Read e-book online DNA Structures Part A: Synthesis and Physical Analysis of PDF

By John N. Abelson, Melvin I. Simon, David M.J. Lilley, James E. Dahlberg

ISBN-10: 0121821129

ISBN-13: 9780121821128

To appreciate the constructions and dynamics of DNA and its interactions with ligands, a whole research of its confirmational flexibility is needed. This quantity and its spouse, quantity 212 of Methods in Enzymology, collate in a single resource all of the tools and methods had to accomplish that aim

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Extra info for DNA Structures Part A: Synthesis and Physical Analysis of DNA

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Treatment with Lawesson's reagent converts the 4-keto oxygen to sulfur. ~5-~s The sulfur atom in d4SU is susceptible to displacement by nucleophiles in an identical manner to the benzenesulfonyl group in dG derivatives. Thus d4nU can be prepared from d4SU by nudeophilic displacement of the sulfur with hydrazine followed by Ag20 oxidation in an analogous fashion to the conversion of benzenesulfonyl-dG derivatives to dZ~mP. 15'16'1s'19 We have, however, found it more convenient to introduce the 5'-dimethoxytrityl group onto d4SU prior to the hydrazine and A g 2 0 steps.

The phosphate (phosphodiester) groups of the DNA backbone are acidic and exist as salts at physiological pH. As the number of acid groups is proportional to the length of the oligonucleotide chain, DNA strands of different lengths can be readily separated by anion-exchange HPLC. 5 to 12 for short periods of time. However, nucleic acids are biological substances and are prone to enzymatic degradation. For this reason, care should be taken to use sterile water throughout HPLC procedures and subsequent purification.

D. Matteucci, Z. Stabinsky, and J. Y. Tang, this series, Vol. 154, p. 287. 7 T. Brown and D. Brown, in "Oligonucleotides and Analogues, a Practical Approach" (F. ), Chap. 1. IRL Press at Oxford Univ. Press, Oxford, 1991. 5%) will fail to react with the activated monomer in solution. A capping step is incorporated into the synthesis cycle to acetylate these "failure" sequences and render them inert to subsequent monomer additions. Without this step, a series of one-base deletion mutations would contaminate the product, but with the step the contaminants are truncated sequences of varying length, forming a mixture much easier to purify.

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DNA Structures Part A: Synthesis and Physical Analysis of DNA by John N. Abelson, Melvin I. Simon, David M.J. Lilley, James E. Dahlberg

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