The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.

/pdf/mfold-web-server-for-nucleic-acid-folding-and-hybridization-3pzoe1h05m.pdf

Mfold web server for nucleic acid folding and hybridization prediction

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

/pdf/the-amber-biomolecular-simulation-programs-e2nyq1ef44.pdf

The Amber biomolecular simulation programs

Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

https://faircloth-lab.org/assets/pdf/untergasser-et-al-2012-nucleic-acids-research.pdf

Primer3—new capabilities and interfaces

http://bio.gsnu.ac.kr/research/miRNA/RNAss/Mfold/miRNAss_JMB_1999_Mathews.pdf

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

Background
Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.

/pdf/viennarna-package-2-0-4q9zpqix5v.pdf

ViennaRNA Package 2.0

DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.

The thermodynamics of DNA structural motifs

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 ΔG°37 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 ΔG°37, ΔH°, ΔS°, 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...

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs

Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson−Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 °C is GC > CG > GG > GA ≈ GT ≈ CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict ΔG°37, ΔH°, ΔS°, and TM within 4%, 7%, 8%, and 2 °C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaCl.

Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability†

Thermodynamics of 39 oligonucleotides with internal G·T mismatches dissolved in 1 M NaCl were determined from UV absorbance versus temperature profiles. These data were combined with literature values of six sequences to derive parameters for 10 linearly independent trimer and tetramer sequences with G·T mismatches and Watson−Crick base pairs. The G·T mismatch parameters predict ΔG°37, ΔH°, ΔS°, and TM with average deviations of 5.1%, 7.5%, 8.0%, and 1.4 °C, respectively. These predictions are within the limits of what can be expected for a nearest-neighbor model. The data show that the contribution of a single G·T mismatch to helix stability is context dependent and ranges from +1.05 kcal/mol for AGA/TTT to −1.05 kcal/mol for CGC/GTG. Several tests of the applicability of the nearest-neighbor model to G·T mismatches are described. Analysis of imino proton chemical shifts show that structural perturbations from the G·T mismatches are highly localized. One-dimensional NOE difference spectra demonstrate tha...

/pdf/thermodynamics-and-nmr-of-internal-g-t-mismatches-in-dna-2kjika9tl9.pdf

Thermodynamics and NMR of Internal G·T Mismatches in DNA

Thermodynamic measurements are reported for 51 DNA duplexes with A·A, C·C, G·G, and T·T single mismatches in all possible Watson−Crick contexts. These measurements were used to test the applicability of the nearest-neighbor model and to calculate the 16 unique nearest-neighbor parameters for the 4 single like with like base mismatches next to a Watson−Crick pair. The observed trend in stabilities of mismatches at 37 °C is G·G > T·T ≈ A·A > C·C. The observed stability trend for the closing Watson−Crick pair on the 5‘ side of the mismatch is G·C ≥ C·G ≥ A·T ≥ T·A. The mismatch contribution to duplex stability ranges from −2.22 kcal/mol for GGC·GGC to +2.66 kcal/mol for ACT·ACT. The mismatch nearest-neighbor parameters predict the measured thermodynamics with average deviations of ΔG°37 = 3.3%, ΔH° = 7.4%, ΔS° = 8.1%, and TM = 1.1 °C. The imino proton region of 1-D NMR spectra shows that G·G and T·T mismatches form hydrogen-bonded structures that vary depending on the Watson−Crick context. The data reported ...

/pdf/nearest-neighbor-thermodynamics-and-nmr-of-dna-sequences-4uxkkvoj3j.pdf

John SantaLucia

Papers

The thermodynamics of DNA structural motifs

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs

Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability†

Thermodynamics and NMR of Internal G·T Mismatches in DNA

Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A·A, C·C, G·G, and T·T Mismatches†