Nucleic acid fragments

Considerable progress has been made in understanding the chemical principles in Pt-nucleic acid interactions since the discovery of Pt antitumor drugs. At the same time, however, new questions have been raised upon development of novel drugs that violate the early structure-activity relationships. A common feature for various Pt drugs is that their initial binding to nucleic acid fragments seems to be controlled by the... 

A variety of buffers is used in electrophoresis. The selected buffer must contain ions to carry the current. Other than current-carrying capacity, the most critical criterion for buffer selection is the stability of the sample to be analyzed. Many proteins are unstable in acidic pHs, so alkaline buffers are frequently employed. Tris-(hydroxymethyl)amino methane (TRIS or THAM), sodium acetate, and ethylenedi-aminetetraacetate (EDTA) are common solutes in buffers, with pHs between 7.9 and 8.9 typical. (Refer to Chapter 5 for a discussion of buffers.) These buffers also work well with nucleic acid fragments. In addition, phosphate buffers, e.g., 10 mMK3P04, are often used with nucleic acid fragments (1.0 mM = 0.0010 M). 

Most HPLC instruments monitor sample elution via ultraviolet (UV) light absorption, so the technique is most useful for molecules that absorb UV. Pure amino acids generally do not absorb UV therefore, they normally must be chemically derivatized (structurally altered) before HPLC analysis is possible. The need to derivatize increases the complexity of the methods. Examples of derivatizing agents include o-phthaldehyde, dansyl chloride, and phenylisothiocyanate. Peptides, proteins, amino acids cleaved from polypeptide chains, nucleotides, and nucleic acid fragments all absorb UV, so derivatization is not required for these molecules. 

Endonucleases cut within the nucleic acid and release nucleic acid fragments. 

Figure 1. Progress curves for renaturation of double-stranded nucleic acid fragments (roughly 400 bases/fragment). From Britten and Kohne with permission.

Berger, I., Kang, C. H., Sinha, N., Wolters, M. and Rich, A. (1996). Ahighly efficient 24-condition matrix for the crystallization of nucleic acids fragments. Acta Crystallogr. D 52, 465 68. 

The agarose concentration depends on the average size of nucleic acid fragments the smaller the fragments, the higher the concentration. 

Disc gel electrophoresis yields excellent resolution and is the method of choice for analysis of proteins and nucleic acid fragments. Protein or nucleic acid bands containing as little as 1 or 2 ju,g can be detected by staining the gels after electrophoresis. 

The electrophoretic techniques discussed up to this point are useful for analyzing proteins and small fragments of nucleic acids up to 350,000 daltons (500 bp) in molecular size however, the small pore sizes in the gel are not appropriate for analysis of large nucleic acid fragments or intact DNA molecules. The standard method used to characterize RNA and DNA in the range 200 to 50,000 base pairs (50 kilobases) is electrophoresis with agarose as the support medium. 

Scoble HA, Brown PR (1983) Reversed-phase chromatography of nucleic acid fragments. High-Performance Liquid Chromatogr 3 1-47... 

Data presented here demonstrate the potential applicability of SPCEs genosensors in the diagnosis of a human infectious pulmonary disease. These electrochemical genosensors are stable and sensitive devices for the detection of specific nucleic acid fragments. Moreover,... 

Binding of Platinum Compounds to Monomeric Nucleic Acid Fragments. 65... 

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