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Duplex Destabilizing Bases

Destabilization of DNA double permits the initiation of transcription event by allowing polymerase complex access to the template DNA, enable construction of complementary RNA molecule. To study regulation of gene expression machnism, regulartory molecules must bind in a single strand-specific manner that requires a pre-existing region of the strand to be separated. The opening and closing of the DNA double helix is regulated at multiple levels in the cell. However, at the level of the duplex itself, for DNA strand separation to occur the hydrogen bonds that hold the complementary chains of DNA together must be broken. These weak chemical bonds that stabilize the double helix exist between the complementary nitrogenous bases that align inside the duplex. When a gene is transcribed or DNA is duplicated, these hydrogen bonds are systematically broken by enzymes called DNA helicases that unravel the DNA duplex into single strands. While the polymerases do their jobs, the single strands are maintained by the presence of single stranded DNA binding proteins that prevent the tendency of the separated strands to reanneal and reestablish hydrogen bonding. After transcription or DNA synthesis and the removal of the binding proteins, the duplex is reformed as the hydrogen bonds restabilize . So the study of gene expression regulation requires stringent in vivo control of the locations and ocassions of strand separation events. Bio-Synthesis offers several kind of duplex destabilizing base to be use for gene regulation study. Contact Bio-Synthesis for dupelx destabiizing base modifications.

Bio-Synthesis metal chelate conjugates can be incorporate at any position of an oligonucleotide. Dual HPLC purification is required. Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

Duplex Destabilization Bases Modification Code 5' Prime Internal 3' Prime
2-Aminopurine-2'-deoxyriboside 2APdR Y Y Y
8-Bromo-2'-deoxyadenosine 8-Br-dA N N Y
8-Bromo-2'-deoxyguanosine 8-Br-dG Y Y Y
7-Deaza-2'-deoxyadenosine 7-Deaza-dA Y Y Y
7-Deaza-2'-deoxyguanosine 7-Deaza-dG Y Y Y
6-Thio-2'-deoxyguanosine 6-Thio-dG Y Y Y
2'-Deoxyuridine dU Y Y Y
N4-Ethyl-2'-deoxycytidine N4-Et-dC Y Y Y
8-Amino-2'-deoxyadenosine 8-Amino-dA Y Y Y
8-Amino-2'-deoxyguanosine 8-Amino-dG 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 :
  1. 1. Bartlett, D. W.; Su, H.; Hildebrandt, I. J.; Weber, W. A.; Davis, M. E., Impact of tumor-specific targeting on the biodistribution and efficacy of siRNA nanoparticles measured by multimodality in vivo imaging. Proc Natl Acad Sci U S A 2007, 104, (39), 15549-54.
  2. Dreyer, G. B.; Dervan, P. B., Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA X Fe(II). Proc Natl Acad Sci U S A 1985, 82, (4), 968-72.
  3. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shionoya, M., A discrete self-assembled metal array in artificial DNA. Science 2003, 299, (5610), 1212-3.
  4. Shionoya, M.; Tanaka, K., Artificial metallo-DNA: a bio-inspired approach to metal array programming. Curr Opin Chem Biol 2004, 8, (6), 592-7.
  5. Weizman, H.; Tor, Y., 2,2’-Bipyridine ligandoside: a novel building block for modifying DNA with intra-duplex metal complexes. J Am Chem Soc 2001, 123, (14), 3375-6.

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