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10.47Methods Used to Purify Synthetic Oligonucleotides ...........

This unit augments the detailed instructions provided by the manufacturersof oligonucleotide synthesizers.

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13.81Mutagenic Oligonucleotides ..................................

The resulting hydrophobically taggedfull-length "trityl-on" oligonucleotide can be separated easily from failuresequences which lack trityl groups and do not efficiently bind the hydrophobicmatrix.

9.92Chapter 10Working with Synthetic Oligonucleotide Probes ................

By using a supportmatrix such as control pore glass (CPG) with a loading capacity of lessthan 40 mmol/g, yields of long oligonucleotide may be greatly increased;furthermore, the pore size of the support should be 1000 angstrom for >100-mersand 2000 angstrom for 200-mers (Gait, 1986) to alleviate molecular crowdingand steric effects.

Syringe method for stepwise chemical synthesis of oligonucleotides.

9.42 Random Priming: Radiolabeling of DNA by Extension of Random Oligonucleotides in the Presence of Melted Agarose ....................................................

Also, very long synthetic oligonucleotides(300-600 bases) have also been synthesized directly, and inspite of incredelylow yields, rare full length products have been successfully amplifiedby PCR (Ciccarelli, R.

Fast cleavage and deprotection of oligonucleotides. 35:4311-4314.

For the casual user of RNA, it is often easierto just purchase small quantities of the required sequence from a ribo-oligonucleotidesynthesis company such as Baron Consulting, Dharmacon Research, Genosys,or Peninsula Labs.

The DIG System is an effective system for the labeling and detection of DNA, RNA, and oligonucleotides. The protocols for labeling with digoxigenin (Figure 1) and subsequent detection are based on well established, widely used methods. DNA, RNA, and oligonucleotide probes are labeled according to the methods (usually enzymatic) used for preparing radioactive probes. Hybridization of digoxigenin-labeled probes (e.g., to target DNA or RNA on a Southern or Northern blot) is also carried out according to standard protocols, except that a special blocking reagent is used to eliminate background. The signal on the nucleic acid blot is detected according to the methods developed for western blots. The incorporation and spacing of digoxigenin in DNA, RNA, and oligonucleotides can be varied by using different labeling protocols.

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  • The Random Oligonucleotide-Primed Synthesis Assay …

    8.253 Removal of Oligonucleotides and Excess dNTPs from Amplified DNA by Ultrafiltration ..........................

  • Directional Random Oligonucleotide Primed (DROP) …

    8.6111 Mixed Oligonucleotide-primed Amplification of cDNA (MOPAC) ...................................................

  • Random Oligonucleotide-Primed Synthesis - Acronym …

    9.367 Synthesis of cDNA Probes from mRNA Using Random Oligonucleotide Primers ...................................

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How is Random Oligonucleotide-Primed Synthesis abbreviated

As is true for all RNA work, equipmentand reagents that will contact unprotected oligonucleotides should be RNasefree () to avoid degradation ofthe synthesized material.

ROPS stands for Random Oligonucleotide-Primed Synthesis

A computerized logbook is especially useful and allows for an organized oligonucleotide nomenclaturesuch as R20.17 which refers to Rebecca's 20-mer, the 17th 20-mer made onthe system.

Oligonucleotide primers for cDNA synthesis (1 mg/ml)

10.308 Hybridization of Oligonucleotide Probes in Aqueous Solutions: Washing in Buffers Containing Quaternary Ammonium Salts ...........................................

Labeling of DNA by random oligonucleotide-primed synthesis

Oligonucleotides of similar size should be combinedin parallel runs since synthesizing many short oligos followed by a longerone is faster than mixing the sets on dual column synthesizers.

What is degenerate oligonucleotide primed PCR? How …

Thus, while virtually any dinucleotide of the form A(5')ppX canbe added to an oligonucleotide, only a few compounds (primarily sterically"small" derivatives of natural bases) can be used by the enzyme to formA(5')ppXp from pXp.

This method is applied to the random oligonucleotide …

13.367 Screening Recombinant Clones for Site-directed Mutagenesis by Hybridization to Radiolabeled Oligonucleotides .........................................

Directional random oligonucleotide primed (DROP) …

The sensitivity of hybridization analysis is determined by how many labeled probe molecules attach to the target DNA. The greater the number of labeled probe molecules that anneal, the greater is the intensity of the hybridization signal. The specific activity is a measure of the incorporation of labeled nucleotides/probe. Modern labeling procedures as nick translation, random priming, PCR or in vitro RNA synthesis routinely provide probes with high specific activity.

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