Oligo Synthesis. Welcome to the IDT family! The oligonucleotide calculator is a very useful tool to help chemists calculate oligonucleotide molecular weight with or without modifications. DNA, RNA, PROTEIN, CHEMICAL MOLECULAR WEIGHT CALCULATOR - Chang Bioscience, Inc. A n, T n, C n, and G n are the number of each respective nucleotide within the polynucleotide. The MBCF Oligo Calculator can also be found on the MBCF LIMS system on the current oligo ordering page. Input the product's amount in µg and the molecular weight in g/mol. Calculate the molecular weight of a formula. Sequence (5'-->3') Memories Calculation. When comparing oligo synthesis services, the O.D. femtomolar picomolar nanomolar micromolar millimolar molar. Molarity Oligo Catalog # Length Stranded (1) Concentration (µM = pmol/µl) Gel Shift Oligos (2) AP1 Consensus Oligonucleotide E3201/E3202 21mer ds 24.0µg/ml 1.75µM AP2 Consensus Oligonucleotide E3211/E3212 26mer ds 29.8µg/ml 1.75µM CREB Consensus Oligonucleotide E3281/E3282 28mer ds 32 . Use our Peptide Molecular Weight Calculator to check the molecular weight of your peptide. base anion mass sugar add mass. Weight to Molar Quantity (for nucleic acids) This is used to convert the weight (weight concentration) into the molar quantity (molar concentration) for nucleic acids, and vice versa. Any spaces in the sequence will be removed automatically. *When preparing stock solutions always use the batch-specific molecular weight of the product found on the vial label and CoA (available online). This calculator requires the user to input the amount of a template present (in ngs) and the length of the template (in bp) and with this information the number of copies of the . Enter Oligo Sequence in Box. Enter the specifications for your oligo modifications . This online tool calculates chemical formula, molecular weight , extinction coefficient , net charge at neutral pH, isoelectric point , grand average of hydropathicity (GRAVY ). The number of molecules in one mole is equal to 6.0221367 x 1023. Note: The molecular weight of A, U, C, G equals to 329.2, 306.2, 305.2 and 345.2 g/mol respectively. Molecular Weight: daltons (g/M) OD of 1 is equal to nanoMolar (pmol/ml). The average MW of a miRIDIAN hairpin inhibitor is 18,500 g/mol How do I convert between nmol to µg of siRNA? Determines all physical properties of an oligo such as GC content, melting temperature (Tm), molecular weight (MW) and extinction . Gain behind-the-scenes insight into the technologies around SARS-CoV-2 testing. To add a modification code, select the Add Mod button to the left of its description. The corresponding highest occupied molecular orbital (HOMO) energies of these polymers were calculated based on their ferrocene-corrected onset oxidation potentials (E onset; Eferrocene onset = −0.33 V), and then these results and the optical band gaps (E g opt s) were used to calculate the lowest unoccupied molecular orbital (LUMO) energies . Exact Mass Calculator, Single Isotope Version. 16th Apr, 2015. 1 * 10 -9 * 6.02 * 10 23 /7449.63 = 80809382479 (copies). Programs for molecular biologists on zbio.net. Reagents in the lab give a molecular weight (abbreviated as M.W. Your product is now available from Integrated DNA Technologies. Step #2: Enter any chemical formula. Molecular Weight Calculations. Access information specific to your industry's workflow. %GC content. Melting Temperature (Tm) °C. Let's assume that we dilute the primer from above 1:200 and the OD260 reading was 0.132. The length of a synthesized base is usually denoted by ' mer ' (from ' Greek ' meros . If you chose another unit of measurement, the program will recalculate the result. If you don't have the sequence on hand, you can only input the sequence length, the calculation will based on the assumption that each base was 325 dalton. Also calculate molarity of solutions, perform molar conversions, calculate dilutions and perform other calculations common in molecular biology labs. Options average mass monoisotopic mass . This calculator calculates the molecular weight for nucleotic acids (DNA or RNA), protein/peptide, or chemicals. Molecular Weight: 1 ml of a sol'n with an Absorbance of at 260 nm is microMolar 4 and contains micrograms. You can draw the structure or edit directly the molecular . Converting mass (weight concentration) into moles (molar concentration) and vice versa for proteins with known molecular weight. This page was written in Javascript by Eugen Buehler. 1 OD 260 Unit = 40 μg/ml ssRNA. 1 OD 260 Unit = 33 μg/ml ssDNA. ¶ T m calculation for DNA oligo is based on the following equation: T m = 81.5° + 0.41°(%GC) - 675°/length of oligo back Calculate the mass or volume required to prepare a nucleic acid solution of specified molar concentration. 