Chemical/biochemical pocket companion designed by the editors of Current Protocols. Type in or copy/paste any nucleic acid base sequence, any protein or peptide amino acid sequence (in one- or three-letter codes accessible from a convenient menu), or any standard chemical formula, and obtain the molecular weight. Allows estimates of the molecular weights of unknown nucleic acid or protein/peptide sequences on the basis of sequence length and average base/amino acid molecular weights. Also includes a list of 1200 of the most commonly encountered organic and inorganic compounds, which may be immediately selected in order to calculate their molecular weights, as well as an easy-to-access list of the chemical elements, which may be plugged into any chemical formula.

Do you (or your students, if you're a teacher) know why the AiDS-causing virus, HIV, is called a retrovirus and how it actually uses the material and machinery of the "host" cell it has invaded to reproduce itself? Do you (or they) have a firm idea what the terms "minus strand, PBS, PPT, and LTR" mean? What does tRNA have to do with retroviruses, anyway?

The simulations of OnScreen Retrovirus use the 3D nucleic acid models of our highly regarded DNA apps to make memorable the crucial steps by which the reverse transcriptase enzyme complex of a retrovirus uses nucleotide building blocks of the host cell to copy the viral genome, initially on a single strand of RNA, to a newly constructed double-stranded DNA molecule, ready to be inserted into the host's DNA as a source of new copies of the virus.

The goal of this app is to convey the conceptual details of the viral genome transfer from RNA to DNA without requiring of the user a deep prior knowledge of molecular biology. Since a ball-and-stick model of nucleic acids is used for the simulations, this is not done at the level of atomic detail, but the simulations are never in conflict with the biochemistry.

Unlike other simulations you might see on the internet, this app shows how the DNA synthesis is at every stage a three-dimensional double-helix-forming process and that it involves several steps, which include the separation of strands and the relative movement of the strands to allow annealing to each other at complementary sections, the steps being dependent on three separate activities of the reverse transcriptase complex: RNA-dependent DNA synthesis, RNA degradation, and DNA-dependent DNA synthesis. The role of the virus's nucleocapsid protein as enhancer of the annealing of strands is also indicated.

Since retrotransposons--which we all have in our DNA!--make use the very same steps to make new copies of their DNA through an intermediate RNA strand before inserting it at another spot in the cell's DNA, the app serves as a simulation of how they work as well.

Background material on viruses, nucleic acids, and enzymes, as well as commentary on each new step in the process of copying the single strand of RNA into a double-stranded DNA molecule are at your fingertips in the app. You can run the simulations with automatic pauses at key steps for convenience in reading of the commentary for the steps or straight through, pausing only when desired.

Updated for the future. National Science Teachers Assoc. (NSTA) Recommends for Grade Level: 6-College (online Feb 2014)

OnScreen DNA Replication shows all of the several steps (indicating the corresponding enzymes responsible for those steps) necessary for one double helix to become two identical to the original. Through the use of engaging 3D animations with a virtual double helix model (not a 2D ladder) it makes clear and memorable how DNA daughter strands are constructed nucleotide by nucleotide in replication.

Students from middle school on up can learn from the app, as no advanced knowledge of chemistry is assumed. The model is exactly the same as the one found in OnScreen DNA Model, a companion app that teaches the structural details of DNA, and in OnScreen Gene transcription, another companion app that shows how protein recipes are copied into messenger RNA. Detailed commentary on what the animations demonstrate in each step is available in a popover view, and a wealth of background material is to be found in a "Useful Stuff" popover.

The sequence of events in DNA replication unfolds in three-dimensional simulations that don't skip over the need for unwinding the DNA after the strands have been separated. The formation of a hybrid DNA-RNA double helix during the first step of primer RNA construction is correctly shown. DNA and RNA nucleotides are seen to move into place and then form hydrogen bonds with their base-pair mates in the template DNA strand. Important details about replication that are often given short shrift or omitted altogether, such as the essential role the enzyme pyrophosphatase plays in the cell, are included.

The concepts of leading and lagging strands and what the Okazaki fragments are and how they are constructed and then joined together through the actions of various replisome enzymes are made clear and memorable through the three-dimensional simulations in the Model View and the representations of enzymes in the Sequence View.

The "end problem" of linear DNA strand replication is not swept under the rug as often happens. Instead, the basic principle of how the enzyme telomerase uses its own RNA to extend the lagging DNA strand by means of reverse transcription is illustrated using simple models with only the RNA and DNA showing.

Set the simulation to pause after each new significant step or pause it only when you want. Commentary on what is happening is literally at your fingertip in a popover. Rotate, translate, or zoom the model during the simulated replication for a better view just by finger slide gestures.

The ball-and-stick model has the advantage of clarity at the expense of atomic detail. The replisome enzyme complex, while not shown in the view with the DNA model, so as not to obscure what is happening with bonds and strands, is depicted in the Sequence View below the model, thus making the point that it moves along the DNA, as it initiates and controls the reactions in replication. Furthermore, the actions of the individual enzymes that make up the replisome are also indicated in the Sequence View.

Built for iOS 11. National Science Teachers Assoc. (NSTA) Recommends for Grade Level: 6-College (online Feb 2014)

OnScreen Gene Transcription shows in a detailed, visual, and memorable way how DNA's genetic code gets copied for use in a living cell.

Through the use of engaging 3D animations with a virtual double helix model, it makes clear and memorable how a recipe for a protein stored in a gene is made available for use by being copied nucleotide by nucleotide in the construction of a messenger RNA molecule. Students from middle school on up can learn from the app, as no advanced knowledge of chemistry is assumed. The model is exactly the same as the one found in OnScreen DNA Model, a companion app that teaches the structural details of DNA. Detailed commentary on what the animations demonstrate is available in a popover view.

The sequence of events in gene transcription unfold in three-dimensional simulations that don't skip over the need for unwinding the DNA after the strands have been separated. The formation of a hybrid DNA-RNA double helix during RNA construction is correctly shown instead of the two-dimensional ladder structure sometimes depicted. Important details about transcription that are often given short shrift or omitted altogether, such as the essential role the enzyme pyrophosphatase plays in the cell, are included.

Set the simulation to pause after each new significant step or pause it only when you want. Commentary on what is happening is literally at your fingertip in a popover. Rotate, translate, or zoom the model during the simulated transcription for a better view just by finger slide gestures. Background material on DNA and RNA are found in the Useful Stuff popover.

The ball-and-stick model has the advantage of clarity at the expense of atomic detail. The RNA Polymerase enzyme complex, while not shown in the view with the DNA model, so as not to obscure what is happening with bonds and strands, is depicted in the Sequence View below the model, thus making the point that it moves along the DNA, as it initiates and controls the reactions in transcription. We know of no other simulation of gene transcription on the internet or anywhere else that shows what happens as thoroughly as OnScreen Gene Transcription does.