What is the ideal Tm should strive for with short stretches of DNA with ligase enzyme activity at 37oC (Also elaborate on Tm in expalanation of solution) *Melting temperature (Tm) for short stretches of DNA, can be estimated as 4*(G+C) + 2*(A+T).
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What is the ideal Tm should strive for with short stretches of DNA with ligase enzyme activity at 37oC
(Also elaborate on Tm in expalanation of solution)
*Melting temperature (Tm) for short stretches of DNA, can be estimated as 4*(G+C) + 2*(A+T).
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- The melting temperature Tm of DNA can be predicted by calculation without actually measuring it. Calculate the Tm of the DNA double strand shown in (1) to (3), and discuss the results. The numbers in parentheses indicate the degree of polymerization of nucleotides.(1) A(10) + T(10), (2) A(15) + T(15), (3) G(10) + C(10)Estimate the viscosith of 1.0 vol % agarose gel solution if it took 58 minutes for 1500 base pairs long DNA molecule to migrate 11cm during gel electrophoresis under 110V. Assume appropriate numerical values for the missing parameters such as the charge and diameter of DNA molecules.Calculate these for 1 ug of plasmid DNA in a final total volume of 20 ul. All enzymes being used here are at a concentration of 10 U/µL. For double digests, give the appropriate volume for each enzyme and decide which buffer to use. (HINT: look up double digest conditions on the NEB website.) You should always calculate all volumes in advance to ensure the correct working concentrations and so that you can prepare the digests as efficiently as possible. It is a good idea to check off each component as it is added to the microfuge tube. Complete the table below, including the volume of DNA sample(s) you will need for 1 pg of the DNA (from two different methods in Experiment #3) based on the concentration(s) you determined from the OD260 value, which you will restriction digest with each of the restriction enzymes singly and in double digests in Part A. For example, the volume of DNA sample that contains 1 µg DNA for DNA sample from Part A, Experiment 3: OD260 = 0.024, dilution 500x…
- An extraction Buffer, EB(200 mM Trish-HCL(Ph 8), 250 mM NaCl, 25 mM EDTA, 0.5% SDS) is used for DNA extraction from cells. Use their stock solutions to prepare their respective working concentrations for the given working volume of EB. Stock Solutions are: 1M Tris-HCL(pH~8) 0.5M EDTA 0.8M NaCl 10% SDS Show final calculaed values in the table given below. Component 1L EB 500 ml EB 250ml EB 100ml EB 200mM Tris-Hcl 250mM NaCl 25mM EDTA 0.5% SDS dH2OPlease give me correct solution for both questions c and d.1) The Nde1 enzyme comes at a concentration of 40 U/ul. According to the manufacturer, the container has enough for 10,000 reactions of 2 ug of DNA, assuming that 1 U/ug of DNA is recommended. How many units in total does the packaging contain? At what concentration in U/ml does the enzyme come? If I had to use 10 U for a reaction of 10 ugs of DNA, how would I serve it? 2) A serially diluted phage solution is used to inoculate an E coli plate in the double-layer plate assay. In 24 hours you count 148 plaques. Considering that the original stock was 0.1, and that you used the sixth dilution of the series, what is the PFU for that phage in this strain of E coli? What is the dilution factor for this plate?
- Show the calculations for the preparation of 0.01%, 0.001%, 0.0001%, 0.00001% standard DNA solutions via serial dilution from a 0.1% stock solution. Prepare 10.0 mL of 0.10% standard DNA solution using acetate buffer pH 4.6 as solvent. Prepare four different concentrations of the 0.10% standard DNA solution from step 1 via serial dilution to obtain 0.01%, 0.001%, 0.0001%, 0.00001% standard DNA solutions. Obtain seven clean and dry test tubes. Place 1.50 mL solutions in each tube as follows: Table 2.1. Set-up for the diphenylamine assay. Test tube # Content 1 (blank) acetate buffer pH 4.6 2 0.10% standard DNA 3 0.01% standard DNA 4 0.001% standard DNA 5 0.0001% standard DNA 6 0.00001% standard DNA 7 DNA extract from Part I Add 3.50 mL diphenylamine reagent to each tube, swirl each tube to thoroughly mix the contents and heat for 10 mins in a boiling water bath. Cool immediately under tap water. Read absorbances at 595 nm.…Give detailed Solution with explanation needed (no need Handwritten answerIn a pUC19 digest for 1 ug of pUC19 (DNA conc. 282ng/ul) using 10X Cutsmart buffer, pure water and BamHI enzyme in a total volume of 40 ul, how much of each solution is added to the total volume?
- Assume the energy of hydrogen bonds per base pair to be 5.86 kJ•mol-1. Given two complementary strands of DNA containing 145 base pairs each, calculate the ratio of two separate strands to hydrogen-bonded double helix in solution at 319 K. ratio = .283Mammalian cells growing in culture were labeled with [3H]-thymidineto estimate the rate of DNA synthesis. The thymidine administered had aspecific activity of 3000 cpm/pmol. At intervals, samples of culture weretaken and acidified to precipitate nucleic acids. The rate of incorporation ofisotope into DNA was 1500 cpm/106 cells /min. A portion of culture wastaken to determine the specific activity of the intracellular dTTP pool, whichwas found to be 600 cpm/pmol.(a) What fraction of the intracellular dTTP is synthesized from the exogenous precursor?(b) What is the rate of DNA synthesis, in molecules per minute per cell ofthymine nucleotides incorporated into DNA?(c) How could you determine the specific activity of the dTTP pool?1.8 Calculations for the Purification of a Recombinant Protein The purification of a recombinant protein is carried out starting with 100 liters of a clarified cell lysate (i.e., the cells have been lysed, and the cell debris has been removed to give a clarified solution), which has a total protein concentration of 0.36 mg/ml and a recombinant protein con- centration of 2.2 U/ml, where U denotes units of biological activity of the recombinant protein. It is known that the completely pure recombinant protein has a specific activity of 40.0 U/mg. Purification is continued until a chromatography step that yields 2.0 liters of a fraction containing the protein, with a total protein concentration of 1.11 mg/ml and a recombinant protein concentration of 43.2 U/ml.For the recombinant protein, calculate the starting and ending purity, the starting and ending specific activity, and the percentage yield and fold purification through the chromatography step.