240 County Road Ipswich, MA 01938-2723 978-927-5054 (Toll Free) 1-800-632-5227 Fax: 978-921-1350 [email protected] 4.How to calculate log2 fold change and does it helps to see the . From this, the final "nmol" yield will vary on the length, sequence and molecular weight of the individual oligo. Step #1: Open molecular formula calculator on desktop or mobile. The OligoSpec calculator outputs the physical properties for a particular oligo design. Molecular mass calculator. This page was written in Javascript by Eugen Buehler. Mongo Oligo Mass Calculator v2.06. To determine what the concentration of the solution is in ng/ul, you will need the molecular mass of the Morpholino oligo (usually about 8200 Da for a 25-base Morpholino). Conversion: mass - moles for proteins. To undo any . . Size of the nucl. To calculate molecular weight of a chemical compound enter it's formula, specify its isotope mass number after each element in square brackets. DNA, RNA, Protein,Chemical Molecular Weight Calculator "…For DNA/RNA molecular weight, users have the option to input sequences or sequence length. One mole of which is 7449.63g. Primo Oligo 1.0 --- Oligo/Primer Calculator. Output close button output summary sequence by 3 10 50 extended output show messages sorted output; written by Jef Rozenski (1999) Length. Oligo Calculators. Oligo Calculator tool calculates melting temperature (Tm), molecular weight (MW), Millimolar Extinction Coeff (OD/μmol, µg/OD) for oligos. This calculator is useful for diluting DNA samples. This is a very primitive exact mass calculator. should be compared (the final yield) and not the initial synthesis scale (in "nmol") which is the quantity of the starting material required before synthesis of the oligo. Degenerate codes can be accepted. Isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an critical parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), X-ray crystallography and liquid chromatography-mass spectrometry (LC-MS) Find your result in nmol (or pmol) in the 'Result' field. As an industry-leading peptide vendor, GenScript offers not only high quality peptides ,but also a variety of free peptide tools to Make Your Research Easy. Oligonucleotides are short sequences of nucleotides ( RNA or DNA ), typically with twenty or fewer bases. The BI-MwA permits routine determination of the weight average molecular weight, M w, the z-average radius of gyration, R g, and the second virial coefficient, A 2. Extinction Coefficient Calculation - The extinction coefficient is calculated with the following method: ε260 = [ (Sum of ε260 for all bases*) + (ε260 for all modifications*)] x 0.9, to adjust for hyperchromicity. DNA Molecular Weight (for instance synthesized Oligonucleotides) Anhydrous Molecular Weight = (A n x 313.21) + (T n x 304.2) + (C n x 289.18) + (G n x 329.21) - 61.96 . xGen NGS—made for you. Detect the presence and manage the impact of SARS-CoV-2 variants. Alternatively, you could think of this of the removal of a phosphate and the addition of a hydroxyl, since this formula calculates the molecular weight of 5' and 3' hydroxylated . It is possible to indicate predefined groups, chemical modification of amino acids, specify a given isotope, and modify the isotopic abundance. This calculator is useful for diluting primers and DNA oligos. Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions. It also facilitates the set up of experiments by calculating the adequate amounts and dilutions for your oligo solutions. (1 u is equal to 1/12 the . 3) If you don't know the molecular weight of your substance, please see the table of example averages in either of the calculator tabs. Protein M 5 kDa 10 kDa 20 kDa 50 kDa 100 kDa 200 kDa 500 kDa; R min (minimum radius) 1.1 nm: 1.42 nm: 1.78 nm: 2.4 nm: 3.05 nm: 3.84 nm: 5.21 nm: For more information, see Erickson, Biological Procedure Online . Conversion: mass - moles for nucleic acids (DNA, RNA, oligonucleotides). %GC content. Use DNA Molecular Weight when calculating molecule copy number. x. M. Wt* g/mol. Micrograms = Molecular Weight × Nanomoles × 10-3 Example: 1 OD 260 unit of primer M13 Forward, 5'-GTA AAA CGA CGG CCA GTG-3' Molecular Weight = 5558.7 The approximate molecular weight of melatonin is 232,278 g/mole. The average MW of a miRIDIAN mimic is 14,100 g/mol. You can also learn more detailed characters such as isoelectric . The procedure to use the molecular weight calculator is as follows: Step 1: Enter the chemical compound in the respective input field. Using Avogadro's number, 6.022x10 23 molecules/mole, . Gain