Bimolecular DNA triplexes: Duplex extensions show implications for H-form DNA stability

被引:10
作者
Mundt, AA
Crouch, GJ
Eaton, BE
机构
[1] WASHINGTON STATE UNIV,DEPT BIOCHEM & BIOPHYS,PULLMAN,WA 99164
[2] WASHINGTON STATE UNIV,DEPT CHEM,PULLMAN,WA 99164
关键词
D O I
10.1021/bi970658y
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
H-form DNA has recently been shown to be biologically relevant by its involvement in the process of homologous recombination [Kohwi, Y., and Panchenko, Y. (1993) Genes Dev. 7, 1766-1778]. A bimolecular DNA triple-stranded structure (tripler) is central to the formation of H-form DNA. Understanding the formation and factors governing the stability of such bimolecular triplexes is necessary to fully elucidate the structure/function relationship of I-I-form DNA. In this study, we extend known information on bimolecular triplexes by examining the effect of a variable CNC base triad (where N = A, C, T, or G) on a 10 base triad tripler that mimics the tripler motif in H-form DNA. We also examine the effect that a duplex extension of four base pairs has on tripler stability and selectivity for the base N. Results from thermal denaturation experiments indicate that the fully complementary tripler is more stable than its duplex counterpart (Delta T-m = 13 degrees C) and is resistant to degradation by bovine spleen phosphodiesterase for at least 24 h at 10 degrees C. A single-base mismatch in the purine strand of the tripler structure is destabilizing (Delta T-m = similar to 20 degrees C), and all structures containing a mismatch were readily degraded by bovine spleen phosphodiesterase. An extension of four duplex base pairs onto the tripler structure affects the stability of the DNA complex and may have implications relevant to H-form DNA.
引用
收藏
页码:13004 / 13009
页数:6
相关论文
共 43 条
[21]   CALCULATING THERMODYNAMIC DATA FOR TRANSITIONS OF ANY MOLECULARITY FROM EQUILIBRIUM MELTING CURVES [J].
MARKY, LA ;
BRESLAUER, KJ .
BIOPOLYMERS, 1987, 26 (09) :1601-1620
[22]   SELF-COMPLEMENTARY OLIGORIBONUCLEOTIDES - ADENYLIC ACID-URIDYLIC ACID BLOCK COPOLYMERS [J].
MARTIN, FH ;
UHLENBECK, OC ;
DOTY, P .
JOURNAL OF MOLECULAR BIOLOGY, 1971, 57 (02) :201-+
[23]   TRIPLE HELIX SPECIFIC LIGANDS [J].
MERGNY, JL ;
DUVALVALENTIN, G ;
NGUYEN, CH ;
PERROUAULT, L ;
FAUCON, B ;
ROUGEE, M ;
MONTENAYGARESTIER, T ;
BISAGNI, E ;
HELENE, C .
SCIENCE, 1992, 256 (5064) :1681-1684
[24]   SEQUENCE SPECIFICITY IN TRIPLE-HELIX FORMATION - EXPERIMENTAL AND THEORETICAL-STUDIES OF THE EFFECT OF MISMATCHES ON TRIPLEX STABILITY [J].
MERGNY, JL ;
SUN, JS ;
ROUGEE, M ;
MONTENAYGARESTIER, T ;
BARCELO, F ;
CHOMILIER, J ;
HELENE, C .
BIOCHEMISTRY, 1991, 30 (40) :9791-9798
[25]   DNA H-FORM REQUIRES A HOMOPURINE HOMOPYRIMIDINE MIRROR REPEAT [J].
MIRKIN, SM ;
LYAMICHEV, VI ;
DRUSHLYAK, KN ;
DOBRYNIN, VN ;
FILIPPOV, SA ;
FRANKKAMENETSKII, MD .
NATURE, 1987, 330 (6147) :495-497
[26]   SEQUENCE-SPECIFIC CLEAVAGE OF DOUBLE HELICAL DNA BY TRIPLE HELIX FORMATION [J].
MOSER, HE ;
DERVAN, PB .
SCIENCE, 1987, 238 (4827) :645-650
[27]   INTERACTION OF OLIGODEOXYRIBONUCLEOTIDES THROUGH FORMATION OF CHIMERIC DUPLEX/TRIPLEX COMPLEXES [J].
NOLL, DM ;
OREAR, JL ;
CUSHMAN, CD ;
MILLER, PS .
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 1994, 13 (04) :997-1005
[28]   BASE-STACKING AND BASE-PAIRING CONTRIBUTIONS TO HELIX STABILITY - THERMODYNAMICS OF DOUBLE-HELIX FORMATION WITH CCGG, CCGGP, CCGGAP, ACCGGP, CCGGUP, AND ACCGGUP [J].
PETERSHEIM, M ;
TURNER, DH .
BIOCHEMISTRY, 1983, 22 (02) :256-263
[29]   THERMODYNAMIC CHARACTERIZATION OF THE STABILITY AND THE MELTING BEHAVIOR OF A DNA TRIPLEX - A SPECTROSCOPIC AND CALORIMETRIC STUDY [J].
PLUM, GE ;
PARK, YW ;
SINGLETON, SF ;
DERVAN, PB ;
BRESLAUER, KJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1990, 87 (23) :9436-9440
[30]  
PLUM GE, 1995, ANNU REV BIOPH BIOM, V24, P319