Dna molecular weight for instance synthesized oligonucleotides anhydrous molecular weight a n x 3. The user can also select options such as single or doublestranded dna and rna molecules ssdna is the default, and the user can select from more than seventy 5. Molecular weight for molecular formula can be calculated with ease. Supply of nucleasefree, dnafree oligos by synthesizing in a clean room and eliminating of truncated failures including n1 mer with our proprietary biorp highpurity purification system. The most frequently used tools list here including rare codon analysis tool, codon frequency table, primer design, restriction enzyme map analysis, sirna design, peptide formula and molecular weight calculater, peptide screening, antigen prediction, psort ii. Other sites referencing the molecular weight calculator program are. If the chemical formula is first calculated, various properties can then be derived from it. Molecular weight calculator free download and software.
Oligocalc provides a convenient web interface for calculating the physical properties of dna and rna oligonucleotides including melting temperature, molecular weight, %gc content and absorbance coefficient for a given oligonucleotide sequence. To calculate the molecular weight of an oligonucleotide, the molecular weights of the individual nucleotides present in the oligo must first be summed. Oligocalc, an online oligonucleotide properties calculator. Oligocalc an online oligonucleotide properties calculator. Pdf determination of oligonucleotide molecular masses by.
However, trying to perform it with swissdock or molegro failed because. Dna and rna molecular weights and conversions thermo fisher. Oligo calculator tool calculates melting temperature tm, molecular weight mw, millimolar extinction coeff od. Molecular weight calculator this program can calculate the molecular weight and percent composition of chemical formulas and amino acids, providing a graphical user interface to edit the formulas and parsing options. Pcr primers design oligocalc is a webaccessible, clientbased computational engine for reporting dna and rna singlestranded and doublestranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, intermolecular self. Dna and rna molecular weights and conversions macromolecular components of e.
Oligocalc is a webaccessible, clientbased computational engine for reporting dna and rna singlestranded and doublestranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, intermolecular selfcomplementarity estimation and intramolecular hairpin loop formation. Filter using one or more categories to focus on specific topics, or use the search bar to perform a text search. In the following boxes, always fill all but one field and click calculate. The oligocalc dna mw calculations assume that there is not a 5 monophosphate anhydrous molecular weight a n x 3. Fdaapproved oligonucleotide therapies price inquiry oligonucleotides oligos have been under clinical development for approximately the past 30 years, beginning with antisense oligonucleotides asos and aptamers and followed about 15 years ago by sirnas. Calculation of molecular weight for synthetic oligonucleotides. For dnarna molecular weight, users have the option to input sequences or sequence length. The molecular weight of an oligonucleotide is calculated from the number of individual nucleotides in the oligonucleotide and from possible modifications of the oligonucleotide. This qc data is available online for oligonucleotides that were ordered on the website once they have shipped. Oligocalc has a familiar x91calculatorx92 look and feel, making it readily understandable and usable. Extensive calculations for molecular mass versus subunit composition have been made for oligonucleotides from rna and dna to determine the extent to which base compositions might be derived from mass spectrometrically determined molecular weights.
Atdbio ltd building 30 school of chemistry university of southampton united kingdom so17 1bj registered in england, no. Compute pimw is a tool which allows the computation of the theoretical pi isoelectric point and mw molecular weight for a list of uniprot knowledgebase swissprot or trembl entries or for user entered sequences. Understanding mass spectrometry of oligonucleotides. This calculator calculates the molecular weight for nucleotic acids dna or rna, proteinpeptide, or chemicals. If you are running linux or windows on an x86 processor, you should probably download the binary distributions rpm for linux, exe for windows. Once the biochemistry and molecular biology behind some of the pharmacology was worked out, new approaches became apparent for using oligonucleotides to treat disease. Our scientific applications support team has assembled a list of frequently asked questions to help you find answers quickly.
Further, the anhydrous molecular weight of both unmodified and modified oligonucleotides can be calculated using oligoanalyzer tool. The accurate molecular weight mw measurements of such molecules, which contain acidlabile moieties, may be easily determined by mass spectrometry using a matrix system, triethanolamine teoanacl, on liquid. Dna rna protein chemical molecular weight calculator. The molecular weight of an oligonucleotide is calculated based on the following formula. Calculating oligonucleotide quantity oligo quantitation. Dnarna proteinchemical molecular weight calculator. Mar 21, 2017 far from existing as a discrete molecule, df is a polydisperse mixture of singlestranded 90% and doublestranded 10% po oligonucleotides approximate length 980mer. How do i calculate the molecular weight of an oligo. Dna molecular weight typically for synthesized dna oligonucleotides. Other options available for the calculation of concentration, dilution, and reaction are unique and interesting. Genscript provides a comprehensive range of online bioinformatics tools for molecular biology, peptide, and protein researchers. Rtprimerdb is a public database for primer and probe sequences used in realtime pcr assays employing popular chemistries sybr green i, taqman, hybridisation probes, molecular beacon to prevent timeconsuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different. Then the weight must be corrected by subtracting 62.