behind-the-scenes insight into the technologies around SARS-CoV-2 testing. Molecular Weight: daltons (g/M) OD of 1 is equal to picoMolar. Using the above calculator you could find that e.g. The calculator is available at the URL . This is used to calculate the Gibbs free energy (ΔG) in the formula: ΔG = ΔH - T ΔS. DNA Molecular Weight accepts one or more DNA sequences and calculates molecular weight. The observed masses, except for the -13 charge state, are within the mass accuracy specification. Length. Conversely, you can calculate the molarity of a nucleic acid solution prepared by dissolving a certain amount of it . Enter Oligo Sequence in Box. a pollution of 1 gram of benzene in a certain amount of water converts to NA/78.11≈ 7.7098 × 1021 molecules polluting that water! Need an oligo calculator? Multiply the number of moles by the MW on the Product Transfer Form, or the average MW for your oligo. x. Molecular Weight: daltons (g/M) OD of 1 is equal to nanoMolar (pmol/ml). Programs for molecular biologists on zbio.net. Adam B Shapiro. The nested oligonucleotide primers designed for the 398 . Also provided are methods for isolating and partially purifying the proteins and . With the calculator and its easy use, peptide chemists can have access to a molecular weight peptide calculator and amino acid calculator, the isoelectric point, a peptide net charge calculator at neutral pH, the average hydrophilicity, the percentage of hydrophilic amino acids . Required Tm= Known Tm + 16.6log (required salt concentration / 0.195M), where the Known Tm is calculated from 0.195M using the OligoCalculator. This web application calculates the molecular mass (average, monoisotopic, and nominal), the elemental composition, and the mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence. DNA Molecular Weight. Calculations are based on the isotopic composition of the elements . Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases. The subtraction of 61.96 gm/mole from the oligonucleotide molecular weight takes into account the . The repeatability of the observations is excellent, with an RSD of 0.02% or less except for the -14 charge state, which had an RSD of 0.07%. The default value = 25.0 °C (298K). This is used to calculate the Gibbs free energy (ΔG) in the formula: ΔG = ΔH - T ΔS. The average molecular weight (MW) of a siRNA is 13,300 g/mol. The sodium equivalent is calculated as follows: [Na +] = Monovalent ion concentration + 4 × (Free Mg 2+) 1/2 (all in molarity) The default value = 382.84 mM. Numbers and blank spaces will be ignored. Used to determine how much liquid is needed to resuspend a number of moles to a . The molecular weight of an oligonucleotide is calculated from the number of individual nucleotides in the oligonucleotide and from possible modifications of the oligonucleotide: MWoligo (DNA) = 313,2*A + 329,2*G + 289,2*C + 304,2*T + MWmod - 62 [g/mol] Many of the Swift products you have grown to love are now part of our new complete portfolio, xGen™ NGS. VERY VERY EXTENSIVE. The Oligo Analysis Tool gives you the option of checking your oligos before ordering. acid [kb]: Peptide Property Calculator. Using the BI-MwA to determine average molecular weight. ScienceLauncher - Scientific e-Books, Tools, Calculators and more! The concentration can be calculated using the following formulas: (OD 260) x (0.02*) x (dilution factor) = µg/µl *Conversion factor for single stranded DNA. Molecular Biology Dilution & Solution Calculators. Molecular Mass Calculator. Degenerate codes can be accepted. Copies=N A xMoles. ), which is the amount of grams/mole (g/mol) for that product. Cite. Register Now to: • Analyze DNA and RNA Sequences • Analyze Sequences with Modifications • Screen Secondary Structures • BLAST Search Sequences Note: N A refers to the Avogadro's constant which value is 6.02x10^23. The MBCF Oligo Calculator can also be found on the MBCF LIMS system on the current oligo ordering page. Dilute solution to a desired Molarity. To use this calculator, you must be using Netscape 2.0 or later. Step 3: Finally, the molecular weight of the chemical compound will be displayed in the new window. Entasis therapeutics. The molecular weight of an oligonucleotide is calculated from the number of individual nucleotides in the oligonucleotide and from possible modifications of the oligonucleotide: MW oligo =313,2*A + 329,2*G + 289,2*C + 304,2*T + MWmod -61 * [g/mol] A,G,C,T: Number of bases in the oligo. Oligo Calculator. Molecular Weight Calculations. Also provides the atomic number, element name, base atomic weight and formula weight for the calcutated molecular formula. For DNA/RNA molecular weight, users