Studies on the Extension of Sequence-independence and the Enhancement of DNA Triplex Formation

Wei, Ming-Tsai; Walter, Axel; Gabrielian, Anna; Schütz, H.; Birch-Hirschfeld, Eckhard; Lin, Shwu‐Bin; Lin, Wei Chen; Fritzsche, H.; Kan, Lou‐Sing

doi:10.1002/jccs.200500056

Cited by 3 publications

(1 citation statement)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The appearance of triplex structures was first reported in RNA by Felsenfeld et al in 1957 (2). Triplex DNA is formed through the binding of a third DNA strand into the major groove of a double helix via Hoogsteen hydrogen bonding to the purine residues (3)(4)(5)(6)(7)(8)(9)(10)(11). The ability of triplex structure formation in cell nuclei has been demonstrated (12).…”

Section: Introductionmentioning

confidence: 99%

The Paperclip Triplex: Understanding the Role of Apex Residues in Tight Turns

Kan

Pasternack

Wey

et al. 2006

Biophysical Journal

Self Cite

View full text Add to dashboard Cite

In this study, we investigate the role of the apex nucleotides of the two turns found in the intramolecular "paperclip" type triplex DNA formed by 5'-TCTCTCCTCTCTAGAGAG-3'. Our previously published structure calculations show that residues C7-A18 form a hairpin turn via Watson-Crick basepairing and residues T1-C6 bind into the major groove of the hairpin via Hoogsteen basepairing resulting in a broad turn of the T1-T12 5'-pyrimidine section of the DNA. We find that only the C6C7/G18 apex triad (and not the T12A13/T1 apex triad) is required for intramolecular triplex formation, is base independent, and occurs whether the purine section is located at the 5' or 3' end of the sequence. NMR spectroscopy and molecular dynamics simulations are used to investigate a bimolecular complex (which retains only the C6C7/G18 apex) in which a pyrimidine strand 5'- TCTCTCCTCTCT-3' makes a broad fold stabilized by the purine strand 5'-AGAGAG-3' via Watson Crick pairing to the T8-T12 and Hoogsteen basepairing to T1-T5 of the pyrimidine strand. Interestingly, this investigation shows that this 5'-AGAGAG-3' oligo acts as a new kind of triplex forming oligonucleotide, and adds to the growing number of triplex forming oligonucleotides that may prove useful as therapeutic agents.

show abstract

Section: Introductionmentioning

confidence: 99%

The Paperclip Triplex: Understanding the Role of Apex Residues in Tight Turns

Kan

Pasternack

Wey

et al. 2006

Biophysical Journal

Self Cite

View full text Add to dashboard Cite

show abstract

Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods

Wey

Lyu

Kan

2010

J Chinese Chemical Soc

Self Cite

View full text Add to dashboard Cite

An imperfect DNA triplex, containing a pyrimidine/purine duplex with two sites of purine/pyrimidine base pair inversions, is formed and recognized. The unusual triplex is examined for the possibility of triplex DNA formation in a living system by way of non‐ideal sequence matching. The duplex part of it consists of a DNA oligomer with 17 nucleotidyl units, 5′‐TTCTTCTGATTCTCTCC‐3′ (C), which has two purine bases flanked by fifteen pyrimidine bases. The sequence of oligomer C is picked from a segment of cell cycle protein cdc25 gene (696 to 712) in Pneumocystis jirovecii, a yeast‐like parasitic fungus, which can cause pneumonia (PCP) in patients with impaired immunity. The complementary oligomer, 5′‐GGAGAGAATCAGAAGAA‐3′ (W), forms a DNA duplex WC with C, accompanied by CG/GC and TA/AT base pair inversions, in contrast to homo pyrimidine/purine duplexes. A third strand, 5′‐CCTCTCTTAGTCTTCTT‐3′ (H), combines with WC, to give an imperfect, but stable, triplex WCH+.UV absorption, circular dichroism, and native gel electrophoresis mobility shift assay are used to monitor the reactions at each stage. The triplex is stable in mild acidic solution, with a 1:1:1 stoichiometric ratio and a UV melting temperature (Tm) of 47.3 °C at pH 4.5. Isothermal titration calorimetry (ITC) and surface Plasmon resonance (SPR) unravel the thermodynamic information (ΔH = −123.1 kcal mol−1, ΔS = −378 cal mol−1K−1 and ΔG = −10.5 kcal mol−1) and kinetic rate constants (ka = 3.71 × 104 M−1 s−1 and kd = 7.49 × 10−4 s−1), respectively, for the WCH+ triplex formation process. WCH+ is termed an imperfect triplex since it contains two non‐canonical, non‐purine/purine/pyrimidine or non‐pyrimidine/purine/pyrimidine, base triads in the middle. This is the first time an imperfect but stable triplex, containing two purine bases in the middle of a pyrimidine‐rich strand (H), is formed and studied. The fact that an imperfect but stable DNA triplex can be formed gives great promise for drug design through more flexible targeting capabilities with much less stringent requirements, e.g., designs against Pneumocystis jirovecii using triplex formation in our example.

show abstract

THE FORMATION AND DETECTION OF TIGHT-TURN IN PYRIMIDINE/PURINE/PYRIMIDINE TYPE DNA TRIPLEXES — NEW FINDINGS ON MOTIFS CC AND TT BY FLUORESCENCE SPECTROSCOPY AT pH 7

Wey¹,

Kan²

2006

Biophys. Rev. Lett.

View full text Add to dashboard Cite

DNA triplexes with 'tight turns', i.e., sharp turns without any intervening bases, are studied by fluorescence resonance energy transfer process (FRET). The particular turning motifs under consideration are CC and TT imbedded in triplexes (5′- F -( TC )3( CT )3- D + 5′- AGAGAG ) and (5′- F -( CT )3( TC )3- D + 5′- GAGAGA ), where F and D are 6-fluorescein and 4-(4-dimethylaminophenylazo) benzoic acid, respectively. The association equilibrium constants of the above two triplexes ranged from 1.7 × 107 to 2.9 × 104 and 0.75 × 107 to 1.8 × 104 from 10 to 35°C, respectively. The thermodynamic parameters of these two triplexes are comparable (△ H : -46.0 vs. -45.0 Kcal/mol ; △ S : -129 vs -127 cal/mol K ; △ G : -7.5 vs. -7.2 Kcal/mol , respectively). Thus, the stability of the tight-turn triplex with a CC motif is comparable to that with a TT motif, but slightly favored over the latter. This is the first report of a py/pu/py type triplex containing such tight turns studied under pH at 7. The importance is manifested in their stabilities maintained under physiological neutral condition, as opposed to previous studies only obtainable in acidic conditions.

show abstract

Studies on the Extension of Sequence-independence and the Enhancement of DNA Triplex Formation

Cited by 3 publications

References 24 publications

The Paperclip Triplex: Understanding the Role of Apex Residues in Tight Turns

The Paperclip Triplex: Understanding the Role of Apex Residues in Tight Turns

Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods

THE FORMATION AND DETECTION OF TIGHT-TURN IN PYRIMIDINE/PURINE/PYRIMIDINE TYPE DNA TRIPLEXES — NEW FINDINGS ON MOTIFS CC AND TT BY FLUORESCENCE SPECTROSCOPY AT pH 7

Contact Info

Product

Resources

About