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’.

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Mfold web server for nucleic acid folding and hybridization prediction

Through the study of transcriptional activation in response to interferon alpha (IFN-alpha) and interferon gamma (IFN-gamma), a previously unrecognized direct signal transduction pathway to the nucleus has been uncovered: IFN-receptor interaction at the cell surface leads to the activation of kinases of the Jak family that then phosphorylate substrate proteins called STATs (signal transducers and activators of transcription). The phosphorylated STAT proteins move to the nucleus, bind specific DNA elements, and direct transcription. Recognition of the molecules involved in the IFN-alpha and IFN-gamma pathway has led to discoveries that a number of STAT family members exist and that other polypeptide ligands also use the Jak-STAT molecules in signal transduction.

https://science.sciencemag.org/content/sci/264/5164/1415.full.pdf

Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins

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

The cloning of genes encoding mammalian DNA binding transcription factors for RNA polymerase II has provided the opportunity to analyze the structure and function of these proteins. This review summarizes recent studies that define structural domains for DNA binding and transcriptional activation functions in sequence-specific transcription factors. The mechanisms by which these factors may activate transcriptional initiation and by which they may be regulated to achieve differential gene expression are also discussed.

https://science.sciencemag.org/content/sci/245/4916/371.full.pdf

Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins

A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented DNA NN DG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used dif- ferent methods of data analysis; used different salt concen- trations; and presented the NN thermodynamics in different formats As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA poly- mers and oligomers Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies re- main Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics Empirical salt dependencies are also derived for oligonucleotides and polymers

/pdf/a-unified-view-of-polymer-dumbbell-and-oligonucleotide-dna-1r0s8psdu0.pdf

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

We describe the use of gel electrophoresis in studies of equilibrium binding, site distribution, and kinetics of protein-DNA interactions. The method, which we call protein distribution analysis, is simple, sensitive and yields thermodynamically rigorous results. It is particularly well suited to studies of simultaneous binding of several proteins to a single nucleic acid. In studies of the lac repressor-operator interaction, we found that binding to the so-called third operator site (03) is 15-18 fold weaker than operator binding, and that the binding reactions with the first and third operators are uncoupled, implying that there is no communication between the sites. Pseudo-first order dissociation kinetics of the repressor-203 bp operator complex were found to be temperature sensitive, with delta E of 80 kcal mol-1 above 29 degrees C and 26 kcal mol-1 below. The half life of the complex (5 min at 21 degrees C) is shorter than that reported for very high molecular weight operator-containing DNAs, but longer than values reported for much shorter fragments. The binding of lac repressor core to DNA could not be detected by this technique: the maximum binding constant consistent with this finding is 10(5) M-1.

Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis

A SIMPLE method for estimating the most stable secondary structure of an RNA molecule from its sequence was proposed earlier1. This method can be used for predicting and assessing possible secondary structures for recently determined RNA sequences2–4. New experimental5–8 and theoretical9, 10 results allow us to improve the method, without making it more complicated.

Improved Estimation of Secondary Structure in Ribonucleic Acids

The bending locus of trypanosome kinetoplast DNA, identified by gel electrophoresis, has tracts of a simple repeat sequence (CA5–6 T) symmetrically distributed about it, with a repeat interval of 10 base pairs The analogous bending induced when catabolite gene activating protein binds to its recognition sequence near the promoter of the Escherichia coli lac operon is centred on a site about 5–7 base pairs away from the centre of the protein binding site

The locus of sequence-directed and protein-induced DNA bending

Intrinsic bending of DNA molecules results from local structural polymorphism in regions of homopolymeric dA · dT which are at least 4 base pairs long; the A · T tracts must be repeated in phase with the helix screw. Bending, in the direction of base-pair tilt rather than roll, occurs at the junctions between the A · T tract and adjacent B-DNA, with a larger angle at the 3′ than at the 5′ end of the A tract.

DNA bending at adenine . thymine tracts.

Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text is for those with only a basic understanding of physical chemistry and molecular biology.

Donald M. Crothers

Papers

Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis

Improved Estimation of Secondary Structure in Ribonucleic Acids

The locus of sequence-directed and protein-induced DNA bending

DNA bending at adenine . thymine tracts.

Nucleic Acids: Structures, Properties, and Functions