Nucleobase

Under oxidative conditions, certain nucleobases (for example, adenine and cytosine) can form N-oxides. Also, the C8 position of guanosine is vulnerable to hydrolytic attack under either strongly acidic or strongly alkaline conditions. The 5,6 double bond of pyrimidine nucleosides also reacts with halogens and halohydrins to give the corresponding addition products (Shabarova and Bogdanov, 1994). Selected examples of the side reactions that occur during oligonucleotide synthesis are given below. Tri-O-acetyluridine (S.1) reacts with MSNT to produce the triazolo derivative S.2 (Figure 2.1.2; Reese and Ubasawa, 1980). During deprotection with ammonium hydroxide, S.2 gives cytidine (S.3). Interestingly, during deprotection with either the tetramethylguanidinium…

Review of Stacking Interactions of Nucleobases: NMR Investigations by H. Sapper and W. Lohmann Introduction Nuclear magnetic resonance (NMR) spectroscopy is often a very useful tool to identify organic molecules based on the atomic nuclei interactions with their environment. Recent advances have made use of the technology in protein, nucleic acid, and complex natural products structure identification. [1, 2, 3] Its origins lie in the works of Felix Bloch and Edward Purcell, who used the…

The cyano-ethoxy carbonyl protection Manoharan et al. (1999) developed 2(cyanoethoxycarbonyloxy)succinimide S.27a a stable, crystalline, and convenient reagent for the protection of pendant akylamines in oligonucleotides (Figure X.X.X). The 2-cyanoethyl (ce) group is the most common phosphate protecting group in oligonucleotides; however, ce and corresponding 2-(cyanoethoxycarbonyl) group were not utilized for the nucleobase protection until 2000. Merk et al. (2000) developed…

It is also conceivable that, at lower pH, depurination can occur via protonation of the purine nucleobase at both N1 and N7. The presence of the 2′-OH has a significant effect on the nucleoside’s susceptibility to depurination. For example, guanosine and adenosine are more resistant to depurination compared to deoxyadenosine and deoxyguanosine. Deoxyadenosine itself depurinates 1200 times faster than adenosine (York, 1981). Interestingly, N-acyl-protected purine nucleosides (particularly…

these degenerate copies, a ORF-prediction cassette with the consensus CsRn1 sequence (CsRn1cons) was constructed, where the consensus gag-pol boundary sequence (from positions 951 to 1433) was replaced with the corresponding region of each CsRn1 copy (fig. 1A). Interestingly, all the 14 sequences were divided into two groups according to their expression strategy; one of which had a single fused ORF (8 copies, 57.1%; Variant A), whereas the other had two overlapping ORFs by -1 frame (6 copies,…

gene is known to be roughly 500 base pairs, therefore a DNA size standard was used that ranged from 50-766 bas pairs. A control is usually used that exhibits no florescence.(Holbrook & Leicht, 2014). There are many different types of software used for sequencing DNA and alighting these sequences. FinchTV is a program that allows one to view DNA sequences trace. This program gives off a chromatogram that has an estimated DNA sequence that can be corrected through analysis of the peaks. Each…

instrument is capable of viewing and exploiting the response of documents/inks when exposed to light of various wavelengths. This is useful for the examination and comparison of inks, security features in documents such as passports and driving licences, and the examination of altered or obliterated entries. 3D Forensic Facial Reconstruction, 3D facial reconstruction takes human remains and extends a possible physical appearance. 3d facial reconstruction is the process of recreating the face of…

“In the beginning was the Word, and the Word was with God, and the Word was God” (John 1:1) and I believe the word was ATGCU. The primary or canonical, nucleobases are cytosine (DNA and RNA), guanine (DNA and RNA), adenine (DNA and RNA), thymine (DNA) and uracil (RNA), abbreviated as C, G, A, T, and U, respectively with their ability to selectively bind formed the basis of life on earth. In 2012 with the discovery of CRISPR/Cas9 science acquired the ability to insert, delete and replace DNA…

clay catalyst. Eventually, these ribonucleotides formed RNA, which, through time, began to fold and replicate itself. As replication got faster, RNA's started to attract amino acids and hold them together. Bonds started forming, and proteins were able to be produced. As more years passed, a lipid membrane enclosed the structure to protect the RNA and proteins, and DNA took RNA's place due to DNA's superior stability. Before metabolism was established, RNA was created and began replicating itself…

3) Reactions were incubated in suitable condition 4) labelled Cas9 was separated from free dye by size-exclusion chromatography. Forster resonance energy transfer (FRET) is a technique used to determine structural and conformational changes and rearrangement in Cas9 protein structure when bind to sgRNA or DNA. They labelled specific residues (in this case in position of D435 and E945) in Cas9 and during binding of sgRNA to Cas9, monitored the transferred energy. They…