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Pseudo Complementary Base Modification

Pseudo-complementary base modified oligonucleotides, originally referred to as selectively binding complementary oligonucleotides, are important tools for the study of duplex structures in RNA and DNA double strands. Oligonucleotides modified with non-standard selective or pseudo-complementary bases show significantly reduced hybridization affinities for the formation of duplexes with each other due the presence of chemical modification. However, many pseudo-complementary modified oligonucleotides can form strong base pairs with natural DNA or RNA target sequences. Consequently, pseudo-complementary nucleic acids show diminished intra-molecular and inter-molecular secondary structures, but can readily hybridize to unmodified nucleic acids. The differential hybridization properties of pseudo-complementary nucleic acids allow for sequence-specific targeting of duplex DNA using various double duplex invasion strategies. Examples are oligonucleotides containing palindromic (self-complementary) sequence stretches that allow the design of hybridization probes that form hairpins in RNA targets.

Bio-Synthesis offers several pseudo-complementary bases to be incorporated at the 5', 3' or internal position of an oligonucleotide. contact Bio-Synthesis for Pseudo-complementary nucleobase oligo modification .

All oligonucleotide synthesized at Bio-Synthesis is quality check by using either MALDI-TOF mass spectrometry, analytical HPLC,or polyacrylamide gel electrophoresis (PAGE). Final yields are determined using UV absorbance at OD260 In addition, we perform custom formulation and quality control tailored to meet your specific requirements.

Pseudocomplementary Nucleobases Modification Code 5 Prime Internal 3 Prime
Pseudouridine (5-Ribosyluracil) Ψ Y Y Y
7-Deaza-2'-deoxyguanosine 7-Deaza-dG Y Y Y
2,6-Diaminopurine-2'-deoxyriboside DAPdR Y Y Y
N4-Ethyl-2'-deoxycytidine N4-Ethyl-dC Y Y Y
2-Thiothymidine 2-Thio-dT Y Y Y
2-Aminopurine-riboside 2-Aminopurine Y Y Y
2,6-Diaminopurine-riboside DAPrR Y Y Y
2'-Deoxyisoguanosine iG Y Y Y
5-Hydroxymethyl-2'-deoxycytidine 5-hmC Y Y Y

Quality Control: Analytical HPLC, Gel eletrophoresis, and  MALDI-TOF Mass Spectrometry

Delivery times: 5-7 Working days

Packaging:    Dried

Shipping conditions: Room temperature

Storage conditions: -20 oC to -70 oC

Oligonucleotides are stable in solution at 4 oC for up to 2 weeks. Properly reconstituted material stored at -20 oC should be stable for at least 6 months. Dried DNA (when kept at -20 oC) in a nuclease-free environment should be stable for years.

References :

  • Biochemistry (1996) 35, 11170-11176.
  • Nucleic Acids Research (1996) 15, 2470-2475.
  • Lohse J, Dahl O, Nielsen PE. Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA. Proc Natl Acad Sci USA. 1999;96:11804–11808.
  • Lonkar P, Kim KH, Kuan JY, Chin JY, Rogers FA, Knauert MP, et al. Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids. Nucleic Acids Res. 2009;37:3635–3644.
  • Kim KH, Nielsen PE, Glazer PM. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids. Nucleic Acids Res. 2007;35:7604–7613.
  • Izvolsky KI, Demidov VV, Nielsen PE, Frank-Kamenetskii MD. Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs. Biochemistry. 2000;39:10908–10913.
  • Demidov VV, Protozanova E, Izvolsky KI, Price C, Nielsen PE, Frank-Kamenetskii MD. Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids. Proc Natl Acad Sci USA. 2002;99:5953–5958.
  • Protozanova E, Demidov VV, Nielsen PE, Frank-Kamenetskii MD. Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes. Nucleic Acids Res. 2003;31:3929–3935.
  • Katada H, Chen HJ, Shigi N, Komiyama M. Homologous recombination in human cells using artificial restriction DNA cutter. Chem Commun. 2009:6545–6547.
  • to K, Katada H, Shigi N, Komiyama M. Site-selective scission of human genome by artificial restriction DNA cutter. Chem Commun. 2009:6542–6544.
  • Katada H, Komiyama M. Artificial restriction DNA cutters as new tools for gene manipulation. Chembiochem. 2009;10:1279–1288.
  • Miyajima Y, Ishizuka T, Yamamoto Y, Sumaoka J, Komiyama M. Origin of high fidelity in target-sequence recognition by PNA-Ce(IV)/EDTA combinations as site-selective DNA cutters. J Am Chem Soc. 2009;131:2657–2662.

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