Aldehyde synthesis by deprotection or hydrolysis

Synthesis, deprotection, analysis and purificationof RNA and ribozymes.

Patent US6649751 - Synthesis, deprotection, analysis …

Also, by replacing thetraditional benzyl protection of cytosine with acetyl and using a 1:1 mixtureof aqueous ammonium hydroxide and aqueous methylamine, oligonucleotidessynthesized with traditional purine protections may be completely deprotectedin 5 minutes at 65°C (Reddy, M.

Synthesis, deprotection, analysis and purification of …

AB - Oligonucleotide microarrays or oDNA chips are effective decoding and analytical tools for genomic sequences and are useful for a broad range of applications. Therefore, it is desirable to have synthesis methods of DNA chips that are highly flexible in sequence design and provide high quality and general adoptability. We report herein, DNA microarray synthesis based on a flexible biochip method. Our method simply uses photogenerated acid (PGA) in solution to trigger deprotection of the 5′-OH group in conventional nucleotide phosphoramidite monomers (i.e. PGA-gated deprotection), with the rest of the reactions in the synthesis cycle the same as those used for routine synthesis of oligonucleotides. The complete DNA chip synthesis process is accomplished on a regular DNA synthesizer that is coupled with a UV-VIS projection display unit for performing digital photolithography. Using this method, oDNA chips containing probes of newly discovered genes can be quickly and easily synthesized at high yields in a conventional laboratory setting. Furthermore, the PGA-gated chemistry should be applicable to microarray syntheses of a variety of combinatorial molecules, such as peptides and organic molecules.

N2 - Oligonucleotide microarrays or oDNA chips are effective decoding and analytical tools for genomic sequences and are useful for a broad range of applications. Therefore, it is desirable to have synthesis methods of DNA chips that are highly flexible in sequence design and provide high quality and general adoptability. We report herein, DNA microarray synthesis based on a flexible biochip method. Our method simply uses photogenerated acid (PGA) in solution to trigger deprotection of the 5′-OH group in conventional nucleotide phosphoramidite monomers (i.e. PGA-gated deprotection), with the rest of the reactions in the synthesis cycle the same as those used for routine synthesis of oligonucleotides. The complete DNA chip synthesis process is accomplished on a regular DNA synthesizer that is coupled with a UV-VIS projection display unit for performing digital photolithography. Using this method, oDNA chips containing probes of newly discovered genes can be quickly and easily synthesized at high yields in a conventional laboratory setting. Furthermore, the PGA-gated chemistry should be applicable to microarray syntheses of a variety of combinatorial molecules, such as peptides and organic molecules.


As a proof of concept orthogonal deprotection is demonstrated in a ..

The cleavage reaction with concentrated ammonium hydroxide (28 to 33% NH3 in water), if carried out separately, is normally considered to be 1 hour at room temperature. Deprotection using ammonium hydroxide is the most traditional method and dates back to the earliest days of oligonucleotide synthesis. One of the critical issues when using ammonium hydroxide, which is water saturated with ammonia gas, is to keep the solution fresh. We aliquot and store ammonium hydroxide in the refrigerator in portions appropriate for use in 1 week. Using an old bottle of ammonium hydroxide is false economy since the resulting oligos are not going to be completely deprotected.

Oligo Synth. Deprotection. Purification

The rate-determining step in oligonucleotide synthesis is more than likely the removal of the protecting group on the G base. Ignore this at your peril since, traditionally, one of the most common reasons for poor performance of oligonucleotides is the presence of a small percentage of the G protecting groups remaining in the final product oligonucleotide. Chromatographic methods may miss the presence of the G protecting groups but these are readily revealed by mass spectral analysis. What are the options with attendant pros and cons for oligonucleotide deprotection?

Protecting Groups List - The Organic Synthesis Database

On classic synthesizers from Applied Biosystems, the cleavage of the oligo from the synthesis support can be carried out separately on the machine, prior to deprotection. As a result, many researchers still carry out the cleavage reaction separately and so the time required to do this is mentioned at the beginning of each Deprotection section. However, most researchers do a one step cleavage/deprotection reaction, which has the advantage of ensuring optimal yields. The only downside to this strategy is the fact that the basic solution at elevated temperatures will dissolve a small amount of silica from CPG and a white insoluble residue will be apparent if the deprotection solution is evaporated to dryness. However, any residual silicate is easily removed by filtration, desalting or any purification procedure.