Oligonucleotide fragmentation

Cleavage in the presence of histidine releases the oligonucleotide fragment containing the random sequence, and this is amplified by PCR and the cycle repeated. This selection procedure produced deoxyribozymes that require no metal cofactor but have a specific requirement for L-histidine, which is presumed (from pH-rate profiles) to act as a general... 

Hofstadler, S.A. Griffey, R.H. Pasa-Tolic, R. Smith, R.D. The Use of a Stable Internal Mass Standard for Accurate Mass Measurements of Oligonucleotide Fragment Ions Using ESI Fourier Transform Ion Cyclotron Resonance-MS With Infrared Multiphoton Dissociation. Rapid Commun. Mass Spectrom. 1998,12, 1400-1404. 

Hong SP, Kim NK, Hwang SG, Chung HJ, Kim S, et al. 2004. Detection of hepatitis B virus YMDD variants using mass spectrometric analysis of oligonucleotide fragments. J Hepatol 40 837. 

Sequencing RNA. The first known RNA sequence, that of an alanine tRNA, was determined by Holley and associates in 1965. The RNA was subjected to partial hydrolysis with pancreatic ribonuclease and ribonuclease Tj (Fig. 5-43). Tire small oligonucleotide fragments were separated by ion exchange chromatography under denaturing conditions (7 M urea) and were then characterized individually.645 Tire availability... 

Elso C, Toohey B, Reid GE, Poetter K, Simpson RJ, Foote SJ. Mutation detection using mass spectrometric separation of tiny oligonucleotide fragments. Genome Res 2002 12 1428-1433. 

The RNA oligomers studied by these authors [115, 116] are several evolved sequences (hepatitis delta virus), synthetic polymers (poly-U), and various random RNA sequences. The random sequences are obtained from the HDV sequence by a permutation of the nucleotides in which base composition is fixed [115, 116]. The lengths of all RNA oligonucleotide fragments are 85 nucleotides [115, 116],... 

Hettich, R.L. and Stemmier, E.A. (1996) Investigation of oligonucleotide fragmentation with matrix-assisted laser desorption ionization Fourier-transform mass spectrometry and sustained off-resonance irradiation. Rapid Commun. Mass Spectrom., 10 (3), 321-7. 

Figure 19-10. Dependence of yield of LEE-induced 5 -oligonucleotide fragments on their length for electron energies of 8 ( A), 28 (O), and 68 eV ( ). The curves represent decaying exponential fits. The inset shows the dependence of the attenuation length (AL) on LEE energy. The error bars represent the uncertainty range of the fitting parameter in the exponential...

Methylases specific for each of the four bases of sRNA (97) and for adenine and cytosine of DNA (98) are available. Selective modification of a nucleic acid or its oligonucleotide fragments before digestion with a specific nuclease gives additional dimensions for selective degradation. Use of C-methyl labelled S-adenosylmethionine permits selective isotopic labelling by these enzymes. 

Figure 6.5. Fluorescence Detection of Oligonucleotide Fragments Produced by the Dideoxy Method. Each of the four chain-terminating mixtures is primed with a tag that fluoresces at a different wavelength (e.g., blue for A). The sequence determined by fluorescence measurements at four wavelengths is shown at the bottom. [From L. M. Smith, J. Z. Sanders, R. J. Kaiser, P. Hughes, C. Dodd, C. R. Connell, C. Heiner, S. B. H. Kent, and L. E. Hood. Nature 321...

Figure 5.5 Fluorescence detection of oligonucleotide fragments produced by the dideoxy method. A sequencing reaction is performed with four chain-terminating dideoxy nucleotides, each labeled with a tag that fluoresces at a different wavelength (e.g., red for T). Each of the four colors represents a different base in a chromatographic trace produced by fluorescence measurements at four wavelengths. [After A. J. F. Griffiths et al., An Introduction to Genetic Analysis, 8th ed. (W. H. Freeman and Company, 2005).]...

---