have the option to input sequences or sequence length. Conversion Factor: Extinction Coefficient: L/(mole.cm) or Single-Stranded DNA, 33ug/OD 260 Double-Stranded DNA, 50ug/OD 260 Single-Stranded RNA, 40ug/OD 260 Molecular Weight: DNA calculations to convert µg to pmol for double-stranded and single-stranded DNA, convert micrograms of DNA to pmol ends, calculate vector:insert molar ratio and convert OD260 readings to µg/ml. In these cases, you can easily calculate the primer concentration from an OD 260 reading. Therefore, provided are methods for treating conditions caused by the deficiency of dopamine and/or by the loss of DA neurons or injury to DA neurons. More SciTools® Web Tools from IDT. The program will chose appropriate unit of measurement. Single-stranded sequences are assumed to have a 5' phosphate. For modified DNA/RNA or for primer/oligo calculations . The inverse of the molecular weight is the number of moles of template present in one gram of material. IDT's free, online OligoAnalyzer tool will analyze an input sequence and provide its molecular weight, as well as GC content, melting temperature, µg/OD, nmole/OD, and extinction coefficient. 2) µg to nmol calculator. Melting Temperature (Tm) °C. The calculator is one of the most useful tool for the peptide chemist to calculate peptide molecular weight and more. How to use Primo Oligo 1.0 Oligo/Primer Calculator (beta-testing) Melting temperature and molecular weight calculations; Input your primer sequences by copy and paste. Click the 'Clear' button to clear all values. you can calculate the Tm of your favourite oligonucleotide amplification primers eg in the Promega PCR buffer (which contains 0.05M monovalent . NGS Target Enrichment; The number of base pairs should be multiplied by the average molecular mass of one base pair (660 g/mol) to get the approximate mass of . You can use DNA Calculator to: Calculate basic physical and chemical parameters of a nucleic acid molecule. Peptides for SARS-CoV-2 Research! Volume. 1 °C (Basic) 2 °C (Salt . The sodium equivalent is calculated as follows: [Na +] = Monovalent ion concentration + 4 × (Free Mg 2+) 1/2 (all in molarity) The default value = 382.84 mM. . It also provides a conversion between single and triple letter amino acid code; peptide titration plot, net charge vs pH. nanoliter microliter milliliter liter. . The molecular weight of an oligonucleotide is calculated from the number of individual nucleotides in the oligonucleotide and from possible modifications of the oligonucleotide: MWoligo (DNA) = 313,2*A + 329,2*G + 289,2*C + 304,2*T + MWmod - 62 [g/mol] Click on the "Calculate" button to start. Length. Input the molecular formula and the weight is calculated. With the Oligo calculator and its easy use, chemists can have access to an oligonucleotide properties calculator, which will provide in one click the mass of the desired oligonucleotide. (Click the Fish.) To use this calculator, you must be using Netscape 2.0 or later. Precise Synthetic Oligo Pools; SARS-CoV-2 RT-qPCR Primers & Probes New! OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. The subtraction of 61.96 gm/mole from the oligonucleotide molecular weight takes into account the . Blanks and numbers will be automatically ignored. Blanks and numbers will be automatically ignored. Temperature for Free Energy Calculation. Molecular Weight: daltons (g/M) OD of 1 is equal to picoMolar. Oligo Calculator. Concentration. you can calculate the Tm of your favourite oligonucleotide amplification primers eg in the Promega PCR buffer (which contains 0.05M monovalent . Sequences can be treated as double-stranded or single-stranded, and as linear or circular. Conversion Factor: Extinction Coefficient: L/(mole.cm) or Single-Stranded DNA, 33ug/OD 260 Double-Stranded DNA, 50ug/OD 260 Single-Stranded RNA, 40ug/OD 260 Molecular Weight: Some Morpholino sequences can be difficult to dissolve completely, so be sure you have the oligo completely in solution. Using the following equation, it is quite simple to calculate the amount in microgram from the nanomole value and the Molecular weight of the oligonucleotide. Heating and vortexing can help if an oligo is slow to . DNA Molecular Weight (for instance synthesized Oligonucleotides) Anhydrous Molecular Weight = (A n x 313.21) + (T n x 304.2) + (C n x 289.18) + (G n x 329.21) - 61.96. Dilute solution to a desired concentration (mass/vol). Promega Oligonucleotide Molecular Weight and Molarity. The additional 159 refers to the existence of a 5'triphosphate residue. Immediately our atomic mass calculator will calculate the Number of atom, Molar mass (g/mol), Subtotal mass (%) and Subtotal mass (g/mol) along with the total molecular weight. 