Oligonucleotide Analogues with Integrated Bases and Backbone

The thiomethylene‐linked U*[s]U⁽*⁾ dimers 9 – 14 were synthesized by substitution of the 6‐[(mesyloxy)methyl]uridine 6 by the thiolate derived from the uridine‐5′‐thioacetates 7 and 8 followed by O‐deprotection. Similarly, the thiomethylene‐linked A*[s]A⁽*⁾ dimers 9 – 14 were obtained from the 8‐(bromomethyl)adenosine 15 and the adenosine‐5′‐thioacetates 16 and 17 . The concentration dependence of both H? N(3) of the U*[s]U⁽*⁾ dimers 9 – 14 evidences the formation of linear and cyclic duplexes, and of linear higher associates, C(8 or 6)CH₂OH and/or C(5′/II)OH groups favouring the formation of cyclic duplexes. The concentration dependence of the chemical shift for both H₂N? C(6) of the A*[s]A⁽*⁾ dimers 18 – 23 evidences the formation of mainly linear associates. The heteroassociation of U*[s]U⁽*⁾ to A*[s]A⁽*⁾ dimers is stronger than the homoassociation of U*[s]U⁽*⁾ dimers, as evidenced by diluting equimolar mixtures of 11 / 20 and 13 / 22 . A 1 : 1 stoichiometry of the heteroassociation is evidenced by a Job's plot for 11 / 20 , and by mole ratio plots for 9 / 18, 10 / 19, 12 / 21, 13 / 22 , and 14 / 23 .     

Oligonucleotide Analogues with Integrated Bases and Backbones. Part 24

Inspection of Maruzen models and force‐field calculations suggest that oligonucleotide analogues integrating backbone and bases (ONIBs) with an aminomethylene linker form similar cyclic duplexes as the analogous oxymethylene linked dinucleosides. The self‐complementary adenosine‐ and uridine‐derived aminomethylene‐linked A*[n ]U dinucleosides 15 – 17 were prepared by an aza‐Wittig reaction of the aldehyde 10 with an iminophosphorane derived from azide 6 . The sequence‐isomeric U*[n ]A dinucleosides 18 – 20 were similarly prepared from aldehyde 3 and azide 12 . The N‐ethylamine 5 , the acetamides 7 and 14 , and the amine 13 were prepared as references for the conformational analysis of the dinucleosides. In contradistinction to the results of calculations, the N‐ethylamine 5 exists as intramolecularly H‐bonded hydroxyimino tautomer. The association in CDCl₃ of these dinucleosides was studied by ¹H‐NMR and CD spectroscopy. The A*[n ]U dinucleosides 16 and 17 associate more strongly than the sequence isomers 19 and 20 ; the cyclic duplexes of 16 form preferentially Watson–Crick‐type base pairs, while 17, 19 , and 20 show both Watson–Crick‐ and Hoogsteen‐type base pairing. The cyclic duplexes of the aminomethylene‐linked dinucleosides prefer a gg‐orientation of the linker. No evidence was found for an intramolecular H‐bond of the aminomethylene group. The CD spectra of 16 and 17 show a strong, those of 19 a weak, and those of 20 almost no temperature dependence.     

Synthesis of nucleoside aminooxy acids

First nucleoside aminooxy acids were synthesized from furanoid sugar phthalimidooxy acids by N-glycosylation with uracil, thymine, N-benzoylcytosine, 6-N-benzoyladenine and 2-N-acetyl-6-O-diphenylcarbamoylguanine. Boc or Fmoc protected uridine aminooxy acid derivatives have also been prepared. As oxyamine protecting group, the phthalimido group was shown to be instable in MeOH, leading to the imide ring-opening product in a reversible way. This reaction was accelerated under acid or basic conditions. A uridine dimer linked by N-oxy amide has also been prepared by coupling of uridine aminooxy ester with uridine phthalimidooxy acid. These nucleoside aminooxy acids might constitute useful building blocks for the development of novel RNA mimics and conjugates with other biomolecules or reporter compounds.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 32

