The Design and Synthesis ofN4-Anthraniloyl-2′-dC, the Improved Syntheses ofN4-Carbamoyl-andN4-Ureidocarbamoyl-2′-dC, Incorporation into Oligonucleotides and Triplex Formation Testing

Guzzo-Pernell, Nancy; Tregear, G. W.; Haralambidis, Jim; Lawlor, J. M.

doi:10.1080/07328319808004232

Cited by 9 publications

(6 citation statements)

References 51 publications

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“…The exo-amino groups of the cytosine and adenine moieties in oligodeoxyribonucleotides have been used as convenient sites to introduce fluorescence groups [16,17] or to attempt to acquire the triplex-forming ability [18] through carbamoyl-type linkers. However, the base-pairing ability as well as the base-recognition ability of these modified bases having the N-carbamoyl structures has never been examined to date.…”

Section: Full Papermentioning

confidence: 99%

Conformational Studies of 4‐N‐Carbamoyldeoxycytidine Derivatives and Synthesis and Hybridization Properties of Oligodeoxyribonucleotides Incorporating these Modified Bases

et al. 2006

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Deoxycytidine derivatives modified with various N‐substituted carbamoyl groups at the 4‐amino group were synthesized. The detailed 1H NMR studies suggest that the 3′,5′‐O‐disilylated N‐carbamoyldeoxycytidine derivative 11 exists as a species having an intramolecular hydrogen bond between the N3 atom and the carbonyl oxygen atom in MeOD but upon addition of CDCl3, the amount of a homodimer species, having intermolecular hydrogen bonds, gradually increases. Oligodeoxyribonucleotides incorporating various 4‐N‐carbamoyldeoxycytidine derivatives were also synthesized. These modified oligodeoxynucleotides can hybridize with the complementary strands without disturbing the structure of DNA duplexes, hence changing the orientation of the carbamoyl group in such a manner that a stable Watson–Crick base pair can be formed with the guanine base at the opposite site. It should be noted that the base recognition ability (G against T, C and A) of these modified cytosine bases can be preserved satisfactorily. These results suggest that the 4‐N‐carbamoyl group is useful as a backbone structure of the linker between various functional residues and oligonucleotides. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

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Section: Full Papermentioning

confidence: 99%

Conformational Studies of 4‐N‐Carbamoyldeoxycytidine Derivatives and Synthesis and Hybridization Properties of Oligodeoxyribonucleotides Incorporating these Modified Bases

et al. 2006

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“…[35] N 4 -(3-Acetamidopropyl)cytosine (R = NHCOMe), for example, could interact selectively with a CG base pair in the triplex DNA at pH 7.0. The modified cytosine nucleobases shown in parts a and b of Figure 11 were developed for a CG base pair by Guzzo-Pernell's group [39] and by McLaughlin's group, [40] Eur. The synthesis was very distinctive and was achieved by transamination of cytosine in the TFO with propane-1,3-diamine in the presence of sodium bisulfite followed by acetylation.…”

Section: Approaches Based On a Parallel Motifmentioning

confidence: 99%

Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

2012

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Triplex formation with double‐stranded DNA (dsDNA) by oligonucleotides has potential for applications in attractive technologies such as gene therapy and genetic diagnosis. However, triplex‐forming oligonucleotides (TFOs) can only recognize homopurine strands in homopurine‐homopyrimidine regions in dsDNA, either through Hoogsteen or through reverse‐Hoogsteen hydrogen bonds. A straightforward and powerful approach to overcoming this sequence limitation is the development of artificial nucleic acids capable of recognizing specific pyrimidine‐purine interruptions (i.e., a CG or TA base pair) in triplex formation. This review describes artificial nucleic acids, especially those containing non‐natural nucleobases, developed to recognize CG or TA base pairs in dsDNA targets.

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“…21,19 However, the difference in the hybridization properties of triplex forming oligonucleotides conjugated to the previously reported basic peptides and our hydrophobic peptide, reported here, is most likely due to different positive charge densities. Triplex stabilization by polyamine analogues is known to be sensitive to the distance between the consecutive charges in the polyamine chain.…”

Section: Triplex Stability Enhanced By Addition Of Intramolecular Spacermentioning

confidence: 55%

“…[8][9][10][11] However, in an endeavour to extend the base recognition, 18,19 for triple helical DNA, we have previously reported the design and synthesis of a number of modified nucleosides to target the CG base pair of duplex DNA. 20,21 Thus, given our interest in antigene, we have considered the application of the hybrid molecule for triple helical DNA. The peptide of interest is the 17 amino acid hydrophobic ter-minal domain of the viral gp41 protein, known as the gp41b fusion peptide.…”

Section: Introductionmentioning

confidence: 99%

Triple helical DNA formation by a hydrophobic oligonucleotide-peptide hybrid molecule

Guzzo-Pernell¹,

Tregear²

2000

Aust. J. Chem.

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Stable triple helical DNA formation with triplex forming oligonucleotide–peptide hybrids, containing hydrophobic peptides, has previously been difficult to achieve. We report hereon stable triplexation with an oligonucleotide–peptide hybrid containing a hydrophobic peptide. The peptide of interest is the gp41b peptide, which is derived from the hydrophobic terminal domain of the HIV transmembrane glycoprotein gp41. Triplex forming oligonucleotides conjugated to the gp41b peptide were prepared with and without intramolecular spacer linkers. Hybrids with appropriate spacers formed stable triplexes whereas those without the linkers did not. Oligonucleotide–peptide conjugates have several applications mainly in control of gene expression, with the peptide enhancing intracellular delivery of the oligonucleotide. The gp41b peptide is one of a number of candidate peptides considered to be potential delivery vectors. Hence, the data presented here may prove to be useful in designing such conjugates. Our data also extend the list of DNA structures known to stabilize triplexes and suggest that triplexation by oligonucleotide–peptide hybrids may be peptide sequence dependent.

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The Design and Synthesis ofN⁴-Anthraniloyl-2′-dC, the Improved Syntheses ofN⁴-Carbamoyl-andN⁴-Ureidocarbamoyl-2′-dC, Incorporation into Oligonucleotides and Triplex Formation Testing

Cited by 9 publications

References 51 publications

Conformational Studies of 4‐N‐Carbamoyldeoxycytidine Derivatives and Synthesis and Hybridization Properties of Oligodeoxyribonucleotides Incorporating these Modified Bases

Conformational Studies of 4‐N‐Carbamoyldeoxycytidine Derivatives and Synthesis and Hybridization Properties of Oligodeoxyribonucleotides Incorporating these Modified Bases

Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

Triple helical DNA formation by a hydrophobic oligonucleotide-peptide hybrid molecule

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