Ribonucleic acid base pairing

A solution leading to a successful algorithm was recently found for the folding of ribonucleic acid (RNA) [36], Natural RNA polymers (figure C2.14.1) are mainly made up from four different bases . A, C, G and U. As with DNA, multiple hydrogen bonding favours the fonnation of G-C and A-U pairs [16, 37, 38] which leads to the appearance of certain characteristic stmctures. Loop closure is considered to be the most important folding event. 

The discovery of the base-paired, double-helical structure of deoxyribonucleic acid (DNA) provides the theoretic framework for determining how the information coded into DNA sequences is replicated and how these sequences direct the synthesis of ribonucleic acid (RNA) and proteins. Already clinical medicine has taken advantage of many of these discoveries, and the future promises much more. For example, the biochemistry of the nucleic acids is central to an understanding of virus-induced diseases, the immune re-sponse, the mechanism of action of drugs and antibiotics, and the spectrum of inherited diseases. 

List of Abbreviations PCR, polymerase chain reaction RT-PCR, reverse transcription polymerase chain reaction DNA, deoxyribonucleic acid RNA, ribonucleic acid RNase, ribonuclease mRNA, messenger RNA GABAa, y-aminobutyric acid type A cRNA, copy RNA dNTPs, deoxy nucleoside triphosphates MMLV, Mouse Moloney murine leukemia vims RT, reverse transcriptase bp, base pair Tm, melting temperature DEPC, diethylpyrocarbonate OD, optical density mL, milliliter SA-PMPs, streptavidin paramagnetic particles dT, deoxy thymidine DTT, dithiothreitol DNase, deoxyribonuclease RNasin, ribonuclease inhibitor UV, ultraviolet TBE, Tris-borate, 1 mM EDTA EDTA, ethylenediaminetetraacetic acid Buffer RET, guanidium thiocyanate lysis buffer PBS, phosphate buffered saline NT2, Ntera 2 neural progenitor cells... 

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. 

Thomas, G. J. Jr. (1969). Determination of the base pairing content of ribonucleic acids by infrared spectroscopy. Biopolymers 7, 325—334. 

The above-mentioned purine-pyrimidine base-pairing scheme consists, as it is well known, of hydrogen bonding between specific, complementary base pairs, namely, adenine-thymine [or uracil in ribonucleic acid (RNA)] and guanine-cytosine (Fig. 1) (shorthand notations A-T or A-U and G-C). The specificity of the bonding concerns both this exclusiveness and the steric arrangement which is... 

Keiderling reported the VCD spectra of triple helices in ribonucleic acids by investigating the temperature dependent VCD features of a mixture of poly(rA) and poly(rU) [54]. The spectra of the triple helix are more complicated than those of a double strand, as expected. We have reported the VCD of a number of oligo deoxynu-cleotides with between four and twelve base pairs. These studies will be elaborated upon after a detailed discussion of the VCD features of polymeric DNA and RNA samples, for which the solution structures are well established. 

DNA) A biopolymer of deoxyribonucleotides that serves as a template for the synthesis of ribonucleic acid. DNA is also the template for its own replication, through uncoiling and the pairing and enzymatic linking of complementary bases, (p. 1140)... 

For reduplication, the chains are separated and on each a new, complementary strand is synthesized by enzymes called DNA polymerases [652J. For protein biosynthesis, the DNA is copied (transcribed) into the messenger ribonucleic acid (mRNA) by the enzyme RNA polymerase (Fig. 20.2) where, in contrast to DNA, the deoxyribose is replaced by ribose and thymine by the equivalent uracil. Here again, the Watson-Crick base pair plays the crucial role so that the mRNA sequence is complementary to the DNA sequence. 

The bases found in RNA (ribonucleic acid) are the purine heterocyclics adenine (6-aminopurine) and guanine (2-amino-6-oxypurine) and their complementary pyrimidine bases uracil (2,4-dioxypyrimidine) and cytosine (2-oxy-4-aminopyrimidine), respectively (Section 1, Appendix). In RNA double-stranded duplexes adenine (A) base-pairs with uracil (U) via two hydrogen bonds (A=U) and guanine base-pairs with cytosine (C) via 3 hydrogen bonds (G=C). Adenine forms the nucleoside adenosine by an N-glycosidic link with the... 

The structure proposed by Watson and Crick has two properties of central importance to the role of DNA as the hereditary material. First, the structure is compatible with any sequence of bases. The base pairs have essentially the same shape (see Figure 1.6) and thus fit equally well into the center of the double-helical structure of any sequence. Without any constraints, the sequence of bases along a DNA strand can act as an efficient means of storing information. Indeed, the sequence of bases along DNA strands is how genetic information is stored. The DNA sequence determines the sequences of the ribonucleic acid (RNA) and protein molecules that carry out most of the activities within cells. 

The mechanism by which genetic information is decoded and used to direct cellular processes begins with the synthesis of another type of nucleic acid, ribonucleic acid (RNA). RNA synthesis occurs by complementary pairing of ribonucleotide bases with the bases in a DNA molecule. 

Ribonucleic acid is a class of polynucleotides, nearly all of which are involved in some aspect of protein synthesis. RNA molecules are synthesized in a process referred to as transcription. During transcription, new RNA molecules are produced by a mechanism similar to DNA synthesis, that is, through complementary base pair formation. The sequence of bases in RNA is therefore specified by the base sequence in one of the two strands in DNA. For example, the DNA sequence 5 -CC(1ATT ACG-3 is transcribed into the RNA sequence 3 -GGCUAAUGC-5. (Complementary DNA and RNA sequences are antiparallel.)... 

When not replicating, DNA serves as the code for synthesis of proteins. During protein synthesis, a small portion of DNA is copied by complementary base pairing of RNA nucleotides (adenine, guanine, cytosine and uracil instead of thymine) to form single stranded messenger ribonucleic acid (mRNA) in the nucleus of the cell. This process is known as transcription and is catalysed by an enzyme called RNA polymerase. 

The two types of natural polynucleotides (nucleic acids) are classified according to the sugars they contain. Ribonucleic acid (RNA) contains exclusively P-o-ribose, while the sugar in deoxyribonucleic acid (DNA) is P-2-deoxy-D-ribose. Different nucleic acids can have from around 80 nucleotides (nt), as in transfer RNA (tRNA), to over 10 nucleotide-pairs in a single eukaryotic chromosome. The unit for size of nucleic acid is the base (for single-stranded species) or the base-pair (bp, for double-stranded species), with the unit Kb (thousand base-pairs) and Mb (million base-pairs). Examples of synthetic homopolynucleotides are poly(uridylate) or poly(deoxyadenylate), in poly(U) or poly(dA)... 

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