PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 2528453-2 1989 These ATP analogues can be classified into two conformations, i.e. syn and anti forms with respect to the N-glycosidic bond between adenine and ribose groups of ATP. Adenine 132-139 synemin Homo sapiens 67-70 6280752-3 1982 One of the separated signals corresponds to the syn amino proton relative to the N(1) nitrogen in the adenine ring and the other to the anti one. Adenine 102-109 synemin Homo sapiens 48-51 6498817-7 1984 All five compounds have the syn-conformational relationship between the sugar (ribose or 2"-deoxyribose) and the base (adenine), in contrast to the anti arrangement in B-DNA and in nonalkylated nucleosides. Adenine 119-126 synemin Homo sapiens 28-31 6786734-2 1981 The major structural features are: (a) the adenine and polycyclic aromatic hydrocarbon residues lie nearly perpendicular to one another; (b) the conformation about the glycosidic bond is syn, rather than anti, and an internal hydrogen bond between the deoxyribose 5"-hydroxyl group and N(3) of the adenine residue is present; and (c) the more planar anthracene portion of the hydrocarbon is stacked between adenine residues of other molecules throughout the crystal. Adenine 43-50 synemin Homo sapiens 187-190 22178760-2 2012 When in the template base position during DNA synthesis the 8-oxoG lesion has dual coding potential by virtue of its anti- and syn-conformations, base pairing with cytosine and adenine, respectively. Adenine 177-184 synemin Homo sapiens 46-49 29522114-2 2018 8-oxo-guanine may bind in the anti-conformation with an opposing cytosine or in the syn-conformation with an opposing adenine paired by transversion, and both conformations may alter DNA stability. Adenine 118-125 synemin Homo sapiens 84-87 228755-5 1979 The NMR-DESERT (Deuterium Substitution Effect on Relaxation Times) method has been utilized for the determination of the syn-anti conformational equilibrium in the monomeric state and for the determination of the mutual orientation of the two adenine rings in the dimeric state of cyclic AMP. Adenine 243-250 synemin Homo sapiens 121-124 29675775-7 2018 Formation of excited state A-T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Adenine 129-136 synemin Homo sapiens 125-128 26148061-7 2015 Crystal structure data of the RNA model resolved at 2.3 A reveals non-canonical pairing of adenine in 5 -CAG/3 -GAC motif samples in different syn and anti conformations. Adenine 91-98 synemin Homo sapiens 143-146 25409153-9 2015 This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Adenine 153-160 synemin Homo sapiens 106-109 24418908-0 2014 Does the tautomeric status of the adenine bases change upon the dissociation of the A* A(syn) Topal-Fresco DNA mismatch? Adenine 34-41 synemin Homo sapiens 89-92 24418908-2 2014 We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A* A(syn) Topal-Fresco base mispair (C(s) symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader"s quantum theory of atoms in molecules. Adenine 198-205 synemin Homo sapiens 103-106 24418908-2 2014 We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A* A(syn) Topal-Fresco base mispair (C(s) symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader"s quantum theory of atoms in molecules. Adenine 198-205 synemin Homo sapiens 232-235 20696268-4 2010 The favored glycosidic syn-conformation exposes the Hoogsteen edge of the base for hydrogen bonding with adenine during DNA synthesis. Adenine 105-112 synemin Homo sapiens 23-26 20696268-9 2010 These structures reveal that flexibility around the template-binding pocket can permit 8-oxoG to assume an anti- or syn-conformation and code for cytosine or adenine incorporation, respectively. Adenine 158-165 synemin Homo sapiens 116-119 17264133-7 2007 This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis-syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. Adenine 242-249 synemin Homo sapiens 114-117 20526335-3 2010 The 2.0-A structure of DNA polymerase (pol) beta bound with 8odGTP opposite template adenine indicates that the modified nucleotide assumes the mutagenic syn conformation and that the nonmutagenic anti conformation would be incompatible with efficient DNA synthesis. Adenine 85-92 synemin Homo sapiens 154-157 18829716-5 2008 The flipped thymine is in the usual anti conformation, but the flipped adenine takes the normally unfavorable syn conformation. Adenine 71-78 synemin Homo sapiens 110-113 18029664-3 2007 For example, 8-oxodG in the syn conformation is complementary to adenine in the hydrogen bonding. Adenine 65-72 synemin Homo sapiens 28-31 19191310-6 2009 Diadenosine triphosphate (Ap(3)A) binds with the adenine in syn conformation, the beta-phosphate as the principal P(1) subsite ligand and without order beyond the gamma-phosphate. Adenine 49-56 synemin Homo sapiens 60-63 16084394-7 2005 The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Adenine 