Praseodymium promotes B–Z transition in self-assembled DNA nanostructures

Bhanjadeo, Madhabi M.; Subudhi, Umakanta

doi:10.1039/c8ra10164g

Cited by 18 publications

(10 citation statements)

References 36 publications

(5 reference statements)

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“…Lanthanide-mediated DNA condensation and structural transition have been reported. 29,35,36 Moreover, it has been proved that monovalent cations stabilize multiplex DNA structures by reducing electrostatic repulsion, thereby increasing the melting temperature. 34 When bDNA USA-1 was denatured in the presence of Na + and K + , the T m increased with increase in cation concentration from 1 mM to 500 mM (Figure 4).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…On the other hand, addition of 10 mM chloride salts of La or Ce caused a similar bDNA condensation observed through band shifting in agarose gel. Lanthanide-mediated DNA condensation and structural transition have been reported. ,, Moreover, it has been proved that monovalent cations stabilize multiplex DNA structures by reducing electrostatic repulsion, thereby increasing the melting temperature …”

Section: Resultsmentioning

confidence: 99%

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Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly

2019

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The construction of functionalizable branched DNA (bDNA) relies on the designing of oligonucleotides and exploitation of their complementary chemistries. The stability of these structures largely depends on the hybridization specificity of the contributing oligonucleotides. However, most of the bDNA structures are not found suitable for in vivo application due to poor yield owing to uncharacterized hybridization efficiency and instability in biological fluids. In this report, our group has explored a mechanistic way for studying the hybridization pathway of genomic sequence derived oligonucleotides that are self-assembled to fabricate robust bDNA structures. The effect of change in nucleotide sequences on bDNA stability was studied by taking oligonucleotides derived from primers of different genes. Additionally, the stability of the bDNA in solutions with different pH, salts, and DNaseI which mimics physiological environment was reported. It was found that genomic sequence derived oligonucleotides self-assembled in a cooperative manner to yield the designed bDNAs, which are stable in physiological environment.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly

2019

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“…Taken together, the kinetics of the Z ‐conformer formation of dsDNA and dsRNA is greatly enhanced by the presence of overhangs and loops in a length‐dependent manner. Interestingly, similar observations have been reported that the B‐Z transition induced by salts such as LaCl 3 is influenced by loops and overhangs, resulting in significantly reduced salt concentrations required for reaching the full B‐Z transition of self‐assembled DNA nanostructures . Why unpaired single‐stranded regions facilitate the formation of Z conformers?…”

Section: The Observed Rate Constants Of the Hzαadar1‐induced B‐z Tranmentioning

confidence: 98%

Protein‐induced B‐Z Transition is Kinetically Accelerated by Introducing Single‐Stranded Regions

Zheng

Lee

Yun

et al. 2020

Bulletin Korean Chem Soc

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B-DNA is a right-handed double-stranded DNA (dsDNA) helix. It is believed that most DNA adopts B-DNA conformation in biological systems. However, DNA can adopt alternative conformations of dsDNA. In Z-DNA, a double helix assumes left-handed conformation that contains a zigzag backbone. 1 Z-DNA formation can be stabilized under certain circumstances such as high salts and negative supercoiling. 2 The formation of thermodynamically disfavored Z-DNA is an interesting subject in the field of nucleic acid research. Much research has been carried out on how B conformation of DNA is structurally transformed into Z conformation (B-Z transition). To date, mainly two mechanisms have been suggested to describe how B-Z transition occurs. The Wang model proposed that the B-Z transition undergoes base pair opening prior to base pair rotation. 1 In contrast, in the Harvey model, the B-Z transition contains base pair rotation without breaking of base pairs. 3 Surely, the identification of Z-DNA binding proteins can provide clues to biological relevance of Z-DNA. The wellcharacterized Z-DNA binding domain named Zα is initially found in human ADAR1 (double-stranded RNA adenosine deaminase 1) and known to be existed in several proteins. 4 Since Zα binds to Z-DNA strongly, it can promote relatively fast B-Z transition through stabilizing Z-DNA and inhibiting re-formation of B-DNA in the B-Z equilibrium. hZα ADAR1 is the first Zα domain present in two tandem Zα domains of human ADAR1, which has been widely used for structural and biochemical studies of Z-DNA/Z-RNA. For example, hZα ADAR1 as a Z-DNA inducer enables to stabilize A-Z, B-Z, and Z-Z junction, 5-8 and Z-RNA by help of hZα ADAR1 successfully forms in physiological salt concentrations so as to solve its structure. 9,10 In addition, hZα ADAR1 has been used to elucidate kinetic behavior of Z-conformer formation of various nucleic acid duplexes by single-molecule studies. 11-13 Here, we reported the effect of the unpaired single-stranded region present in DNA duplexes such as overhangs and loops on the B-Z transition induced by hZα ADAR1 .For this study, we used d(CG) 6 sequence as a core Zforming DNA sequence (ZFD) that forms self-complementary dsDNA with overhangs, which may contain either 5 0 -or 3 0 -overhangs composed of 1-6 nucleotides (Supporting Information Figure S1 and Table S1). First, dT-overhang ZFDs with different overhang-lengths placed at the 5 0 -ends of ZFD (referred to as T1-, T2-, T3-, T4-, and T6-ZFD, respectively) were designed and tested (Supporting Information Table S1). The B-Z transition in the presence of hZα ADAR1 was monitored under the physiological pH condition (pH 7.4) with a relatively low salt concentration (10 mM NaCl). All of 5 0 -dToverhang ZFD substrates readily form Z conformation when hZα ADAR1 is added (Supporting Information Figure S2).For the kinetic analysis, CD measurements performed at 5 C to observe fast hZα ADAR1 -induced B-Z transition. The CD signals at 255 nm were collected immediately after adding hZα ADAR1 . As shown in Figur...

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“…Significant factors influencing the B-Z transition have been identified, such as alternating (CG) n sequences, high salt concentrations, multivalent cations or polycations, and Z binding proteins [14,[80][81][82][83]. In addition, steric effects are also important.…”

Section: Z-dnamentioning

confidence: 99%

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Balasubramaniyam

Jin

Ahn

et al. 2021

IJMS

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Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

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Praseodymium promotes B–Z transition in self-assembled DNA nanostructures

Abstract: Millimolar concentrations of PrCl3 can induce sequence-specific B–Z transition in various-self-assembled branched DNA (bDNA) nanostructures.

Cited by 18 publications

References 36 publications

Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly

Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly

Protein‐induced B‐Z Transition is Kinetically Accelerated by Introducing Single‐Stranded Regions

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

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