Polymerase recognition of 2-thio-iso-guanine·5-methyl-4-pyrimidinone (iGs·P)—A new DD/AA base pair

Abstract

Polymerase specificity is reported for a previously unknown base pair with a non-standard DD/AA hydrogen bonding pattern: 2-thio-iso-guanine·5-methyl-4-pyrimidinone. Our findings suggest that atomic substitution may provide a solution for low fidelity previously associated with enzymatic copying of iso-guanine.

Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo

“…Substitution of ap olar functional group (NH 2 ,O H) of nucleobases by am ethyl group at positions that are normally involved in H-bonding of canonical bases (the 6-carbonylg roup of pyrimidine base, the 2-amino and 6-carbonyl group of purine base) readily leads to orthogonality (absence of base pairing with canonical bases). As demonstrated with the T H :G S base pair [16] base pairingb etween methylated bases or bases with at hiocarbonyl group might easier occur when aH -atom is present in the opposite base (Figure 1c). However,t he latter bases might not be really orthogonal.…”

“…Leu Ala Pro Cys His Ala ON 16,20,24 5'-p-C TA GC* CCG TGCC AT GCA À3' ON 17,21,25 5'-p-C TA GC* C*GT GC CATG CA À3' ON 18, 22,26 5'-p-C TA GC** CG TGCC AT GCA À3' ON 19,23,27 5'-p-C TA GC** * GT GC CATG CA À3' Table 8. In vivo recognition of modified bases by canonical bases in the GCG (Pro) codon (aa:amino acid).…”

“…As econd small hydrophobic functionality that is involved in this study is at hiocarbonyl group (replacing ac arbonyl group),f or its potential to interact with the methyl group present in opposite bases in ad uplex.B yi ntroducing such methyl and thiocarbonyl group, we willm ake the major (or minor groove) more hydrophobic which may not be favourable for duplex stabilization and could contribute to orthogonality.H owever,t here are severalp recedents of the involvement of ah ydrophobic thiocarbonyl group in base pair stabilization and some natural t RNA contain sulphur modifiedn ucleobases such as 2-thio-U, 4-thio-U,2 -thio-C. [13] Rappaport has studied the 6-thioguanine (G S ): 5-methyl-2-pyrimidone (T H )b ase pair (Figure 1a). [14] The laboratory of Switzer has investigated the 2-thio-isoguanine (iG S ):5-methyl-isocytosine (iC Me )b ase pair [15] (Figure 1b)a nd the 2-thio-isoguanine(iG S ):5-methyl-4-pyrimidone (P) [16] base pair (Figure 1c). In all these cases the thiocarbonyl group was placed opposite an NH 2 group or an H-atoma nd the stability of the base pair (G S :T H , iG S :iC Me and iG S :P)w as found to be similart ot he canonical A:Tp air.…”

A concise synthesis of isoguanine 2ʹ-deoxyriboside and its adenine-like triplex formation when incorporated into DNA

“…Although not a DNA base, isoguanine (isoG) occurs naturally and various methods have been reported for the preparation of derivatives [1][2][3][4] including its riboside, 5 2'-deoxyriboside [6][7][8][9] and other analogues. 10,11 Isoguanine has been widely studied and when incorporated into nucleic acids, [12][13][14][15][16][17][18][19][20][21][22][23] has been shown to form stable base pair 7,[24][25][26][27][28] (Figure 1 left) and triplex motifs 29 (Figure 1 middle) as its N1-H tautomer. These experimental observations are supported by theoretical calculations.…”

Disclosing the role of C4-oxo substitution in the photochemistry of DNA and RNA pyrimidine monomers: Formation of photoproducts from the vibrationally-excited ground state

“…This modified nucleobase has been proposed together with 2-thio-iso-guanine as a nonstandard Watson-Crick base pair, successfully recognized and copied by polymerase. 12 Interestingly, 4OPy also appears in the list of potential nucleobase ancestors suggested by Cafferty and Hud 10 and has been identified in model prebiotic reactions. [13][14][15][16] In fact, 4OPy was identified, in significant amounts, as a product of the condensation reaction of formamide catalyzed by cosmic dust analogues 15 or alumina and silica, both used as model inorganic oxides present in early Earth.…”