4-11 synemin Homo sapiens 54-57 16084394-7 2005 The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Adenine 101-108 synemin Homo sapiens 54-57 12371855-4 2002 Simulations in both explicit and implicit solvent were carried out, with each converging to either anti or syn conformation for adenine and base pairing in all cases. Adenine 128-135 synemin Homo sapiens 107-110 12851932-9 2003 In contrast, in the case of d<pCATTCATT>, the stem is formed by two A-T base pairs with the glycosidic angles of the adenine bases in a syn conformation, most probably forming Hoogsteen base pairs. Adenine 123-130 synemin Homo sapiens 142-145 12459895-0 2003 Cooperative effects in long-range 1,4 DNA-DNA interstrand cross-links formed by polynuclear platinum complexes: an unexpected syn orientation of adenine bases outside the binding sites. Adenine 145-152 synemin Homo sapiens 126-129 12459895-4 2003 NMR analysis of the adduct shows strong H8/H1" intraresidue crosspeaks observed for the A1 and A7 resonances, consistent with a syn conformation for these bases which is usually not observed for adenine residues and bases not directly involved in the cross-link in oligonucleotides. Adenine 195-202 synemin Homo sapiens 128-131 11867468-8 2002 The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Adenine 91-98 synemin Homo sapiens 4-7 12012449-6 2002 A physical mechanism of the anti-like to syn-like conformational transition of the solute PMEA that is due to adenine protonation and the flexibility of the (phosphonomethoxy)ethyl group is proposed and discussed. Adenine 110-117 synemin Homo sapiens 41-44 11747549-10 2002 The results are consistent with the hypothesis that the observed local changes of the double helix structure in A*C are due to the pairing of the oxidized adenine in a syn conformation with the cytosine. Adenine 155-162 synemin Homo sapiens 168-171 11459484-10 2001 The latter stems from conformational heterogeneity involving a syn-anti equilibrium of the glycosidic bond in the modified adenine residue. Adenine 123-130 synemin Homo sapiens 63-66 10772708-3 2000 Formation of the intramolecular pyrophosphate linkage by a conformation-restriction strategy in a syn-form using a halogen substitution at the 8-position of the adenine ring. Adenine 161-168 synemin Homo sapiens 98-101 10860726-6 2000 The overhang residues are looped out and the penultimate adenines of the two residues at the top end (A15) are anti and at the bottom (A7) end are syn. Adenine 57-65 synemin Homo sapiens 147-150 10860726-7 2000 The syn adenine bases form minor groove A*(G.C) base triples with C8-H...N2 hydrogen bonds. Adenine 8-15 synemin Homo sapiens 4-7 8673615-1 1996 The 8-hydroxyguanine:adenine mispairing scheme that spontaneously occurs in vivo through oxidative metabolism of DNA was edited to obtain a pair closely fitting the Watson-Crick geometry in which 2 purine bases of identical structure but oppositely rotated in the syn and anti configurations are hydrogen-bonded. Adenine 21-28 synemin Homo sapiens 264-267 10052954-8 1999 The G.A mispairs are protonated at N1 of the adenines as in the C.A+ mispairs, and two hydrogen bonds in the G(syn).A+(anti) conformation are formed. Adenine 45-53 synemin Homo sapiens 111-114 9746368-0 1998 Characterization of the interaction of myosin with ATP analogues having the syn conformation with respect to the adenine-ribose bond. Adenine 113-120 synemin Homo sapiens 76-79 9746368-1 1998 Numerous analytical experiments have shown that, in solution, ATP analogues with bulky substitutions at the eighth position of the adenine ring predominantly assume the syn conformation with respect to the adenine-ribose bond. Adenine 131-138 synemin Homo sapiens 169-172 9746368-1 1998 Numerous analytical experiments have shown that, in solution, ATP analogues with bulky substitutions at the eighth position of the adenine ring predominantly assume the syn conformation with respect to the adenine-ribose bond. Adenine 206-213 synemin Homo sapiens 169-172 9514254-5 1998 The adenine bases of both the structures are in syn conformation contrasting with the anti geometry in 3"-AMP, 5"-AMP and the enzyme bound state. Adenine 4-11 synemin Homo sapiens 48-51 9438017-15 1998 By contrast, 1H NMR and IR spectra of bromo ester 21 are indicative of syn-conformation of adenine. Adenine 91-98 synemin Homo sapiens 71-74 1930146-24 1991 The stabilization of the A(anti).G(syn) conformation by protons is consistent with models invoking N1 protonation of adenine. Adenine 117-124 synemin Homo sapiens 35-38 8404869-2 1993 Three base pairings are known to occur between adenine and guanine: AH+ (anti).G(syn), A(anti).G(anti) and A(syn).G(anti). Adenine 47-54 synemin Homo sapiens 81-84 8404869-2 1993 Three base pairings are known to occur between adenine and guanine: AH+ (anti).G(syn), A(anti).G(anti) and A(syn).G(anti). Adenine 47-54 synemin Homo sapiens 109-112