PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 10793758-5 1974 It is concluded that the flexibility of the glycosidic linkage in conjunction with the pseudo-rotation of the sugar residue is responsible for these changes; the thermodynamic values which can be deduced from these decreases are compatible with an oscillatory motion around the glycosidic bond, but exclude anti-syn transformations in pyrimidine nucleosides. Sugars 110-115 synemin Homo sapiens 312-315 7370262-4 1980 In the absence of any such hydrogen bonding, the imidazole nucleosides expectedly exhibit nearly "free" rotation around the glycosyl bond for the commonly found C(3") endo and C(2") endo sugar ring conformations, thus increasing the probability of anti in equilibrium high-anti in equilibrium syn conformational interconversions as compared to common purine and pyrimidine nucleosides. Sugars 187-192 synemin Homo sapiens 293-296 497209-8 1979 The comparison has been extended to syn nucleosides which show opposite trends in the sugar conformation and g+ distribution. Sugars 86-91 synemin Homo sapiens 36-39 626748-8 1978 It is considered that the bulky, tetrahedral, neutral 8-substituent, with an effective van der Waals radius of 3.5--4.0 A, provides an adenosine analogue which should exhibit the syn conformation about the glycosidic bond in solution as well as in solid state, irrespective of the nature of the sugar pucker. Sugars 295-300 synemin Homo sapiens 179-182 856281-4 1977 The purine base ring was shown to be in a predominant syn conformation with respect to the sugar ring by 100 MHZ 1H nuclear Overhauser experiments, by analysis of 3J(13C,H1") magnitudes observed in proton-coupled 13C NMR experiments and by CD measurements. Sugars 91-96 synemin Homo sapiens 54-57 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. Sugars 74-79 synemin Homo sapiens 125-128 22962845-8 2013 For the first time purine-purine planar H-bonded mispairs containing Hyp in the anti-orientation with respect to the sugar moiety--Hyp Ade(syn), Hyp Gua*(syn), and Hyp Gua(syn), that closely resembles the geometry of the Watson-Crick base pairs, have been suggested as the source of transversions. Sugars 117-122 synemin Homo sapiens 141-144 29861990-2 2016 A general and highly syn-stereoselective aldol reaction directed by the "super silyl" group catalyzed by triflimide (HNTf2) is developed providing alpha,beta-dioxyaldehydes and 1,2,3-triol fragments which can be a useful platform for the elaboration of natural and unnatural sugar derivatives. Sugars 275-280 synemin Homo sapiens 21-24 27308197-3 2015 The methodology presented can be expanded to the synthesis of various higher sugars by means of syn-selective carbon-carbon-bond-forming aldol reactions promoted by primary-based organocatalysts. Sugars 77-83 synemin Homo sapiens 49-52 28986322-3 2017 Since the SYN-004 drug substance is a buffered liquid, several binder excipients in different ratios were tested to facilitate binding of SYN-004 to sugar spheres. Sugars 149-154 synemin Homo sapiens 138-141 22962845-8 2013 For the first time purine-purine planar H-bonded mispairs containing Hyp in the anti-orientation with respect to the sugar moiety--Hyp Ade(syn), Hyp Gua*(syn), and Hyp Gua(syn), that closely resembles the geometry of the Watson-Crick base pairs, have been suggested as the source of transversions. Sugars 117-122 synemin Homo sapiens 158-161 22962845-8 2013 For the first time purine-purine planar H-bonded mispairs containing Hyp in the anti-orientation with respect to the sugar moiety--Hyp Ade(syn), Hyp Gua*(syn), and Hyp Gua(syn), that closely resembles the geometry of the Watson-Crick base pairs, have been suggested as the source of transversions. Sugars 117-122 synemin Homo sapiens 158-161 18092770-4 2008 At 420 K in the majority of conformers, the base is anti oriented and the population of North (N) sugars increases: syn/anti=39.3%:60.7% and S/N=63.0%:37.0%. Sugars 98-104 synemin Homo sapiens 116-119 21873463-3 2011 