Base-modified oligodeoxynucleotides. I. effect of 5-alkyl, 5-(1-alkenyl) and 5-(1-alkynyl) substitution of the pyrimidines on duplex stability and hydrophobicity

Sági, János; Szemzö, Attila; Ebinger, Katalin; Szabolcs, Anna; Sági, Gyula; Ruff, Éva; Ötvös, László

doi:10.1016/s0040-4039(00)60379-9

Cited by 66 publications

(27 citation statements)

References 19 publications

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“…50 One exception to this rule is the recent finding that addition of C-5 methyls on cytidines is destabilizing in all-RNA (but not DNA) triple helices. 53 Also in this vein is the finding that pyrimidine C-5 propyne groups are also stabilizing to double (and in some cases, triple) helices, 54,55 although some exceptions are known. 56 For example, addition of propyne to dU thermally stabilizes duplexes with RNA (in one report) by 1.7 °C per substitution and triplexes by 2.4 °C ( Figure 6).…”

Section: A Addition Of Simple Substituents To Dna Basesmentioning

confidence: 99%

“…[50][51][52][53][54][55][56][57][58][59] All the substituents shown are stabilizing relative to deoxyuridine (which has hydrogen at the C-5 position), including the C-5 methyl group of thymidine (1). Structures of deoxycytidine (9) and some modified deoxycytidine nucleosides which have increased surface area by addition of extra rings (10)(11)(12).…”

Section: Figurementioning

confidence: 99%

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Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

1997

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Section: A Addition Of Simple Substituents To Dna Basesmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

1997

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“…The distinct influence of the linkers on thermal stability of DNA helix was supposed to be closely related to their inherent properties. [11,14] In our study, the stabilities of base pairs 3-dT > 4-dT > 1-dT ∼ 2-dT, reflected the contribution of the 7-positioned linkers of 8-aza-7-deaza-2 -deoxyadenosine in the order of propargyl > H > alkyl ∼ (Z )-alkenyl. Computer aided calculation on the duplexes 5·9, 5·12, 5·13 was conducted with AMBER 8.0 (University of California, San Francisco, CA, USA), employing the Amber 2003 force field (15-17) on a SGI Altix 350 workstation (SGI, Freemont, CA, USA).…”

Section: Thermal Stability Of Hydroxyl-functionalized Dna Duplexesmentioning

confidence: 54%

Hydroxyl-Functionalized DNAs with Different Linkers and Their Complmentary Duplex Stability

Zhang

Xu³

et al. 2010

Nucleosides, Nucleotides and Nucleic Acids

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Tert-butyldiphenylsilyl (TBDPS) was testified to be an appropriate orthogonal protecting group for novel 7-hydroxyl-functionalized 8-aza-7-deaza-2'-deoxyadenosine analogues. It was stable in partial and complete hydrogenation reactions used for the different linker preparation. The corresponding phosphoramidites and hydroxyl-functionalized oligodeoxynucleotides were synthesized and identified. The thermal effect of the hydroxyl group with different linkers on DNA duplexes was evaluated. It provided a feasible strategy for the preparation of hydroxyl-functionalized DNAs for the nucleic acid research.

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“…According to our and others' earlier studies on the biophysical and biochemical properties of base-modified DNA-s, the 5-alkynyl substitution of pyrimidine bases results in a significant duplex stabilization [16,17] and a higher resistance to enzymatic cleavage. [18] However, propynyl residues introduced into the 7-position of 8-aza-7-deazapurines were found to be even more stabilizing than those at the 5-position of pyrimidine bases.…”

Section: Introductionmentioning

confidence: 88%

PNA-DNA Chimeras Containing 5-Alkynyl-pyrimidine PNA Units. Synthesis, Binding Properties, and Enzymatic Stability

Bajor

Sági

Tegyey

et al. 2003

Nucleosides, Nucleotides & Nucleic Acids

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Three chimeric dimer synthons (oeg_t(NH)T, oeg_up(NH)T and oeg_uh(NH)T) containing thymine (t), 5-(1-propynyl)-uracil (up) and 5-(1-hexyn-1-yl)-uracil (uh) PNA units with N-(2-hydroxyethyl)glycine (oeg) backbone were synthesized in solution and incorporated into T20 oligonucleotide analogues, using standard P-amidite chemistry. Insertion of dimer blocks led to destabilization of duplexes with dA20 target. The smallest Tm drops were found for chimeras containing oeg_up(NH)T dimers. Incorporation of the chimeric synthons into the 3'-end of T20 brought about growing resistance to 3'-exonucleolytic (SV PDE) cleavage in the order of oeg_t(NH)T < oeg_up(NH)T < oeg_uh(NH)T. Due to different endonuclease activities of 3'- and 5'-exonucleases applied, placing of five consecutive dimers at the 5'-terminus resulted in a relatively smaller, but also side-chain dependent, stabilization towards the hydrolysis by 5'-exonuclease (BS PDE). Neither exonucleases (SV and BS PDE) nor an endonuclease (Nuclease P1) could hydrolyse the unnatural phosphodiester bond linking the 3'-OH of thymidine to the terminal OH of N-(2-hydroxyethyl)glycine PNA backbone.

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Base-modified oligodeoxynucleotides. I. effect of 5-alkyl, 5-(1-alkenyl) and 5-(1-alkynyl) substitution of the pyrimidines on duplex stability and hydrophobicity

Cited by 66 publications

References 19 publications

Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

Hydroxyl-Functionalized DNAs with Different Linkers and Their Complmentary Duplex Stability

PNA-DNA Chimeras Containing 5-Alkynyl-pyrimidine PNA Units. Synthesis, Binding Properties, and Enzymatic Stability

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