Self-complementary DNA

The Rayner group has reported several examples of the use of dynamic nucleic acid decoration for stabilizing structures of interest. In the first of these, described in 2004 [45], a mixture consisting of a self-complementary DNA hexamer bearing a 2 -amino-2 -deoxyuridine at the 3 -terminus with a pool of three aldehydes (51-53, Fig. 19) and sodium cyanohydride was generated. Analysis of aliquots of the... 

Figure 4.5. Crystal structure of the self-complementary DNA oligonucleotide 5 -CATGGCCATG-3, downloaded from the Protein Data Bank (ID 126D) and visualized in RasMol [58].

The choice of hybridization probes should take into consideration a balanced sequence region because a sequence region that is nearly equal tends to bind probes tightly, but not too tightly. It should not contain monotonous or repetitive sequences because such sequences can form hybrids and the sequence should not be self-complementary. DNA sequences can form loops and therefore be less accessible to hybridization. In principle, those probes can be cheaper than probes bearing two fluorescent labels. 

Probes 5 and 6 (Table 1) covering a region of DNA beyond the 3 -end of the gene for the b subunit were used to map the 3 -end of the atg 2 operon mRNA. The protected fragments in the SI nuclease experiment corresponds to a termination site at nucleotide 3615. This nucleotide falls in a region with self-complementary DNA sequences and a run of thymidylate residues, both characteristic of a transcription termination signal in E. coli (Fig. 3). 

FIGURE 12.27 The formation of a cruciform structure from a paliudromic sequence within DNA. The self-complementary Inverted repeats can rearrange to form hydrogen-bonded cruciform loops. 

In 2004, Rayner and coworkers reported a dynamic system for stabilizing nucleic acid duplexes by covalently appending small molecules [34]. These experiments started with a system in which 2-amino-2 -deoxyuridine (U-NH ) was site-specifically incorporated into nucleic acid strands via chemical synthesis. In the first example, U-NH was incorporated at the 3 end of the self-complementary U(-NH2)GCGCA DNA. This reactive amine-functionalized uridine was then allowed to undergo imine formation with a series of aldehydes (Ra-Rc), and aldehyde appendages that stabilize the DNA preferentially formed in the dynamic system. Upon equilibration and analysis, it was found that the double-stranded DNA modified with nalidixic aldehyde Rc at both U-NH positions was amplified 34% at the expense of Ra and Rb (Fig. 3.16). The Rc-appended DNA stabilizing modification corresponded to a 33% increase in (melting temperature). Furthermore, imine reduction of the stabilized DNA complex with NaCNBH, resulted in a 57% increase in T. ... 

The tertiary structure of DNA is the structural level that is most relevant to 3-D reality. Traditionally, ODNs in a physiologically relevant aqueous solution are considered to be in a random-coiled ssDNA state or in the form of dsDNA helix in the presence of a complementary DNA, including the case of self-complementarity. The double helix is the dominant tertiary structure for biological DNA that can be in one of the three DNA conformations found in nature, A-DNA, B-DNA, and Z-DNA. The B-conformation described by Watson and Crick (11) is believed to predominate in cells (12). However other types of nucleic acid tertiary structures different from random or classical double-stranded helix forms can also be observed. Among them are triplexes, quadruplexes, and several other nucleic acid structures (13, 14). 

We have investigated the reactions of the COs " radicals with double-stranded DNA by laser flash photolysis techniques [15]. In these time-re-solved experiments, the COs radicals were generated by one-electron oxidation of HCOs by sulfate radical anions, SO4 the latter were derived from the photodissociation of persulfate anions, S20s initiated by 308-nm XeCl excimer laser pulse excitation. In air-equilibrated buffer solution containing the self-complementary oligonucleotide duplex d(AACGCGAATTCGCGTT), 208 , and an excess of HCO3., the decay of the CO3 radical anion absorption band at 600 nm is associated with the concomitant formation of the characteristic narrow absorption band of the G(-H) radicals near 310 nm. 

The bending observed with this and other sequences may be important in the binding of some proteins to DNA A rather common type of DNA sequence is a palindrome. A palindrome is a word, phrase, or sentence that is spelled identically read either forward or backward two examples are ROTATOR and NURSES RUN. The term is applied to regions of DNA with inverted repeats of base sequence having twofold symmetry over two strands of DNA (Fig. 8-20). Such sequences are self-complementary within each strand and therefore have the potential to form hairpin or cruciform (cross-shaped) structures (Fig. 8-21). When the inverted repeat occurs within each individual strand of the DNA, the sequence is called a mirror repeat. Mrror repeats do not have complementary sequences within the same strand and cannot form hairpin or cruciform structures. Sequences of these types are found... 

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