Sequence specific recognition and cleavage of DNA by synthetic molecules

DNA recognition is an essential biological process responsible for the regulation of cellular functions including protein synthesis and cell division and is implicated in the mechanism of action of some anticancer drugs. Studies directed towards defining the elements responsible for sequence specific DNA recognition through the study of the interactions of synthetic organic ligands with DNA are described.

DNA recognition by poly-N-methylpyrrolecarboxamides was studied by the synthesis and characterization of a series of molecules where the number of contiguous N-methylpyrrolecarboxamide units was increased from 2 to 9. The effect of this incremental change in structure on DNA recognition has been investigated at base pair resolution using affinity cleaving and MPE•Fe(II) footprinting techniques. These studies led to a quantitative relationship between the number of amides in the molecule and the DNA binding site size. This relationship is called the n + 1 rule and it states that a poly-N methylpyrrolecarboxamide molecule with n amides will bind n + 1 base pairs of DNA. This rule is consistent with a model where the carboxamides of these compounds form three center bridging hydrogen bonds between adjacent base pairs on opposite strands of the helix. The poly-N methylpyrrolecarboxamide recognition element was found to preferentially bind poly dA•poly dT stretches; however, both binding site selection and orientation were found to be affected by flanking sequences. Cleavage of large DNA is also described.

One approach towards the design of molecules that bind large sequences of double helical DNA sequence specifically is to couple DNA binding subunits of similar or diverse base pair specificity. Bis-EDTA-distamycin-fumaramide (BEDF) is an octaamide dimer of two tri-N methylpyrrolecarboxamide subunits linked by fumaramide. DNA recognition by BEDF was compared to P7E, an octaamide molecule containing seven consecutive pyrroles. These two compounds were found to recognize the same sites on pBR322 with approximately the same affinities demonstrating that fumaramide is an effective linking element for Nmethylpyrrolecarboxamide recognition subunits. Further studies involved the synthesis and characterization of a trimer of tetra-N-methylpyrrolecarboxamide subunits linked by β-alanine ((P4)_(3)E). This trimerization produced a molecule which is capable of recognizing 16 base pairs of A•T DNA, more than a turn and a half of the DNA helix.

DNA footprinting is a powerful direct method for determining the binding sites of proteins and small molecules on heterogeneous DNA. It was found that attachment of EDTA•Fe(II) to spermine creates a molecule, SE•Fe(II), which binds and cleaves DNA sequence neutrally. This lack of specificity provides evidence that at the nucleotide level polyamines recognize heterogeneous DNA independent of sequence and allows SE•Fe(II) to be used as a footprinting reagent. SE•Fe(II) was compared with two other small molecule footprinting reagents, EDTA•Fe(II) and MPE•Fe(II).

Theoretical studies of novel organic systems : biradicals, polyradicals, and conducting polymers

Chapter 1

Cyclobutanediyl has been studied in both its singlet and triplet states by ab initio electronic structure theory. The triplet, which is the ground state of the molecule, exists in both C_(2h) and C_(2v) forms, which interconvert via a C_s transition state. For the singlet, only a C_(2h) form is found. It passes, via a C_s transition state, onto the C_(2v) surface on which bicyclobutane is the only minimum. The ring-flipping (inversion) process in bicyclobutane includes the singlet biradical as an intermediate, and involves a novel, nonleast motion pathway. Semiclassical periodic orbit theory indicates that the various minima on both the singlet and triplet surfaces can interconvert via quantum mechanical tunneling.

Chapter 2

The dimethylenepolycyclobutadienes (n) are the non-Kekulé analogues of the classical acenes. Application of a variety of theoretical methods reveals several novel features of such structures. Most interesting is the emergence of a parity rule. When n is even, n is predicted to be a singlet, with n disjoint NBMOs. When n is odd, theory predicts a triplet ground state with (n+1) NBMOs that are not fully disjoint.

Chapter 3

Bi(cyclobutadienyl) (2), the cyclobutadiene analogue of biphenyl, and its homologues tri- (3) and tetra(cyclobutadienyl) (4) have been studied using electronic structure theory. Ab initio calculations on 2 reveal that the central bond is a true double bond, and that the structure is best thought of as two allyl radicals plus an ethylene. The singlet and triplet states are essentially degenerate. Trimer 3 is two allyls plus a dimethylenecyclobutanediyl, while 4 is two coplanar bi(cyclobutadienyl) units connected by a single bond. For both 3 and 4, the quintet, triplet, and singlet states are essentially degenerate, indicating that they are tetraradicals. The infinite polymer, polycyclobutadiene, has been studied by HMO, EHCO, and VEH methods. Several geometries based on the structures of 3 and 4 have been studied, and the band structures are quite intriguing. A novel crossing between the valence and conduction bands produces a small band gap and a high density of states at the Fermi level.

