Virtual PCR and DNA sequencing experiment

PCR-DNA Experiment

Abstract- Science and Biology have not been the same since the discovery and subsequent research on the mechanisms of DNA, the gene, and the way that chemicals combine to form traits. Numerous projects have stemmed from the original work, among which the Human Genome Project is possibly the most famous. For our purposes, using a virtual laboratory simulation, DNA samples were extracted and amplified for analysis. Computer analysis found the samples to be pure enough to allow for a strong statistical probability that they were Bartonella henselae, a common animal vector bacterial transfer.

Introduction- DNA, or deoxyribonucleic acid, is a fascinating modern subject that has implications far beyond science and technology. Since 1953, when the double helix was discovered by James Watson and Francis Crick, science has never been the same. In fact, Crick is known to have remarked shortly after they confirmed their findings, "We have found the secret of life!" (Nobel). DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription (Walker and Jones).

Materials and Methods - In this simulation, all laboratory materials were virtual, but the technique and methods were appropriate techniques to sequence DNA. The experiment was designed to first extract DNA, take it through the steps of amplification and detachment, and then prepare it for analysis. The question was what type of bacteria was being sequenced. The steps used were: 1) Extraction of genomic DNA, 2) Amplification of genetic region, 3) Verification, 4) Clean PCR Products, 5) Quantify DNA concentration, 6) Cycle the sequence, and, 7) Precipitate cycle-sequenced products for analysis. In this case, a virtual laboratory was used, with the user being guided to the appropriate tools and equipment (Virtual Bacterial Identification).

Results

Accession

Description

Max score

Total score

Query coverage

E value

Max ident gi|39295|Z11684.1

R.henselae 16S rRNA gene

0.0

gi|6626180|AF214556.1

Bartonella henselae 16S ribosomal RNA, partial sequence

0.0

99%

Discussion- The BLAST search displays the matching sequences in the database in descending order of the degree of the match. Most of the top scorers are either Bartonella henselae or Rochalimaea henselae. The latter is an older name for this species. Bartonella species are demanding in their nutritional requirements for culture; as a result, normal culturing techniques do not yield vigorously growing bacterial colonies.