DNA MELTING Two antiparallel single strands form a DNA duplex according to the following model: SA SB SASH a) You have carried out melting studies at various concentrations for an unknown DNA. Here is the fitted data (1) (ii) (iii) (iv) " y=0.0000271x + 0.00282. Based on the best-fit equation above, find the unknown sequence from the options below given the free energy data at 37°C. Show your work AGGCGATCGG and its complement AGCAATGGCC and its complement GGAGAACTTA and its complement GGCCAAGGCC and its complement AºG - 9.50 kcal/mol 35.97 kJ/mol 30.55 kJ/mol -10.20 kcal/mol - b) Thermodynamically speaking, AS and AH can both drive processes. What happens to these parameters as double stranded DNA is melted? Explain.
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- Biochemist Erwin Chargaff was the first to note that, in DNA, [A] = [T] and [G]= [C], equalities now called Chargaff’s rule. Using this rule, determine the percentages of all the bases in DNA that is 20% thymine.Which conformation of DNA – (i) totally double helix, (ii) minimally unwound or (iii) largely unwound – would have the highest relative absorbance at 260 nm. Would a molecule of DNA having a higher content of guanine and cytosine than of adenine and thymine have a higher or lower melting temperature (Tm) than one with the reverse composition?Agarose gels with different average pore sizes areneeded to separate DNA molecules of different sizeclasses. For example, optimal separation of 1100 bpand 1200 bp fragments would require a gel with alarger average pore size than optimal separation of8500 bp and 8600 bp fragments. How do you thinkthat scientists prepare gels of different average poresizes? (Hint: Agarose gels are made in a mannersimilar to gelatin desserts such as JELL-O.)
- When DNA is heated, it denatures; that is, the strands separate because hydrogen bonds are broken and some base-stacking and hydrophobic interactions are disrupted. The higher the temperature, the larger the number of hydrogen bonds that are broken. After reviewing DNA base pair structure, determine which of the following molecules will denature first as the temperature is raised. Explain your reasoning. a. 5′-GCATTTCGGCGCGTTA-3′ 3′-CGTAAAGCCGCGCAAT-5′ b. 5′-ATTGCGCTTATATGCT-3′ 3′-TAACGCGAATATACGA-5′Compare the melting temperature of a 1-kb segment of DNA containing20% A residues to that of a 1-kb segment containing 30% A residues under the same conditions.DNA solution is viscous because of the nature of chemical substance that can intercalate into the DNA helix. An example of such substance is acridine orange. experiments revealed that acridine orange causes an increase in the viscosity of DNA solution.how would you account for this effect?
- One of the useful rules of thumb that you may have learned in Biochemistry, is that a 50 g/ml solution of DNA has an absorbance of about 1.0 in a 1 cm cell. A. I have a solution of DNA that has a transmittance of 0.15 when it is placed in a cell with a 200 um pathlength. What is the concentration of DNA in this solution? (in units of g/ml) B. Assume that this DNA is a synthetic oligo containing 25 base pairs, and that the MW of a single base pair has a molecular weight of 330. What is the molar concentration of duplex DNA molecules in the solution? C. What is the Molar absorptivity of DNA in units of L cm (mol base pair) -1 -1Ethanol promotes bonding between Na+ ions from the salt and charged phosphate group of the DNA due to a higher dielectric constant than water. True or False?When the helix axis of a closed circular duplex DNA of 2310 bp is constrained to lie in a plane, the DNA has a twist (T) of 207. When released, the DNA takes up its normal twist of 10.5 bp per turn. Indicate the values of the linking number (L), writhing number (W), and twist for both the constrained and unconstrained conformational states of this DNA circle. What is the superhelix density, σ = W/T, of both the constrained and unconstrained DNA circles?
- Spectroscopy is a useful tool to determine the concentration of DNA in a solution by measuring the UV absorbance at a wavelength of 260nm. When analyzing the purity of a DNA sample, an additional measurement of UV absorbance at 280nm is often taken to determine if proteins are is present as well. The ratio of 260/280 is then taken, and the closer this value is to 2 the more pure your DNA sample.a) Given that the aromatic rings present in the nitrogenous bases of DNA cause DNA to absorb UV light at 260nm, predict what might be responsible for proteins absorbing UV light at 280nm.b) You purify two DNA samples and measure the absorbance at 260nm and 280nm. For the first sample (Sample A) the absorbance at 280nm is 0, and for the second sample (Sample B) the absorbance at 260nm is 0.5. You are skeptical that Sample A is really that pure, and upon further testing you identify contaminating protein sequences (shown below) in both samples! Sample A contaminating protein: MSTSILEGAASTLSample B…In Noll’s experiment , explain where DNase I cuts the DNA. Why were the bands on the gel in multiples of 200 bp at lower DNase I concentrations?When a double-stranded DNA molecule is exposed tohigh temperature, the two strands separate, and themolecule loses its helical form. We say the DNA hasbeen denatured. (Denaturation also occurs whenDNA is exposed to acid or alkaline solutions.)a. Regions of the DNA that contain many A–T basepairs are the first to become denatured as the temperature of a DNA solution is raised. Thinkingabout the chemical structure of the DNA molecule, why do you think the A–T-rich regionsdenature first?b. If the temperature is lowered, the original DNAstrands can reanneal, or renature. In addition to thefull double-stranded molecules, some molecules ofthe type shown here are seen when the moleculesare examined under the electron microscope. Howcan you explain these structures?