Occasionally, nucleobases in these regions populate the syn conformation wherein the base resides close to or over the ribose sugar, which leads to a more compact state. Sugars 126-131 synemin Homo sapiens 56-59 20387889-2 2010 This first total synthesis, which proceeds in 8.2% yield over 23 steps, features two 1,4-syn boron aldol reactions, a Sonogashira coupling, and an alpha-glycosylation to append the L-evalose sugar moiety. Sugars 191-196 synemin Homo sapiens 17-20 22827513-1 2013 Radical cationic repair process of cis-syn thymine dimer has been investigated when (1) sugar-phosphate backbones were substituted by hydrogen atoms, (2) phosphate group was substituted by two hydrogen atoms each on a sugar ring and (3) sugar-phosphate backbone was taken into account. Sugars 88-93 synemin Homo sapiens 39-42 26286151-1 2012 Nucleosides that consist of base and sugar moieties can adopt two main conformations, syn and anti, about the glycosidic bond. Sugars 37-42 synemin Homo sapiens 86-89 26286151-3 2012 In guanosine, syn conformation is preferred as a result of internal hydrogen bonding between the 5"-OH group of the sugar and the N3 site of the guanine moiety. Sugars 116-121 synemin Homo sapiens 14-17 19726854-0 2009 A toyocamycin analogue with the sugar moiety in a syn conformation. Sugars 32-37 synemin Homo sapiens 50-53 19191710-8 2009 Finally ROM-RCM of 10a-d and 11a-d with Grubbs" catalyst afforded the cis-syn-cis and cis-anti-cis bicyclo-annulated sugars 21a-d and 23a-d, respectively, containing 7-9 membered rings. Sugars 117-123 synemin Homo sapiens 74-77 18092770-3 2008 Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti=62.3%:37.7% and S/N=77.2%:22.8%. Sugars 62-67 synemin Homo sapiens 0-3 18092770-3 2008 Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti=62.3%:37.7% and S/N=77.2%:22.8%. Sugars 62-67 synemin Homo sapiens 90-93 17655217-4 2007 Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature: syn/anti = 61.6%:38.4% and S/N = 74.5%:25.5%. Sugars 62-67 synemin Homo sapiens 0-3 18776272-1 2008 Chiral syntheses of a series of hexahydroisobenzofuran (HIBF) nucleosides have been accomplished via glycosylation of a stereo-defined (syn-isomer) sugar motif with the appropriate silylated bases. Sugars 148-153 synemin Homo sapiens 7-10 17655217-5 2007 However, at 420 K, the majority of conformers contain anti base and the population of North (N) sugars increases: syn/anti = 38.0%:62.0% and S/N = 59.5%:40.5%. Sugars 96-102 synemin Homo sapiens 114-117 17655217-4 2007 Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature: syn/anti = 61.6%:38.4% and S/N = 74.5%:25.5%. Sugars 62-67 synemin Homo sapiens 98-101 12643728-8 2003 The change in the sugar pucker from S to N decreases (3)J(C2/4-H1") and (3)J(C6/8-H1"), while increasing (1)J(C1"-H1") for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. Sugars 18-23 synemin Homo sapiens 127-130 16852085-4 2005 It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. Sugars 138-143 synemin Homo sapiens 20-23 16852085-4 2005 It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. Sugars 138-143 synemin Homo sapiens 185-188 16852085-4 2005 It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. Sugars 150-155 synemin Homo sapiens 20-23 16852085-4 2005 It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. Sugars 150-155 synemin Homo sapiens 185-188 15690428-9 2005 With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3"-endo) conformation, and the C3"-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop. Sugars 49-55 synemin Homo sapiens 113-116 14961666-2 2004 Oligodeoxynucleotides (ODNs) modified by (Br)G were synthesized as Z-DNA in which the syn-conformation deoxyguanosine is stabilized by steric interference between the 8-bromo group of (Br)G and the sugar moiety. Sugars 198-203 synemin Homo sapiens 52-55 12758081-4 2003 Besides, the sugar pucker of the syn cytidine is still located in the regular C2"-endo domain, unlike the C3"-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. Sugars 