Universal base analogues and their applications in DNA sequencing technology

Abstract

Universal base analogues are an important class of compounds which pair with all natural bases without discrimination. Since 1990s, a variety of compounds known as universal bases, including hypoxanthine, nitroazoles, isocarbostyril analogues, azole carboxamides and aromatic triazole analogues have been developed and employed in degenerate PCR primers, microarray probes, ligation and triplexes. There are a number of excellent reviews on the applications of universal base analogues in biochemistry and molecular biology, but their use in DNA sequencing has been overlooked, which was the original impetus for the authors to develop universal bases. In this manuscript, the status quo of universal base analogues and their applications in DNA sequencing are discussed, including Sanger sequencing, sequencing by hybridization, sequencing by ligation and sequencing by recognition tunneling. This should be of interest to those working in DNA sequencing technologies, molecular recognition and molecular biology.

Conformational Preferences of 2-Acylpyrroles in Light of FT-IR and DFT Studies

“…However, the spectrum of the synthetic compound differs slightly from the spectra of the compound of natural origin [21]. In such cases, it is helpful to know the structure of small structural elements that build large molecules of natural origin [22,23].…”

“…ΔE cis/trans of 2-substituted pyrroles vary in a range of 1.06-8.04 kcal/mol. ΔE cis/trans of the N-H moieties (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19) range from 1.06 to 5.15, whereas those of the N-CH 3 moieties [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] range from 1.93 to 8.08 kcal/mol. The lowest energy difference bacteria [9][10][11].…”

“…However, the spectrum of the synthetic compound differs slightly from the spectra of the compound of natural origin [21]. In such cases, it is helpful to know the structure of small structural elements that build large molecules of natural origin [22,23].It is noted that pyrrol-2-yl carbonyl compounds consist of parallel aligned N-H and C=O groups separated by one carbon atom. It promotes the formation of centrosymmetric dimers with two equivalent N-H … O hydrogen bonds [24].…”

Molecular-Size Fluorescence Emitters

“…They found applications in probing the local structure and dynamics of nucleic acids, typing single nucleotide polymorphism (SNP), investigations of DNAproteins interactions, to name a few (Sinkeldam et al 2010;Wilson and Kool 2006). Universal nucleoside analogues, which form stable base pairs with all natural nucleobases without discrimination, are especially important in the probing of nucleic acids (Liang et al 2013). A nucleoside analogue incorporating a 3-hydroxychromone fluorophore as a nucleobase mimic was synthesized and incorporated into oligonucleotide chains (Dziuba et al 2012).…”

Optimization of the Alkyl Linker of TO Base Surrogate in Triplex‐Forming PNA for Enhanced Binding to Double‐Stranded RNA

“…[14][15][16] As with TO, nucleobase analogues that pair with any natural bases in an on-discriminatory manner,o ru niversal bases, [17] are very important analyticalt ools. Such compounds can be recognized as an extended genetica lphabet, and they have been utilized in the design for primers in the polymerase chain reaction (PCR) [18][19][20] and hybridization probes. [18,19,21] Fluorescent universal bases, such as pyrene, [22,23] um, [24,25] and 7-(2,2'-bithien-5-yl)imidazo [4,5-b]pyridine( Dss) [26] have also been reported, offering ag reat opportunity for sequence-selective detection of target DNA or RNA for the purpose of gene analysis.…”