Nucleic sequence dependence

The nucleic acids known as deoxyribonucleic acid (DNA) are the molecules that store genetic information. This information is carried as a sequence of bases in the polymeric molecule. Remarkably, the interpretation of this sequence depends upon simple hydrogen bonding interactions between base pairs. Hydrogen bonding is fundamental to the double helix arrangement of the DNA molecule, and the translation and transcription via ribonucleic acid (RNA) of the genetic information present in the DNA molecule. 

The structure of nucleic acids depends on the sequence of individual nucleotides. The actual base sequences for many nucleic acids from various species are available to date. Instead of writing the full name of each nucleotide, abbreviations are used, e.g. A for adenine, T for thymidine, G for guanosine and C for cytidine. Thus, a typical DNA sequence might be presented as TAGGCT. 

Just as the structure of a protein depends on its sequence of individual amino acids, the structure of a nucleic acid depends on its sequence of individual nucleotides. To carry the analogy further, just as a protein has a polyamide backbone with different side chains attached to it, a nucleic acid has an alternating sugar-phosphate backbone with different amine base side chains attached. 

The message for assembling life in three dimensions is two-dimensional, meaning that the information it contains is sequence-dependent, and since the nucleic acid polymers in all primordial reactors would have different sequences the new model... 

Miller, T. R., et ah (1995). A probe for sequence-dependent nucleic acid dynamics. J. Am. 

The molecule of DNA is like a coded message. This message, the genetic information contained in and transmitted by nucleic acids, depends on the sequence of bases from which they are composed. It is somewhat like the message sent by telegraph, which consists only of dots, dashes, and spaces in between. The key aspect of DNA structure that enables storage and replication of this information is the famed double helix structure of DNA mentioned above. 

Langley DR (1998) Molecular dynamic simulations of environment and sequence dependent DNA conformations the development of the BMS nucleic acid force field and comparison with experimental results, J Biomol Struct, 16 487—509... 

The interaction of biologically active molecules like dyes with nucleic acids is of great interest because such molecules are used as drugs in chemotherapy (e.g. antibiotics, antitumor substances) other ones can induce mutations and tumors. They form intermolecular complexes with nucleic acids. A special class are dyes interacting with DNA by intercalation. These dye molecules are inserted between two base pairs (Fig. 10). A peculiarity of such complexes are base-sequence-dependent effects, for example, the fluorescence behaviour or the energy transfer inside the complex. These processes can depend on the type of base pairs between which the dye molecules are inserted. The quantum yield of fluorescence for some dyes after intercalation is much higher in AT-AT than in AT-GC or GC-GC sequences. 

The exciting properties of nucleic acids have opened new scenarios in the field of nanotechnology and sensor development. In particular, the dynamic properties of nucleic acids and the thermally indnced sequence-dependent separation of double-stranded DNA allow the utilization of nucleic acids with machinelike functions that can perform different motions or act as switches and motors (Beissenhirtz and Willner, 2006). The same principles have been applied for the development of aptamer-based machines, which can amplify the recognition event between the aptamer and the substrate through operation of the machine (Shlyahovsky et al., 2007). A scheme for the assay developed for cocaine is reported in Figure 8.10. 

Umezawa, Y. Nishio. M. Thymine-methyl/7c interaction implicated in the sequence-dependent deformability of DNA. Nucleic Acids Res. 2002, 30, 2183-2192. 

Wu C, Carta R, Zhang L (2005) Sequence dependence of cross-hybridization on short oligo microarrays. Nucleic Acids Res 33 e84... 

Nucleic acids in solution can be detected and quantified readily on the basis of ultraviolet (UV) absorbance. Nucleic acids exhibit strong absorbance with a peak at 260 nm in a manner that is sensitive to chemistry and bonding. For accurate quantification of small oligonucleotides, a sequence-dependent extinction coefficient can be computed, but for all other routine laboratory analysis, approximate values are almost universally employed (Table 2). 

The nucleotides which consist of three parts, namely a nitrogenous base, a pentose sugar and a phosphate radical, are a very important group of compounds since one or more of them is involved in virtually every biochemical process. The adenosine di- and tri-phosphates which play an essential part in cellular energy exchanges have a nucleotide-type structure as do many of the coenzymes. Furthermore, nucleotides constitute the monomeric units of which the nucleic acids are composed that is to say nucleic acids are polynucleotides. The nucleic acids which are of two types, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are responsible for directing the synthesis of proteins. They specify the unique sequence of amino acids in any particular protein and consequently should be regarded as primordial molecules on whose existence that of the proteins depends. However, since the synthesis of the nucleic acids depends on enzymes which are themselves proteins, this poses the fundamental evolutionary question as to which came first - the biochemical version of the problem of the chicken and the egg ... 

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