The G[s ]G dinucleoside 6 and the G[s ]G* dinucleoside 8 were prepared by alkylation of the guanosine thiols derived from 2 and 5 , respectively, by the C(8)‐chloromethylated guanosine 4 that was obtained from alcohol 3 . Dinucleosides 6 and 8 were deacylated to 7 and 9 , and fully deprotected to 10 and 11 , respectively. The G[n ]G dinucleoside 16 was obtained by reductive amination of aldehyde 13 with an iminophosphorane derived from azide 14 and deprotection of the resulting dimer 15 . In the solid state of 6 , and in a solution of 6 and 8 in CDCl₃, H? N(1/I) and H? N(1/II) are engaged in intramolecular H‐bonds to the C?O of the isobutyryl protecting groups, and HN of the isobutyryl group of unit I forms an interresidue, intramolecular H‐bond to N(7/II), leading to a syn orientation of the nucleobase at unit I, to a tg orientation of the sulfanyl moiety, and to an orthogonal orientation of the nucleobases, preventing any base pairing. The silylated and isopropylidenated dinucleosides 7 and 9 are present in DMSO solution as solvated monoplexes. Broad ¹H‐NMR signals of the nucleosides 7 and 16 in CHCl₃ solution evidence equilibrating G‐quadruplexes. The quadruplex formation of 7 and 16 was established by ¹H‐NMR spectroscopy (only of 16 ), vapour pressure osmometry, mass spectrometry, and CD spectroscopy. The C(6(I))‐hydroxymethylated analogue 9 in CDCl₃ and the fully deprotected dinucleosides 10 and 11 in H₂O form only weakly π? π stacked associates, but no G‐quadruplexes, as evidenced by CD spectroscopy.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 16

The self‐complementary, ethylene‐linked U*[c_a]A⁽*⁾ dinucleotide analogues 8, 10, 12, 14, 16 , and 18 , and the sequence‐isomeric A*[c_a]U⁽*⁾ analogues 20, 22, 24, 26, 28 , and 30 were obtained by Pd/C‐catalyzed hydrogenation of the corresponding, known ethynylene‐linked dimers. The association of the ethylene‐linked dimers was investigated by NMR and CD spectroscopy. The U*[c_a]A⁽*⁾ dimers form linear duplexes and higher associates (K between 29 and 114M ^?1). The A*[c_a]U⁽*⁾ dimers, while associating more strongly (K between 88 and 345M ^?1), lead mostly to linear duplexes and higher associates; they form only minor amounts of cyclic duplexes. The enthalpy–entropy compensation characterizing the association of the U*[c_x]A⁽*⁾ and A*[c_x]U⁽*⁾ dimers (x=y, e, and a) is discussed.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 15

The self‐complementary (Z)‐configured U*[c_e]A⁽*⁾ dinucleotide analogues 6, 8, 10, 12, 14 , and 16 , and the A*[c_e]U⁽*⁾ dimers 19, 21, 23, 25, 27 , and 29 were prepared by partial hydrogenation of the corresponding ethynylene linked dimers. Photolysis of 14 led to the (E)‐alkene 17 . These dinucleotide analogues associate in CDCl₃ solution, as evidenced by NMR and CD spectroscopy. The thermodynamic parameters of the duplexation were determined by van't Hoff analysis. The (Z)‐configured U*[c_e]A⁽*⁾ dimers 14 and 16 form cyclic duplexes connected by Watson–Crick H‐bonds, the (E)‐configured U*[c_e]A dimer 17 forms linear duplexes, and the U*[c_e]A⁽*⁾ allyl alcohols 6, 8, 10 , and 12 form mixtures of linear and cyclic duplexes. The C(6/I)‐unsubstituted A*[c_e]U allyl alcohols 19 and 23 form linear duplexes, whereas the C(6/I)‐substituted A*[c_e]U* allyl alcohols 21 and 25 , and the C(5′/I)‐deoxy A*[c_e]U⁽*⁾ dimers 27 and 29 also form minor amounts of cyclic duplexes. The influence of intra‐ and intermolecular H‐bonding of the allyl alcohols and the influence of the base sequence upon the formation of cyclic duplexes are discussed.     

Oligonucleotide Analogues with Integrated Bases and Backbone (ONIB). Part 31

The self‐complementary guanosine‐ and cytidine‐derived aminomethylene‐linked C*[n ]G dinucleoside 9 was synthesized by reductive amination of aldehyde 3 with an iminophosphorane derived from azide 7 . Deacylation of 9 gave the isopropylidene‐protected dinucleoside 10 . The sequence‐isomeric G*[n ]C dinucleoside 11 was similarly prepared from aldehyde 8 and azide 5 , and deacylated to 12 . The association of 10 and 12 in CHCl₃ or in CHCl₃/DMSO mixtures, and the structure of the associates were studied by ¹H‐NMR, ESI‐MS, CD, and vapor pressure osmometry (VPO). Broad ¹H‐NMR signals of dinucleosides 10 and 12 evidence an equilibrium between duplexes and quadruplexes (Hoogsteen base pairing between the Watson? Crick base‐paired duplexes). The quadruplex dominates for the G*[n ]C dinucleoside 12 between ?50° and room temperature. The sequence‐isomeric C*[n ]G 10 forms mostly only a cyclic duplex in CDCl₃ and in CDCl₃/(D₆)DMSO 9 : 1.