Conformational Heterogeneity in PNA:PNA Duplexes

Totsingan, Filbert; Jain, Vipul; Bracken, W. Clay; Faccini, Andrea; Tedeschi, Tullia; Marchelli, Rosangela; Corradini, Roberto; Kallenbach, Neville R.; Green, Mark M.

doi:10.1021/ma902797f

Cited by 28 publications

(38 citation statements)

References 61 publications

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“…The phenomena discussed above will pertain to varieties of systems, consistent with the several examples given above, but within the restriction that chiral information input does not act as a structural modifier 19. There are many more examples in the literature where these general ideas have found value and a proper review of the subject, rather than an overview of the principles as intended here, may be of interest.…”

Section: Discussionmentioning

confidence: 68%

Chiral Cooperativity in Helical Polymers

Jain¹,

Cheon²,

Tang³

et al. 2011

Israel Journal of Chemistry

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Human experience informs us of the two extreme consequences of crowding: random behavior of the individuals, in which each takes a singular path; and cooperative behavior, in which the individuals in the crowd act in a predictable uniform manner, such as in a military organization These extremes find parallels in the crowded situations encountered at the molecular level, exemplified for the former by glassy states, such as often encountered in polymeric materials,1 or for the latter, in the uniform archetypal arrangements of crystals or liquid crystals. Here we review the cooperative characteristics of uniform arrangements that take a chiral form and explore how these characteristics lead to left‐ and right‐handedness. These studies lead us to understand the basis of amplification of chirality in regular arrays, in which small influences have large consequences, and how chiral cooperativity acts in the resolution of conflict between influences favoring left‐ and right‐handedness.2

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Section: Discussionmentioning

confidence: 68%

Chiral Cooperativity in Helical Polymers

Jain¹,

Cheon²,

Tang³

et al. 2011

Israel Journal of Chemistry

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“…It has been shown by some of us that PNA containing three intrinsically chiral monomers, bearing either a D‐ or L‐lysine side chain at the C2–(α) carbon atom, form parallel PNA:PNA duplexes with achiral complementary PNA of handedness opposite to that of the corresponding antiparallel duplexes . Later on, we studied the propagation of the helicity generated by a terminal chiral amino acid in antiparallel PNA:PNA duplexes . In order to better understand the structural features of PNA parallel duplexes and the induction of chirality in these systems by a terminal chiral amino acid, we explored the possibility to use porphyrins covalently linked to the N‐terminus of PNA ( P1P and P2P ) as a CD reporter of supramolecular chirality upon duplex formation (Scheme ).…”

Section: Resultsmentioning

confidence: 99%

“…In recent years, these artificial DNA mimics have also found attractive applications in nanotechnology as programmable helical structures with different helical pitch and increased stability towards chemical and enzymatic degradation, as tools in molecular computing, and as new self‐assembled materials for optical and optoelectronic applications . One of the key features of PNA is the possibility to form homo‐duplexes, where the helix handedness can be controlled by insertion of suitable chiral centers, so that either right‐ or left‐handed helices can be obtained . While the structural features of antiparallel PNA duplexes (formed by two strands with opposite N‐terminus → C‐terminus orientation) have been extensively studied, parallel PNA:PNA duplexes are still not fully characterized .…”

Section: Methodsmentioning

confidence: 99%

Structural Studies on Porphyrin–PNA Conjugates in Parallel PNA:PNA Duplexes: Effect of Stacking Interactions on Helicity

et al. 2015

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Parallel PNA:PNA duplexes were synthesized and conjugated with meso-tris(pyridyl)phenylporphyrin carboxylic acid at the N-terminus. The introduction of one porphyrin unit was shown to affect slightly the stability of the PNA:PNA parallel duplex, whereas the presence of two porphyrin units at the same end resulted in a dramatic increase of the melting temperature, accompanied by hysteresis between melting and cooling curves. The circular dichroism (CD) profile of the Soret band and fluorescence quenching strongly support the occurrence of a face-to-face interaction between the two porphyrin units. Introduction of a L-lysine residue at the C-terminal of one strand of the parallel duplex induced a left-handed helical structure in the PNA:PNA duplex if the latter contains only one or no porphyrin moiety. The left-handed helicity was revealed by nucleobase CD profile at 240-280 nm and by the induced-CD observed in the presence of the DiSC2 (5) cyanine dye at ~500-550 nm. Surprisingly, the presence of two porphyrin units led to the disappearance of the nucleobase CD signal and the absence of CD exciton coupling within the Soret band region. In addition, a dramatic decrease of induced CD of DiSC2 (5) was observed. These results are in agreement with a model where the porphyrin-porphyrin interactions cause partial loss of chirality of the PNA:PNA parallel duplex, forcing it to adopt a ladder-like conformation.

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“…Gupta et al Journal of Biotechnology 259 (2017) 148-159 therapeutics. Totsingan and group (Totsingan et al, 2010) synthesized and studied the chiral optical properties of different oligomers of PNA/ PNA duplexes, where different amino acids were attached at the terminal of a single strand of each duplex. In this statistical theoretical model, it was observed that the PNA/PNA double helix had access to a dynamic ensemble of conformational states in solution which varied as a function of oligomer length.…”

Section: Pna/pna Duplexesmentioning

confidence: 99%

Peptide nucleic acids: Advanced tools for biomedical applications

Gupta

Mishra

Puri³

2017

Journal of Biotechnology

139

120

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Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively. Hence, several methods based on PNAs have been developed for designing various anticancer and antigene drugs, detection of mutations or modulation of PCR reactions. The duplex homopurine sequence of DNA may also be recognized by PNA, forming firm PNA/DNA/PNA triplex through strand invasion with a looped-out DNA strand. PNAs have also been found to replace DNA probes in varied investigative purposes. There are several disadvantages regarding cellular uptake of PNA, so modifications in PNA backbone or covalent coupling with cell penetrating peptides is necessary to improve its delivery inside the cells. In this review, hybridization properties along with potential applications of PNA in the field of diagnostics and pharmaceuticals are elaborated.

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Conformational Heterogeneity in PNA:PNA Duplexes

Cited by 28 publications

References 61 publications

Chiral Cooperativity in Helical Polymers

Chiral Cooperativity in Helical Polymers

Structural Studies on Porphyrin–PNA Conjugates in Parallel PNA:PNA Duplexes: Effect of Stacking Interactions on Helicity

Peptide nucleic acids: Advanced tools for biomedical applications

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