Influence of Neighboring Base Pairs on the Stability of Single Base Bulges and Base Pairs in a DNA Fragment

Abstract

Temperature-gradient gel electrophoresis (TGGE) was used to determine the relative thermal stabilities of 32 DNA fragments that differ by a single unpaired base (base bulge) and 17 DNAs differing by a base pair. Homologus 373 and 372 bp DNA fragments differing by a single base pair substitution or deletion were employed. Heteroduplexes containing a single base bulge were formed by melting and reannealing pairs of 372 and 373 bp DNAs. Product DNAs were separated on the basis of their thermal stability by parallel and perpendicular TGGE. The order of stability was determined for all single unpaired bases in four different nearest neighbor environments: (GXT).(AYC), (GXG).(CYC), (CXA).(TYG), and (TXT).(AYA) with X = A, T, G, or C, and Y = no base, or visa versa. DNA fragments containing a base bulge were destabilized by 2-3.6 degrees C (+/- 0.2 degrees C) with respect to homologous DNAs with complete Watson-Crick base pairing. Both the identity of the unpaired base and the sequence of the flanking base pairs influenced the degree of destabilization. The range of temperature shift correspond to estimated unfavorable free energies from 2.5 to 4.6 kcal/mol. Purine base bulges were generally not as destabilizing as pyrimidine base bulges. An unpaired base which was identical to one of its adjacent bases generally caused less destabilization than an unpaired base with an identity differing from its nearest neighbors. This implies that positional degeneracy of an unpaired base within a run of two or more identical bases is an important factor effecting stability.(ABSTRACT TRUNCATED AT 250 WORDS)

Bulged Guanine is Uniquely Sensitive to Damage Caused by Visible-Light Irradiation of Ethidium Bound to DNA: A Possible Role in Mutagenesis

“…In the absence of EB, these oligomers melt reversibly at 54.9 and 46.38, respectively. The bulged guanine in DNA 2 reduces the T m by 8.68, which is consistent with the previously reported destabilization caused by introduction of a single bulged base [10] [16] [20] [21].…”

“…The insertion of a single-base bulge into one strand of duplex DNA destabilizes the molecule by approximately 4 kcal/mol at 378 [10] [16] [20] [21]. The destabilization depends upon interactions with the base pairs directly neighboring the bulge and also with more distal base pairs [22].…”

Role of the Structure of the Top Half of HIV-1 cTAR DNA on the Nucleic Acid Destabilizing Activity of the Nucleocapsid Protein NCp7

“…The higher stability with C 35 may tentatively be related to the fact that bulges having at least one neighboring nucleotide identical to the bulged nucleotide show an increased stability. 51,52 Indeed, if the bulged nucleotide is identical to its neighbor, the bulge may change position with its neighbors. This results in conformational freedom, which increases the entropy and stabilizes the sequence.…”

A New CoII Complex as a Bulge-Specific Probe for DNA

“…The melting temperature of DNA containing a single-base DNA bulge is destabilized by 2.0 ± 3.6 8C relative to that of the corresponding totally Watson ± Crick base-paired structure. [3] Although many synthetic chemical nucleases have been developed to explore a variety of DNA/RNA structures, [4] probes specific for the DNA bulge site are still rare. Recently, two types of DNA-targeting antitumor drugs, neocarzinostatin chromophore (NCS-C) and bleomycin (BLM), were shown to have a preference for a DNA nick site near the bulge.…”