Chapter 4

At the level of Hückel theory, polyfulvene has a HOCO-LUCO degeneracy much like that seen in polyacetylene. Higher levels of theory remove the degeneracy, but the band gap (E_g) is predicted to be significantly smaller than analogous structures such as polythiophene and polypyrrole at the fulvenoid geometry. An alternative geometry, which we have termed quinoid, is also conceivable for polyfulvene, and it is predicted to have a much larger E_g. The effects of benzannelation to produce analogues of polyisothianaphthene have been evaluated. We propose a new model for such structures based on conventional orbital mixing arguments. Several of the proposed structures have quite interesting properties, which suggest that they are excellent candidates for conducting polymers.

Chapter 5

Theoretical studies of polydimethylenecyclobutene and polydiisopropylidene- cyclobutene reveal that, because of steric crowding, they cannot achieve a planar, fully conjugated structure in either their undoped or doped states. Rather, the structure consists of essentially orthogonal hexatriene units. Such a structure is incompatible with conventional conduction mechanisms involving polarons and bipolarons.

Studies on T-even bacteriophage DNA

Part I. The regions of sequence homology and non-homology between the DNA molecules of T2, T4, and T6 have been mapped by the electron microscopic heteroduplex method. The heteroduplex maps have been oriented with respect to the T4 genetic map. They show characteristic, reproducible patterns of substitution and deletion loops. All heteroduplex molecules show more than 85% homology. Some of the loop patterns in T2/T4 heteroduplexes are similar to those in T4/T6.

We find that the rII, the lysozyme and ac genes, the D region, and gene 52 are homologous in T2, T4, and T6. Genes 43 and 47 are probably homologous between T2 and T4. The region of greatest homology is that bearing the late genes. The host range region, which comprises a part of gene 37 and all of gene 38, is heterologous in T2, T4, and T6. The remainder of gene 37 is partially homologous in the T2/T4 heteroduplex (Beckendorf, Kim and Lielausis, 1972) but it is heterologous in T4/T6 and in T2/T6. Some of the tRNA genes are homologous and some are not. The internal protein genes in general seem to be non-homologous.

The molecular lengths of the T-even DNAs are the same within the limit of experimental error; their calculated molecular weights are correspondingly different due to unequal glucosylation. The size of the T2 genome is smaller than that of T4 or T6, but the terminally repetitious region in T2 is larger. There is a length distribution of the terminal repetition for any one phage DNA, indicating a variability in length of the DNA molecules packaged within the phage.

Part II. E. coli cells infected with phage strains carrying extensive deletions encompassing the gene for the phage ser-tRNA are missing the phage tRNAs normally present in wild type infected cells. By DNA-RNA hybridization we have demonstrated that the DNA complementary to the missing tRNAs is also absent in such deletion mutants. Thus the genes for these tRNAs must be clustered in the same region of the genome as the ser-tRNA gene. Physical mapping of several deletions of the ser-tRNA and lysozyme genes, by examination of heteroduplex DNA in the electron microscope, has enabled us to locate the cluster, to define its maximum size, and to order a few of the tRNA genes within it. That such deletions can be isolated indicates that the phage-specific tRNAs from this cluster are dispensable.

Part III. Genes 37 and 38 between closely related phages T2 and T4 have been compared by genetic, biochemical, and hetero-duplex studies. Homologous, partially homologous and non-homologous regions of the gene 37 have been mapped. The host range determinant which interacts with the gene 38 product is identified.

Part IV. A population of double-stranded ØX-RF DNA molecules carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under conditions where the phage lysozyme gene is nonessential. The structures of deleted monomers, dimers, and trimers have been studied by the electron microscope heteroduplex method. The dimers and trimers are shown to be head-to-tail repeats of the deleted monomers. Some interesting examples of the dynamical phenomenon of branch migration in vitro have been observed in heteroduplexes of deleted dimer and trimer strands with undeleted wild-type monomer viral strands.