pH-Dependent Assembly of DNA–Gold Nanoparticles Based on the i-Motif: A Switchable Device with the Potential of a Nanomachine

Seela, Frank; Budow, Simone

doi:10.1002/hlca.200690189

Cited by 23 publications

(23 citation statements)

References 29 publications

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“…The immobilization of 19 on the 15 nm gold nanoparticles was performed as described recently. 50 Prior to functionalization, the pH of the gold nanoparticle solution was raised from pH 5.5 to pH 9.5 avoiding i-motif formation of the non-bound oligonucleotides. The DNA-modified gold nanoparticle sample 20 was prepared by mixing the alkaline gold nanoparticle solution (6.4 ml) with the oligonucleotide solution of 19 (3.5 ml) obtained after trityl group removal and purification.…”

Section: Preparation and Properties Of Dna-gold Nanoparticle Conjugatesmentioning

confidence: 99%

Oligonucleotides forming an i-motif: the pH-dependent assembly of individual strands and branched structures containing 2′-deoxy-5-propynylcytidine

2007

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Non-branched and branched oligonucleotides incorporating consecutive runs of 2'-deoxy-5-propynylcytidine residues () instead of 2'-deoxycytidine () were synthesized. For this, phosphoramidite building blocks of 2'-deoxy-5-propynylcytidine () were prepared using acetyl, benzoyl or N,N-di-n-butylaminomethylidene protecting groups. The formation of the i-motif assemblies incorporating 2'-deoxy-5-propynylcytidine residues was confirmed by temperature-dependent CD- and UV-spectra as well as by ion-exchange chromatography. The low pK(a)-value of nucleoside (pK(a) = 3.3) compared to dC (pK(a) = 4.5) required strong acidic conditions for i-motif formation. Branched oligonucleotide residues with strands in a parallel orientation lead to a strong stabilization of the i-motif allowing aggregation even at non-optimal pH conditions (pH = 5). The immobilization of oligonucleotides incorporating multiple residues of on 15 nm gold nanoparticles generated DNA-gold nanoparticle conjugates which are able to aggregate into i-motif structures at pH 5.

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Section: Preparation and Properties Of Dna-gold Nanoparticle Conjugatesmentioning

confidence: 99%

Oligonucleotides forming an i-motif: the pH-dependent assembly of individual strands and branched structures containing 2′-deoxy-5-propynylcytidine

2007

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“…Recent interest has been shown in the study of i-motif structures due to their potential application in nanotechnology [9][10][11][12] and their possible roles in gene transcription [13]. Although low pH favours the formation of i-motif structures and they have not been reported in vivo, the sequences with the potential to form i-motifs are frequent in the human genome.…”

Section: Introductionmentioning

confidence: 99%

Solution equilibria of the i-motif-forming region upstream of the B-cell lymphoma-2 P1 promoter

et al. 2007

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The 5'-end of the P1 promoter of the B-cell lymphoma-2 (bcl-2) gene contains a highly guaninecytosine-rich region, which has a role in the regulation of bcl-2 transcription. Whereas the guanine-rich region has been the focus of recent studies, little attention has been paid to the cytosine-rich strand. Here we examine the structural transitions of the cytosine-rich sequence by means of acid-base, mole-ratio and melting experiments monitored by molecular absorption, circular dichroism, and NMR spectroscopies. Two intramolecular i-motif structures have been detected in the pH range 2-7, with maximal formation at pH 4 and 6, respectively. At pH 7.6 the majority species has been associated with a hairpin involving Watson-Crick base pairs. Upon addition of the quadruplex-interacting ligand TmPyP4, bcl-2c structures at pH 6.1 and 7.6 yield identical interaction species with stoichiometries 1:2 (DNA:ligand) and logarithms of formation constant 12.4+/-0.2 and 11.7+/-0.1, respectively. The initial i-motif structure at pH 6.1 is lost upon interaction with TmPyP4.

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“…[6] The oligonucleotides 1-3 were immobilized on the surface of 15 nm gold nanoparticles according to the procedure TABLE 1 Thiol-modified oligonucleotides 1-3 utilized for the immobilization on gold nanoparticles, DNA gold nanoparticle conjugates 4-6, and the branched oligonucleotide 7 described previously. [3] The resulting DNA gold nanoparticle conjugates 4-6 ( Table 1) …”

Section: Functionalization Of Gold Nanoparticlesmentioning

confidence: 99%

“…[2] Recently, our laboratory reported on the immobilization of cytosine-rich oligonucleotides on 15 nm gold nanoparticles. [3] Cytosine-rich oligonucleotides form a complex tetrameric structure (i-motif) under weak acidic conditions that is stabilized by the intercalation of two parallel duplexes and hemiprotonated base pairs 756 F. Seela and S. Budow (dC·dCH + ) ( Figure 1, motif I). [4] The construction of a DNA gold nanoparticle sytem based on the pH-dependent four strand assembly of the i-motif generates a switchable nanoscopic device.…”

Section: Introductionmentioning

confidence: 99%