Formation of stable DNA triplexes

Abstract

Triple-helical nucleic acids are formed by binding an oligonucleotide within the major groove of duplex DNA. These complexes offer the possibility of designing oligonucleotides which bind to duplex DNA with considerable sequence specificity. However, triple-helix formation with natural nucleotides is limited by (i) the requirement for low pH, (ii) the requirement for homopurine target sequences, and (iii) their relatively low affinity. We have prepared modified oligonucleotides to overcome these limitations, including the addition of positive charges to the sugar and/or base, the inclusion of cytosine analogues, the development of nucleosides for recognition of pyrimidine interruptions and the attachment of one or more cross-linking groups. By these means we are able to generate triplexes which have high affinities at physiological pH at sequences that contain pyrimidine interruptions.

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

“…We note that the guanidine group of arginine is often utilized in proteins for the sequence specific recognition of the Hoogsteen edge of a G base with two hydrogen bond acceptors (carbonyl and N7, Figure 1D) (24,32), and have been utilized in modified nucleic acids to enhance the recognition of the Hoogsteen edge of a G base (25,26). …”

“…Extensive research has been done to design and synthesize TFOs with modified nucleobases to enhance the recognition of C-G inversions in DNA duplexes (25–28). A guanidine functionalized C base, N 4 -(2-guanidoethyl)-5-methylcytosine (27) has been previously incorporated into relatively long TFOs (17-mer) with 2′-O-methyl (2′-OMe) and 2′-O-aminoethoxy (2′-AE) RNA backbones for TFO·DNA 2 triplex formation.…”

Synthesis of C-5, C-2′ and C-4′-neomycin-conjugated triplex forming oligonucleotides and their affinity to DNA-duplexes

“…3 Due to the limited number of suitable Hoogsteen base pairs (usually only the homopurine stretches of the duplex can be targeted) and their pH dependency (C:G*C H+ ), 4,5 a remarkable effort to increase the thermodynamic stability of triple helical structure, especially under physiological conditions, has been done. Sugar/phosphate backbone-and base-modified TFOs [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] but also with the aid of triplex stabilizing ligands, which by covalent incorporation into TFOs may provide a sequenceindependent extra binding motif, have been studied. [23][24][25][26][27][28][29][30] Regarding the ligand discovery, the ability of aminoglycosides in stabilizing the DNA and RNA triplexes and their hybrid triplexes has thoroughly been studied by Arya et al [31][32][33][34] Among this carbohydrate family, neomycin has proven to be the most effective triplex stabilizing groove binder.…”

Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides

“…Thus, extensive studies have been carried out to use chemically modified TFOs to enhance the binding affinity with DNA duplexes (29,30). For example, 2′- O methyl (2′-OMe) (Figure 1B) modification in TFOs favors triplex formation (31,32) with parental DNA duplexes.…”