Use monoisotopic masses not isotopic averages methionine to selenomethionine cysteine to selenocysteine. If you are running linux or windows on an x86 processor, you should probably download the binary distributions. The biochemistry of small nucleic acids is outlined in section 2. Nucleoside phosphoramidites pas are the most widely used building blocks in contemporary solidphase synthesis of oligonucleotides. Molecular weight molecular weight scan mass spectrometry result. Oligonucleotide properties calculator biosynthesis, inc. Download32 is source for chemical formula calculator shareware, freeware download chemical reagent calculator, magicplot calculator, formulacalc for pocket pc, formulacalc for p800p900, formulacalc for palm os, etc. Percent difference maximum difference daltons min max. Lurie comprehensive cancer center, the feinberg school of medicine, northwestern university, chicago, il 60611, usa we developed oligocalc as a webaccessible, clientbased computational engine for reporting dna and rna singlestranded and doublestranded properties, including molecular weight. Supply of nucleasefree, dnafree oligos by synthesizing in a clean room and eliminating of truncated failures including n1 mer with our. Oligo calculators try our oligo calculator to determine volumes needed to resuspend your dna oligos to desired concentrations, estimate the percentage of fulllength product for different oligo lengths, and calculate final yield based on oligo length, synthesis scale, and purification method. Fdaapproved oligonucleotide therapies boc sciences.
Oligo calculator calculate oligonucleotide properties. Lurie comprehensive cancer center, the feinberg school of medicine, northwestern university, chicago, il 60611, usa we developed oligocalc as a webaccessible, clientbased computational engine for reporting dna and rna singlestranded and doublestranded properties, including molecular weight, solution. Ms data available for idt orders idt offers esi ms qc free of charge on all standard oligonucleotides. The latest version of the molecular weight calculator for windows is version 6. Software for molecular docking with oligonucleotides. Molecular weight calculator free download windows version. A total of 7 malditof spectrometers used for performing full qc inspection. Oligocalc is a webaccessible, clientbased computational engine for reporting dna and rna singlestranded and doublestranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter molecular selfcomplementarity estimation and intra molecular hairpin loop formation. There is excellent agreement between the manually calculated value of 29.
Jul 01, 2007 the user can also select options such as single or doublestranded dna and rna molecules ssdna is the default, and the user can select from more than seventy 5. Promega oligonucleotide molecular weight and molarity promega oligonucleotide molecular weight and molarity. From the standpoint of correlation of nucleotide composition with mass spectrometrically determined molecular weight, accuracy of 0. Dna and rna oligonucleotides are usually synthesized through phosphoramidite pa chemistry on polymeric support by sequential addition of nucleoside building blocks to a growing oligonucleotide chain which is covalently attached to the solid support. Oligoarrayaux is a subset of the unafold package for use with oligoarray. A n, t n, c n, and g n are the number of each respective nucleotide within the polynucleotide. As a comparison, here is the value as determined by oligoevaluator, our online oligonucleotide sequence calculator. Compute pimw is a tool which allows the computation of the theoretical pi isoelectric point and mw molecular weight for a list of uniprot knowledgebase swiss. The simplest way of calculating the chemical formula is to add the unit formulae of each base, listed in table 1, then substract p o 3 h because there is no phosphate linkage at the 3. Oligocalc is a webaccessible, clientbased computational engine for reporting dna and rna singlestranded and doublestranded properties, including molecular weight, solution concentration, melting temperature, intra molecular hairpin loop formation, etc. The molecular weight of each oligonucleotide is presented on that oligos specification sheet. The elements are searched in order of probable occurence, beginning the c, h, o then n.
I am trying to do molecular docking studies for metal complexes using crystal structure of oligonucleotide from pdb 2o1i. Far from existing as a discrete molecule, df is a polydisperse mixture of singlestranded 90% and doublestranded 10% po oligonucleotides approximate length 980mer. The molecular weight, typically for synthesized dna oligonucleotides, uses the following formula. Accurate molecular weight measurements of nucleoside. For example, 4hhb contains two chains a, two chains b, two po4 ligands, and four hem ligands for a molecular weight of 215150. Promega oligonucleotide molecular weight and molarity. Dna and rna molecular weights and conversions thermo. Determination of oligonucleotide composition from mass. List of dna and rna molecular weights and conversions including nucleotide molecular weight and rna molecular weight.
776 617 1228 409 833 1030 779 1227 269 1446 880 505 1278 1361 896 1297 570 341 1405 181 157 1027 729 1258 1426 1154 878 334 727 986 340 572 870 640 936 27 913 1211 796 218 611 891 1347 1226 1005 1187 44