13-18 synemin Homo sapiens 33-36 6498175-6 1984 Conformational analysis by means of 1H NMR spectroscopy showed that, in dimethyl sulfoxide, the sugar ring exhibits a marked preference for the C(2")-endo conformation (approximately 70%) and a conformation about the glycosidic bond predominantly syn (approximately 90%), hence similar to that in the solid state. Sugars 96-101 synemin Homo sapiens 247-250 11870304-1 2002 In the title compound, C(13)H(13)N(5)O(4) x H(2)O (4,5"-cyclowyosine x H(2)O), the cyclization forces a syn arrangement of the aglycon with respect to the sugar moiety. Sugars 155-160 synemin Homo sapiens 104-107 7647551-1 1995 The effect of the glycosidic torsion angle on 13C and 15N shifts of the sugar and base moieties of guanosine nucleotides was investigated by comparing the sites in two model G-tetrad oligodeoxynucleotides that contain guanosine residues alternately with syn and anti bases. Sugars 72-77 synemin Homo sapiens 254-257 7742328-6 1995 The syn glycosidic torsion angle at [AF]dG6 is supported by both carbon and proton chemical shift data for the sugar resonances of the modified guanine residue. Sugars 111-116 synemin Homo sapiens 4-7 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. Sugars 72-77 synemin Homo sapiens 28-31 9669563-4 1998 For these sugar puckers the difference between the minimum energies of the anti and syn conformations is in the range of 0.1-2.0 kcal/mole, with the minimum syn energy being lower in the case of the 4E, 1E and 2E sugar puckers. Sugars 10-15 synemin Homo sapiens 84-87 9669563-4 1998 For these sugar puckers the difference between the minimum energies of the anti and syn conformations is in the range of 0.1-2.0 kcal/mole, with the minimum syn energy being lower in the case of the 4E, 1E and 2E sugar puckers. Sugars 10-15 synemin Homo sapiens 157-160 9669563-4 1998 For these sugar puckers the difference between the minimum energies of the anti and syn conformations is in the range of 0.1-2.0 kcal/mole, with the minimum syn energy being lower in the case of the 4E, 1E and 2E sugar puckers. Sugars 213-218 synemin Homo sapiens 84-87 9669563-4 1998 For these sugar puckers the difference between the minimum energies of the anti and syn conformations is in the range of 0.1-2.0 kcal/mole, with the minimum syn energy being lower in the case of the 4E, 1E and 2E sugar puckers. Sugars 213-218 synemin Homo sapiens 157-160 9669563-5 1998 It is particularly significant that cytosine can assume the syn conformation for the 3E sugar pucker commonly observed for the syn nucleotides in Z-DNA with both alternating pyrimidine/purine (APP) and non-APP sequences. Sugars 88-93 synemin Homo sapiens 60-63 9669563-5 1998 It is particularly significant that cytosine can assume the syn conformation for the 3E sugar pucker commonly observed for the syn nucleotides in Z-DNA with both alternating pyrimidine/purine (APP) and non-APP sequences. Sugars 88-93 synemin Homo sapiens 127-130 8527437-6 1995 The syn glycosidic torsion angle at [AF]dG6 is supported by both carbon and proton chemical shift data for the sugar resonances of the modified deoxyguanosine residue. Sugars 111-116 synemin Homo sapiens 4-7 8257675-13 1993 In general, it appears that in order to relieve the energetically unfavorable steric contacts between the cytosine base in the syn conformation and the deoxyribose sugar, the base is forced into a highly buckled conformation, and that this large buckle in turn alters the conformation of neighboring residues. Sugars 164-169 synemin Homo sapiens 127-130 1617149-4 1992 The conformation of the sugars and glycosidic torsion angles are S type and syn, respectively. Sugars 24-30 synemin Homo sapiens 76-79 3248218-2 1988 In some energy minima corresponding to the arrangement of the bases with one of the bases being in the syn-orientation with respect to the sugar two bases are linked through one H-bond and one or two water bridges. Sugars 139-144 synemin Homo sapiens 103-106