Matrix nucleic acids

Singh, G. B., Kramer, J. A., Krawetz, S. A. (1997) Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res. 25, 1419-1425. 

Material/Matrix Nucleic Acid Result Gene Species/Delivery Ref. 

Both the ease of use of this method for characterization of proteins and nucleic acids, and the abiHty to analyze many samples simultaneously for comparative purposes, have led to the prevalence of this technique. The drawbacks of a polyacrylamide matrix is that acrylamide is a neurotoxin, the reagents must be combined extremely carefiiUy, and the gels are not as pHable as most agarose gels. 

High matrix rigidity is offered by porous sihca, which can be deriva-tized to enhance its compatibility with proteins, but it is unstable at alkaline pH. Hydroxyapatite particles have high selectivity for a wide range of proteins and nucleic acids. 

Classical gel electrophoresis has been used extensively for protein and nucleic acid purification and characterization [9, 10], but has not been used routinely for small molecule separations, other than for polypeptides. A comparison between TLC and electrophoresis reveals that while detection is usually accomplished off-line in both electrophoretic and TLC methods, the analyte remains localized in the TLC bed and the mobile phase is immediately removed subsequent to chromatographic development. In contrast, in gel electrophoresis, the gel matrix serves primarily as an anti-... 

Nordhoff, E. Ingendoh, A. Cramer, R. Overberg, A. Stahl, B. Karas, M. Hillenkamp, F. Crain, P. F. Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the UV and IR. Rapid Comm. Mass Spectrom. 1992, 6,771-776. 

The scientific world was amazed to hear that David Lee, from the laboratory of Reza Ghadiri (Scripps Research Institute, La Jolla, California), had found a self-replicating peptide (Lee et al., 1996) there are analogies to the experiments with oligonucleotides (see Sect. 6.4). Lee was able to show that a certain peptide, containing 32 amino acids, can both function as a matrix and also support its own synthesis autocatalytically. The information transfer is clearly more complex than that involved in nucleic acid replication. In the case of this particular peptide, both the... 

Leslie Orgel and co-workers took up this problem and studied the non-enzymatic polymerisation of mononucleotides, i.e., the question as to whether single nucleic acid building blocks can undergo polycondensation on a corresponding complementary matrix. The substrates used were the 5 -phosphoimidazolides of adenosine (ImpA) and guanosine (ImpG), the matrices poly(U) and poly(C). 

The result was quite disappointing, as instead of the required 3 -5 -phosphodiester linkage, which is found in nucleic acids today, the main products obtained were those with the unnatural 2 -5 -bond between the nucleotides. Further experiments showed that the presence of divalent metal ions had a clear positive effect on the matrix-dependent polycondensation. The addition of l-10mMPb2+ to 100 mM of poly(U) as the matrix and 50 mM of ImpA monomer caused the yield of oligomeric product (pentamers and longer) to increase by a factor of four (Sleeper et al., 1979). 

A further unusual feature of the matrix-dependent polycondensation lies in the character of the nucleobases themselves. Purine mononucleotides undergo polycondensation, in good yields, at complementary matrices consisting of pyrimidine polymers. However, the synthesis of pyrimidine oligonucleotides from their mononucleotides at purine matrices is not effective. This important fact means that a pyrimidine-rich matrix leads to a purine-rich nucleic acid, which is itself not suitable to act as a matrix. This phenomenon also occurs when matrices are used which contain both basic species, i.e., purines and pyrimidines. An increase in the amount of purine in a matrix leads to a clear decrease in its effectiveness (Inoue and Orgel, 1983). However, the authors note self-critically that the condensation agent used cannot be considered to be prebiotic in nature. 

We still need to clear up one or two points of nomenclature in normal replication of nucleic acids, the matrix (the + strand) and the newly formed daughter strand (- strand) are held together by Watson-Crick hydrogen bonding. This process is also referred to as cross-catalytic . Normal autocatalysis is different it leads to a product which corresponds in structure to the matrix, so that there is no difference between the + and - strands. Such self-complementary sequences are called palindromes. 

The growing interest for the identification and characterization of polar and large compounds caused the development and the introduction of new ionization techniques, such as electrospray ionization (ESI)[4], and matrix assisted laser desorption ionization (MALDI),[5] and their more recent improvements, thus establishing new MS based approaches for studying large molecules, polymers and biopolymers, such as proteins, carbohydrates, nucleic acids. 

An array or a matrix of nucleic acid probes immobilized at discrete locations on a silicon or glass surface provides a convenient means to simultaneously probe a sample for the presence of many different target sequences. Microarray biochip scanning devices, mostly based on fluorescent labels, are now currently available, and could also be used with CL labels to take advantage of the higher sensitivity of this detection principle. 

Fig. 1. An overview of the DCLD tier/triage flow chart Boxes 1, 2, and 3 are taken from the Office of Device Evaluation decision tree, which is routinely used to determine whether a product can be reviewed as a 510(k) and found substantially equivalent to a predicate (currently marked) device or whether the product must be handled as a fundamentally new product and submitted to a PMA review. Box 4 determines the novelty of the product in terms of analyte, matrix, and/or technology. If new issues of safety and effectiveness are raised, a highly novel product might require review as a PMA. If the issues of safety and effectiveness are not new but require high-level scrutiny, then a tier III review is warranted. Examples of products requiring a tier III review would include 1. Analyte troponin for diagnosis of MI (with creatinine kinase as the predicate) 2. Matrix sweat patches for drugs of abuse (with urine drugs of abuse tests as the predicate) and 3. Technology nucleic acid...

Affinity (AC) Aqueous, usually buffered Specific affine ligand bonded to support matrix. (See also Section 19.6.2). Proteins (enzymes, antibodies, antigens, lectins), peptides, nucleic acids, oligonucleotides, viruses, cells. 

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