分子量计算的例子： C[14]O[16]2 , S[34]O[16]2 . Redirecting to https://www.atdbio.com/tools/oligo-calculator (308) Pivot as your targets change with scalable chemistries and automated workflows. MW ssRNA = N A xMW A +N U xMW U +N C xMW C +N G xMW G +159. The most useful formula you will be using is: M1 V 1 = M 2 V 2, Starting . Step #3: Press "GO" button. Molecular weight of double stranded DNA sequence "TTAACCGGTTAA" is 7449.63 (Dalton). This tool allows calculating the theoretical isotopic distribution and monoisotopic mass from a Molecular Formula. Step 2: Now click the button "Calculate Molecular Weight" to get the weight. (Click the Fish.) Molecular Weight to Size Calculator How big is a protein molecule? %GC content. OligoCalc. The program will chose appropriate unit of measurement. OligoCalc will use the currently entered sequence, selected options and entered conditions to calculate the length, molecular weight, estimated absorbance at 260 nm, the micromolar concentration and micrograms of oligonucleotide present in a 1 ml solution with an absorbance of one for the sequence entered. DNA Calculator. . ss oligo concentration (ug/ml) = OD 260 x MW x 1000 / ε 260. where MW = molecular weight of oligo (non-phosphorylated) and ε 260 = extinction coefficient of oligo at 260nm. Degenerate nucleotide codes can be accepted. The present invention provides a novel proteinaceous composition that increases the levels of dopamine (DA) in neurons. Detect the presence and manage the impact of SARS-CoV-2 variants. The default value = 25.0 °C (298K). In contrast, "Molarity" measures the concentration of mole units in solution. molecular weight of each oligonucleotide was used to calculate the expected mass of each charge state. If you chose another unit of measurement, the program will recalculate the result. Molecular mass (molecular weight) is the mass of one molecule of a substance and is expressed in the unified atomic mass units (u). Readily prepare Zimm, Berry, or Debye plots to calculate these parameters with the optional BI-ZPMwA software. Access information specific to your industry's workflow. qPCR Oligos New! The isotope selected has the property that each atom in the species is the most abundant . Enter Oligo Sequence in Box. dsDNA ssDNA RNA olig. Pivot as your targets change with scalable chemistries and automated workflows. An example includes Parkinson's disease. Melting Temperature (Tm) °C. A path length of 1 cm is assumed for the absorbance. Enter a sequence in the text box and click 'Calculate properties' to calculate the oligonucleotide's properties. The subtraction of 61.96 gm/mole from the oligonucleotide molecular weight takes into account the removal of HPO 2 (63.98) and the addition of two hydrogens (2.02). MW mod: Molecular weight of a modification, if present Temperature for Free Energy Calculation. Molecular Weight: daltons (g/M) OD of 1 is equal to nanoMolar. Converting mass (weight concentration) into moles (molar concentration) and vice versa. Try our oligo calculator to determine volumes needed to resuspend your DNA oligos to desired concentrations, estimate the percentage of full-length product for different oligo lengths, and calculate final yield based on oligo length, synthesis scale, and purification method. adding an adjustment for salt gives the equation that the Oligo Calculator uses: No adjustment constant for salt concentration is needed, since the various parameters were determined at 1 Molar NaCl, and the . A n, T n, C n, and G n are the number of each respective nucleotide within the polynucleotide. The code will automatically be placed onto the appropriate position of the sequence, but you also can move and rearrange any internal modification codes you select. ε260 of bases = dA (ε260=15,200), dC . Given the formula of a chemical species, the calculator determines the exact mass of a single isotope of that species and the relative abundance of that isotope. Vs pH path length of 1 gram of benzene in a certain amount grams/mole! 16 ] 2 //iprdb.com/patent-2527-US2005148500A1.html '' > Oligo Calculator can also be found on the product Transfer Form or... Readily prepare Zimm, Berry, or the average MW of a modification code select... ( g/mol ) for that product to start the set up of experiments by calculating the isotopic. The OD260 reading was 0.132 except for the -13 charge state, within... Is 14,100 g/mol Probes new, Single isotope Version 61.96 gm/mole from the Oligonucleotide molecular weight of,... Moles to a sequences of nucleotides ( RNA or DNA ), dC nmol ( or ). 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