19)(20)(21)(22)(23)(24) for predicting the thermodynamics of hybridization and folding of long nucleic acid sequences, the free energy contributions from all natural Watson-Crick basepairs including the nearestneighbor effects as well as all possible alternative basepairing modes, mismatches, and higher ordered structural motifs such as bulges, loops, and dangling ends must be known.…”

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confidence: 99%

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A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

Isaksson

Chattopadhyaya

2005

Biochemistry

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The geometry of the dangling base in 105 published structures (from X-ray/NMR) containing single-stranded overhangs has been analyzed and correlated to the thermodynamic stabilization found (UV) for the corresponding dangling base/closing basepair combination in short oligonucleotides. The study considers most combinations of closing basepairs, sequence and dangling base residue type, attached in both the 3′-and 5′-ends of both DNA and RNA. Linear regression analysis showed a straightforward correlation (R ) 0.873) between the degree of screening for the hydrogen bonds of the closing basepair provided by the dangling base and the resulting thermodynamic stabilization in both DNA and RNA series with dangling ends either at the 3′-or at the 5′-terminus. Regression analysis of only the datasets from RNA gives an improved correlation, R ) 0.934, showing that dangling ends on RNA are more ordered than the dangling ends on DNA, R ) 0.376. This study highlights the gain in the free energy of stabilization owing to the favorable stacking between the dangling nucleobase and the neighboring basepair and the resulting strengthening of the hydrogen bond of the closing basepair. By acting as a hydrophobic cap on the terminal of the DNA or RNA duplex, the dangling-end residue restricts the bulk water access to the terminal basepair, thereby providing it with a microenvironment devoid of water, which consequently enhances its thermodynamic stability, making it energetically comparable to the corresponding internal basepair. Thus, one single structural model consisting of the interplay of the above electrostatic interactions can be used to explain the molecular basis of the observed thermodynamic effects for dangling-end attachment to the 3′-and 5′-ends of both DNA and RNA duplexes, which is a key step toward accurate dangling-end effect prediction.Unpaired terminal nucleotides naturally occur in various biologically important RNA structures: The acceptor stem in tRNA (1-3) has a characteristic 3′-NCCA nucleobase overhang that determines its structure, stability, and function. The dangling ends neighboring the codon-anticodon pair have also been found to stabilize the interaction between tRNA and mRNA (4, 5) for protein synthesis in the ribosomal machinery. The efficiency of down regulation of gene expression by RNA interference (RNAi) has been shown to be dependent on a two to three nucleotide overhang (6-9). Similarly, the structures of pseudoknots (10) are stabilized by a complicated interplay between single-stranded and double-stranded motifs. A multitude of literature on the stabilizing interactions of native single-stranded oligonucleotides is available (9,(11)(12)(13)(14).Accurate prediction of nucleic acid secondary structure and stability from its primary sequence is a key interest for probe binding optimization in biotechnological applications such as microarrays (15) and molecular beacons (16). To develop an accurate algorithm (14,(17)(18)(19)(20)(21)(22)(23)(24) for predicting the thermodynamics of hybridi...

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Mathematical Models on RNA Evolution, Simulations In Silico , and Concepts for In Vitro Selection

Schuster

2006

The Aptamer Handbook

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Sol Spiegelman and his group carried out the first successful evolution experiments in vitro in the 1960s (for a review see, for example, Spiegelman, 1971). These experiments were based on replication of single-strand RNA through catalysis by a bacteriophage-specific enzyme, mostly Qb replicase. A sample of RNA molecules carrying the recognition site for the replicase is introduced into a buffer solution that contains the four nucleotide triphosphates (ATP, CTP, GTP, and UTP) as well as the replicase. Consumed materials are replenished through transfer of small samples into fresh stock solution. After a sufficient number of repeated transfers RNA molecules are isolated that are adapted to the stock solution, in the sense that they replicate most efficiently. Although the molecular details of the replication process and the nature of the optimization process were largely unknown in the early days, the interpretation of the serial transfer experiments as Darwinian evolution in the test was essentially correct. The Qb RNA evolution experiments were repeated and put on a firm molecular basis later on, and finally, they were applied to the design of RNA molecules with predefined properties (for a collection of reviews see Watts and Schwarz, 1997).The mechanism of RNA replication by virus-specific enzymes like Qb replicase consists of two multistep RNA polymerization cycles, each synthesizing the complementary strand of an RNA template molecule, plus-I or minus-I, respectively (Biebricher and Eigen, 1988): plus-I + activated monomers p minus-I + plus-I minus-I + activated monomers p plus-I + minus-I

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The Thermodynamics of DNA Structural Motifs

Cited by 1,160 publications

References 97 publications

Thermodynamic Behavior of Short Oligonucleotides in Microarray Hybridizations Can Be Described Using Gibbs Free Energy in a Nearest-Neighbor Model

Thermodynamic Behavior of Short Oligonucleotides in Microarray Hybridizations Can Be Described Using Gibbs Free Energy in a Nearest-Neighbor Model

A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

Mathematical Models on RNA Evolution, Simulations In Silico , and Concepts for In Vitro Selection

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