Polycation comb-type copolymer reduces counterion condensation effect to stabilize DNA duplex and triplex formation

Maruyama, Atsushi; Ohnishi, Yu Ichiro; Watanabe, Haruo; Torigoe, Hidetaka; Ferdous, Anwarul; Akaike, Toshihiro

doi:10.1016/s0927-7765(99)00078-8

Cited by 33 publications

(26 citation statements)

References 37 publications

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“…We avoided LNA modifications of S-arms and added PLL- g -Dex ( Fig. 2 a) to improves substrate association since the copolymer stabilizes nucleic acid duplexes by increasing the association rate rather than by decreasing the dissociation rate ( Maruyama et al, 1999 ; Torigoe et al, 1999 ). The addition of the copolymer significantly enhanced the activity of MNAzymes.…”

Section: Resultsmentioning

confidence: 99%

“…Modification of the S-arms of DNAzymes with locked nucleic acids (LNA) improves substrate hybridization as the LNA residues have high binding affinity for complementary DNA and RNA ( Braasch and Corey, 2001 ; Kaur et al, 2007 ; Koshkin et al, 1998 ; Obika et al, 1998 ; Petersen and Wengel, 2003 ) and yields DNAzymes with enhanced cleavage activity relative to unmodified versions ( Donini et al, 2007 ; Kaur et al, 2010 ; Schubert et al, 2003 ; Vester et al, 2002 ). We reported that the addition of cationic comb-type copolymer, poly(L-lysine)- graft -dextran (PLL- g -Dex), promotes nucleic acids assembly and enhances thermal stability of duplex and triplex nucleic acids ( Maruyama et al, 1999 , 1998 , 1997 ; Hanpanich and Maruyama, 2020 ). The copolymer also significantly enhances activity and stability of DNAzymes ( Gao et al, 2015a ; Hanpanich et al, 2020 ) and MNAzymes ( Gao et al, 2015b ; Hanpanich et al, 2019 ; Rudeejaroonrung et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer

Hanpanich

Saito

Shimada

et al. 2020

Biosensors and Bioelectronics

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RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer

Hanpanich

Saito

Shimada

et al. 2020

Biosensors and Bioelectronics

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“…Hence, we describe the activity of the copolymers as "chaperone-like" activity. Shielding of the electrostatic potential along anionic DNA strands by the cationic copolymer appears to be responsible for these thermodynamic and kinetic observations [24,28].…”

Section: Introductionmentioning

confidence: 94%

“…and assembling DNA to ordered structures. In the wsIPEC, DNA duplex and triplex conformations were thermodynamically stabilized [21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Inter-polyelectrolyte nano-assembly induces folding and activation of functional peptides

Shimada

Kinoshita

Tokunaga

et al. 2015

Journal of Controlled Release

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Insufficient solubility, fragile folding structure and short half-life frequently hamper use of peptides as biological reagents or therapies. To enhance the peptide function, the effect of complexation of the peptides with ionic graft copolymers with water-soluble graft chains was tested in this study. Amphiphilic anionic peptide E5 acquires membrane disrupting activity at acidic pH due to folding from the random coil state to an ordered α-helical structure. Aggregation and imprecise folding of the peptide limited membrane disrupting activity of the peptide. In the presence of a cationic graft copolymer, E5 and its analogs adopted an ordered conformation without aggregation. The mixture of the peptides and the copolymer functioned more efficiently than peptide alone at not only acidic pH but also neutral pH at which the peptide alone had no activity. Similarly, a cationic peptide was successfully folded and activated by an anionic graft copolymer. Thus, our analysis indicated that spontaneous nano-assembly of ionic peptides with graft copolymers having opposite ionic charges triggers the folding of peptides without loss of solubility, leading to enhanced bioactivity.

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“…We have previously reported that cationic comb-type copolymers (PLL- g -Dex) composed of a cationic poly( L -lysine) backbone (<20 wt%) and abundant hydrophilic dextran side chains (>80 wt%) form completely soluble complexes with DNA ( 14–16 ), and stabilize DNA hybrids such as duplexes and triplexes ( 16 , 17 ). Our spectroscopic study indicated that the copolymers interact with DNAs without changing DNA base-pair structures (bp) ( 18 ).…”

Section: Introductionmentioning

confidence: 99%

Activation of DNA strand exchange by cationic comb-type copolymers: effect of cationic moieties of the copolymers

Choi

Kano

Maruyama

2007

Nucleic Acids Research

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We have previously reported that poly(l-lysine)-graft-dextran cationic comb-type copolymers accelerate strand exchange reaction between duplex DNA and its complementary single strand by >4 orders of magnitude, while stabilizing duplex. However, the stabilization of the duplex is considered principally unfavourable for the accelerating activity since the strand exchange reaction requires, at least, partial melting of the initial duplex. Here we report the effects of different cationic moieties of cationic comb-type copolymers on the accelerating activity. The copolymer having guanidino groups exhibited markedly higher accelerating effect on strand exchange reactions than that having primary amino groups. The high accelerating effect of the former is considered to be due to its lower stabilizing effect on duplex DNA, resulting from its increased affinity to single-stranded DNA. The difference in affinity was clearly demonstrated by a fluorescence correlation spectroscopy study; the interaction of the former with single-stranded DNA still remained high even at 1 M NaCl, while that of the latter completely disappeared. These results suggest that some modes of interactions, such as hydrogen bonding, other than electrostatic interactions between the copolymers having guanidino groups and DNAs may be involved in strand exchange activation.

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Polycation comb-type copolymer reduces counterion condensation effect to stabilize DNA duplex and triplex formation

Cited by 33 publications

References 37 publications

One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer

One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer

Inter-polyelectrolyte nano-assembly induces folding and activation of functional peptides

Activation of DNA strand exchange by cationic comb-type copolymers: effect of cationic moieties of the copolymers

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