Determination of sequences

An elegant method of determination of sequence using monophosphatase, exonuclease, and alkaline hydrolysis has been proposed by... 

Farinas ET,Tan JD, Mascharak PK. Photoinduced DNA cleavage reactions by designed analogues of Co(III)-bleomycin the metalated core is the primary determinant of sequence specificity. Inorg Chem 1996 35 2637-43. 

Direct determination of sequences cloned into plasmid pBR322... 

Synthesis of a specific DNA segment via the PCR is directed by two oligonucleotide primers. Multiple rounds of extension from the primers amplify the target sequence exponentially, with termini defined by the 5 ends of the two primers. This process allows the determination of sequences from a very small number of target molecules. Unique sequences can be amplified from a complex mixture of nucleic acids because of the high specificity of the primer-template hybridization. 

Ni, J.S., Pomerantz, S.C., Rozenski, J. et al. (1996) Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem., 68 (13), 1989-99. 

Note Added in Proof. Model II, as discussed in Section X,B,4, was suggested first by Dayhoff (1972) prior to its development and extension by Wilson et al. (1977). The most recent refinement follows from the first determination of sequences of fish lysozymes (rainbow trout, Oncorhynchus mykiss), resulting in a new proposed divergence date of ca.400 MY ago (Daotigny et al., 1991). 

In section 2.1 the contact interface between TBP and the minor groove of DNA was characterized as anhydrous. This is a common characteristic in all the TBP-DNA complexes available to date. As TBP presents a primarily hydrophobic surface to DNA, most of the hydrogen bond donors and acceptors at this surface are not satisfied by the complexation. Hence, there is likely to be an enthalpic penalty associated with the dehydration of this surface. This penalty is compensated by the favorable increase in entropy associated with the liberation of the surface-bound water molecules into bulk solution. Following this reasoning, there are two aspects of hydration that could contribute to the determination of sequence specificity the ideal sequence would be one which coordinates a large number of water molecules, but binds them least tightly. 

Tosi, C., P. CoRRADiNi, A. Valvassori, and F. Ciampelli Infrared determination of sequence distribution and randomness in copolymers. International Symposium on Macromolecular Chemistry, Bruxelles 1967, Preprint IX-91 (in press in J. Polymer Sci. Part C). 

Brownlee, G. G. (1972) Determination of sequences in RNA, In T. S. Work and E. Work, eds.. Laboratory Techniques in Biochem. and Molecular Biology, Vol. 3, Part 1 (North Holland, Amsterdam). 

Actually deciphering the complete sequence from the MS fragmentation pattern is an extremely complex task that is beyond the scope of this chapter. However, verification of a proposed sequence should be possible, even for facilities just being introduced to peptide analysis by MS. In the case of the ABRF study described above, with the availability of MS/MS data it should have been obvious to the participating laboratories that the requested peptide had not been synthesized. With the results of this study as an example, it can be concluded that when other quality assurance mechanisms are in place in a peptide synthesis laboratory, molecular weight determination by either MALDI-TOF or ESI-MS can provide an excellent means of verifying the integrity of a synthetic product. When questions do arise about a specific peptide, MALDI-PSD and ESI-MS/MS then can permit rapid determination of sequence information that should yield valuable clues about the nature of a synthetic sequence. 

Eoley and SUbert (1989) define a human-computer interface as the determination of all user inputs into a computer, the determination of all computer outputs to the user, and the determination of sequences of inputs/outputs made accessible to the user. 

Montaudo, M.S. and Samperi F., Determination of Sequence and Composition in Poly(butylene adipate-co-butyleneterephthalate) by MALDI-TOF, Europ. Mass Spectrom, 4, 459 (1999). 

Ballistreri, A., Giuffrida, M., Lenz, R.W., Fuller, C.R., Kim, Y.B., and Montaudo, G., Determination of Sequence Distributions in Bacterial Copolyesters Containing Higher Alkyl and Alkenyl Pendant Groups, Macrotnolecules, 25,1845, 1992. 

At the lower right of the two-dimensional map, nuclear Overhauser enhancement spectroscopy (NOESY) demonstrates a set of through space proton-proton contacts that allow determination of sequence. As listed at the top of Figure 9.10, there are four types of through space proton-proton contacts. Contact between the aCH proton of residue i and the NH proton of residue i -i-1 is defined as d dy and... 

Copolymers can vary in their average composition and mean monomeric unit sequence length, as well as in the distributions in composition and sequences. It is useful to consider sequences of polymers with a small number of different monomeric units (e.g., proteins). Since the determination of sequence is very specific of multipolymers with many different monomeric units, this will be discussed under the relevant polymer. 

Nguyen, G Matlengiewicz, M. Nicole, D. Incremental method for determination of sequence distribution of poly(methyl methacrylate) by NMR spectroscopy. Analusis 1999, 27, 847-853. 

Hazard and risk assessment Determination of sequence of event leading to hazard, hazard events with risk involvement with the same, risk reduction and safety fimction for risk reduction. 8... 

Rao and co-workers [62] applied Py-GC and C-NMR to the determination of sequence distribution of butadiene (B) - acrylonitrile (A) - methacrylic acid (M) terpolymers. Sequence distribution was described in terms of six triads (BBB, ABA, ABB, BBA, MBR and AMB) and found to vary with the mode of addition of methacrylic acid monomer. 

T. Mitsuhashi and M. Oki. Borohydride reduction of methyleneanthrones Determination of sequence of hydride addition. Ghem. letters, 1978, 373. 

Thom-Csanyi, E., Hohnk, H.D., and Pflug, K.P. (1993) Ring-opening metathesis copolymerization of cyclopentene and [2.2] paracyclophane-l,9-diene UV-Vis-spectroscopic determination of sequence-length distribution of p-pheny-lenevinylene units. Journal of Molecular Catalysis, 84,253. 

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