Conformational Control of Dual Emission by Pyrrolidinyl PNA–DNA Hybrids

Sezi, Sabrina; Varghese, Reji; Vilaivan, Tirayut; Wagenknecht, Hans‐Achim

doi:10.1002/open.201200016

Cited by 7 publications

(3 citation statements)

References 31 publications

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“…Over the many years, because of the sensitivity of pyrene fluorescence to its environment, pyrene and its derivatives have been frequently utilized as a fluorescence probe for the detection of the dynamics or structural properties of synthetic polymers, 1,2 phospholipids, 3-6 polypeptides [7][8][9] and DNA. [10][11][12][13][14] Recently, pyrene and its π-stack assembly have attracted much interest in applications as organic semiconductors. 15 Organized pyrene π-stacks are important to control their electronic properties, such as the energy gap and charge carrier mobility in the development of electronic and optoelectronic devices.…”

Section: Introductionmentioning

confidence: 99%

Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence

et al. 2012

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The binding and fluorescence properties of complementary RNA sequences attached to different numbers of pyrenes via one carbon linker at the 2'-O-positions have been investigated. Upon hybridization of the pyrene-modified RNA sequences, the modified RNA duplexes with normal thermal stability are formed, and the pyrene arrays are assembled in an inter-strand manner. Because hypochromic effects in the pyrene absorption band and the exciton coupled circular dichroism signals were observed for the pyrene assemblies, the formation of the pyrene array occurs via a π-stacking interaction between the pyrene rings. The pyrene assemblies exhibit strong excimer fluorescence that is characterized by a broad and structureless excitation spectrum. Hence, the excimer is a static excimer due to the direct excitation of the associated pyrenes in the ground state. Based on several spectroscopies, it is revealed that the spatial configuration of the pyrenes in the association is more regulated by the increase in the attached pyrene.

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Section: Introductionmentioning

confidence: 99%

Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence

et al. 2012

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“…Understanding factors contributing to these unusual behaviors through a combination of structural and theoretical studies will contribute to targeted, tailored "new generation" pyrrolidinyl PNAs with improved/customizable properties. Finally, while diagnostic applications of pyrrolidinyl PNA have been clearly demonstrated, its therapeutic/biological applications 67 and other areas such as functional materials 68 are only emerging. We invite others to join us as we continue to explore the full potential of utilizing acpcPNA and related pyrrolidinyl PNAs in these cutting-edge research areas and beyond.…”

Section: Discussionmentioning

confidence: 99%

Pyrrolidinyl PNA with α/β-Dipeptide Backbone: From Development to Applications

Vilaivan

2015

Acc. Chem. Res.

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The specific pairing between two complementary nucleobases (A·T, C·G) according to the Watson-Crick rules is by no means unique to natural nucleic acids. During the past few decades a number of nucleic acid analogues or mimics have been developed, and peptide nucleic acid (PNA) is one of the most intriguing examples. In addition to forming hybrids with natural DNA/RNA as well as itself with high affinity and specificity, the uncharged peptide-like backbone of PNA confers several unique properties not observed in other classes of nucleic acid analogues. PNA is therefore suited to applications currently performed by conventional oligonucleotides/analogues and others potentially beyond this. In addition, PNA is also interesting in its own right as a new class of oligonucleotide mimics. Unlimited opportunities exist to modify the PNA structure, stimulating the search for new systems with improved properties or additional functionality not present in the original PNA, driving future research and applications of these in nanotechnology and beyond. Although many structural variations of PNA exist, significant improvements to date have been limited to a few constrained derivatives of the privileged N-2-aminoethylglycine PNA scaffold. In this Account, we summarize our contributions in this field: the development of a new family of conformationally constrained pyrrolidinyl PNA having a nonchimeric α/β-dipeptide backbone derived from nucleobase-modified proline and cyclic β-amino acids. The conformational constraints dictated by the pyrrolidine ring and the β-amino acid are essential requirements determining the binding efficiency, as the structure and stereochemistry of the PNA backbone significantly affect its ability to interact with DNA, RNA, and in self-pairing. The modular nature of the dipeptide backbone simplifies the synthesis and allows for rapid structural optimization. Pyrrolidinyl PNA having a (2'R,4'R)-proline/(1S,2S)-2-aminocyclopentanecarboxylic backbone (acpcPNA) binds to DNA with outstanding affinity and sequence specificity. It also binds to RNA in a highly sequence-specific fashion, albeit with lower affinity than to DNA. Additional characteristics include exclusive antiparallel/parallel selectivity and a low tendency for self-hybridization. Modification of the nucleobase or backbone allowing site-specific incorporation of labels and other functions to acpcPNA via click and other conjugation chemistries is possible, generating functional PNAs that are suitable for various applications. DNA sensing and biological applications of acpcPNA have been demonstrated, but these are still in their infancy and the full potential of pyrrolidinyl PNA is yet to be realized. With properties competitive with, and in some aspects superior to, the best PNA technology available to date, pyrrolidinyl PNA offers great promise as a platform system for future elaboration for the fabrication of new functional materials, nanodevices, and next-generation analytical tools.

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“…Due to its solvatochromic properties, Nile red is a potential candidate to be used in combination with PNA to develop a hybridization probe which not only differentiates between complementary and non-complementary DNA, but can also report on local structural variations. Except for an example from our group on the conformation control of Nile red-labeled DNA by acpcPNA [ 32 ], no combination of the Nile red label and PNA has yet been reported in the literature. It is therefore our purpose to develop a facile method for synthesizing Nile red-labeled acpcPNA based on the click strategy [ 33 – 36 ] and to investigate its optical properties.…”

Section: Introductionmentioning

confidence: 99%

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

Yotapan¹,

Charoenpakdee²,

Wathanathavorn³

et al. 2014

Beilstein J. Org. Chem.

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SummaryDNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.

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Conformational Control of Dual Emission by Pyrrolidinyl PNA–DNA Hybrids

Cited by 7 publications

References 31 publications

Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence

Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence

Pyrrolidinyl PNA with α/β-Dipeptide Backbone: From Development to Applications

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

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