Nucleic acids from sequences

We have learned previously that the synthesis of exactly our proteins on Earth is doomed by conhngency - we cannot hope to hnd out the exact condihons that deternuned the hnal sequence of a given protein or a nucleic acid from our Earth. Once this biher assertion is accepted, we should at least attempt experiments that show that the prebiotic synthesis of some specihc sequence in many identical copies is possible. Also, it is perhaps surprising that there has been so little reported in the... 

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. 

Hybridization measurements have been used in many studies of homology of nucleic acids from different species. A nucleic acid is cut (e.g., by sonic oscillation) into pieces of moderate length ( 1000 nucleotides) and is denatured. The denatured DNA fragments are mixed with denatured DNA of another species. Nucleotide sequences that are closely similar between species tend to hybridize, whereas sequences that are... 

There are several different methods based on 16S rRNA sequences that can be used to study bacterial community structure. The first approach involves extracting bulk nucleic acids from samples and then using this material in subsequent molecular analyses. A large number of these methods involve the polymerase chain reaction (PCR). Using PCR, target gene sequences... 

Differences in the sequence of homologous proteins in different species are derived from the primordial pools and are a product of the redundancy of nucleic acid polymerization and reiterations by complementary reproduction of nucleic acid strands. Sequence repeats in different proteins that could not have come about by chance (here I agree with Darwinians) do arise quite naturally from untargeted reiteration in the primordial pool. 

Part of the EMBL, the European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The mission of the EBI is to ensure that information from molecular biology and genome research is placed in the public domain and is accessible freely to all facets of the scientific community. The Institute manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. 

Comparison of Nucleic Acids from Microorganisms Sequencing Approaches... 

The covalent structure of nucleic acids accounts for their ability to carry information in the form of a sequence of bases along a nucleic acid chain. Other features of nucleic acid structure facilitate the process of replication —that is, the generation of two copies of a nucleic acid from one. These features depend on the ability of the bases found in nucleic acids to form spe-cific base pairs in such a way that a helical structure consisting of two strands is formed. The doublehelical structure of DNA facilitates the replication of the genetic material (Section 5.2.2). 

Some of the bases in DNA and RNA can be chemically modified via methylation. Enzymes, similar to proteases, called exo- and endo-nucleases can cleave RNA and DNA. Exonucleases cleave nucleic acids from the ends. Endonucleases recognize specific sequences of duplex DNA and cleave at a specific site within... 

Step 2 Gene isolation (three alternative methods) Nucleic acid triplet sequencing for amino acid sequence mRNA isolation, with reverse transcriptase and complementary DNA DNA probes from genetic library... 

This chapter illustrates the characterizations of technical procedures necessary in the course of these molecular evaluations, describing our laboratory experience and suggesting different diagnostic approaches microdissection techniques, extraction of nucleic acids from paraffin-embedded tissues, polymerase chain reaction (PCR), direct sequencing, and allelic separation by cloning [4-7],... 

In this section we discuss the change that occur in the melting of DNA and RNA. The term melting is used to refer a thermally induced transition of a double-helical nucleic acid from an ordered double helix to a disordered state. Native RNA is usually single stranded, but it folds back on itself to form double helical sequences. Raman spectroscopy does not appear to be sensitive to the tertiary structure of RNA, but it can tell what fraction of the RNA is in double-helical form. ... 

All macromolecules are chain-like polymers built up from smaller monomers. Usually only one family of subunits is used to construct each chain [3]. Amino acids are hnked to other amino acids to form proteins, sugars are linked to form polysaccharides and nucleic acids are sequences of nucleotides. 

Fig. 5 An overview of different steps involved in microbial community analysis by DGGE (modified after [53]). Nucleic acids from an environmental sample are extracted, amplified and analyzed by DGGE. The obtained bands are cut, re-amplified and then sequenced...

Primary structure of nucleic acids The sequence of bases along the pentose-phosphodiester backbone of a DNA or RNA molecule, read from the 5 end to the 3 end. 

Clones containing genomic DNA of a particular sequence may be identified by plaque hybridization, which is similar in principle to colony hybridization for detection of particular plasmid recombinants. A lawn of E. coli containing several thousand plaques of independent recombinants is blotted on to a nitrocellulose filter. The DNA is released from the blotted recombinant phage, denatured by alkali, and neutralized. A radioactive probe of nucleic acid containing sequences of the gene of interest is then hybridized to the DNA plaques on the filter. Positive plaques, detected by autoradiography as radioactive DNA-RNA or DNA—DNA hybrids, are then picked off and amplified at lower plaque density (approx. 100 per plate). 

If the nucleic acids from the hypocotyl of the soya bean are separated in this way, the following sequence of fractions is obtained (Fig. 17) tRNA, DNA, rRNA, and a further RNA fraction which is presumed to contain mRNA. If the nucleic acids of our sections are analyzed after treatment with 5-fluorouracil, it becomes apparent that the synthesis of tRNA and rRNA is strongly inhibited. In contrast, the synthesis of the supposed mRNA remains unimpaired. This is not the case after treatment with actinomycin Ci. In this instance,-as already mentioned, growth is inhibited, and the synthesis of the supposed mRNA is also strongly im-... 

Each tobacco mosaic virus particle consists of one long thread of nucleic acid embedded in protein. The protein surrounds the nucleic acid in loops or in the fashion of screw threads making up the super-molecule. Treatment with phenol separates nucleic acids from protein. The nucleic acid obtained in this mild way remains infectious, and in a host cell can cause virus multiplication and consequent symptoms of disease. About 95% of the material is protein it consists of individual subunits with a molecular weight of 17,500, which exhibit a marked tendency to aggregate At neutral or slightly acidic pH the protein molecules aggregiite to little rozls, very similar to the intact virus particles both in shape and size. The amino acid sequence is now known. Mutants obtained by nitrous acid treatment (see above) show up differences in the amino acid sequence usually only one amino acid has been replaced, for example, serine by leucine, or leucine by phenylalanine. 

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