The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences

2015 ◽  
Vol 71 (10) ◽  
pp. 2119-2126 ◽  
Author(s):  
Arunachalam Thirugnanasambandam ◽  
Selvam Karthik ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Hydrogen Bonds ◽  
Dna Sequences ◽  
Single Strand ◽  
Triplet Repeat ◽  
The Novel ◽  
Base Pairs ◽  
Purine Base ◽  
Ion Interactions ◽  
Folded Structure ◽  
Triplet Repeat Sequences

The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson–Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.

scholarly journals Construction of a novel phagemid to produce custom DNA origami scaffolds

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Parsa M Nafisi ◽  
Tural Aksel ◽  
Shawn M Douglas
Keyword(s):  
Dna Sequences ◽  
Dna Origami ◽  
Single Strand ◽  
Base Pairs ◽  
Fixed Sequence ◽  
Design Processes ◽  
Low Level ◽  
Structural Details ◽  
Filamentous Bacteriophages ◽  
Fixed Region

Abstract DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the ‘scaffold’ to template assembly of numerous short DNA oligonucleotide ‘staples’. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.

scholarly journals New Code for DNA Nucleotide Sequences

2020 ◽  
Author(s):  
Charles Schaper
Keyword(s):  
Hydrogen Bonds ◽  
Gene Transcription ◽  
Dna Sequences ◽  
Structural Characteristics ◽  
Intermolecular Hydrogen Bond ◽  
Regulatory Elements ◽  
Initiation Site ◽  
Nucleotide Sequences ◽  
Base Pairs ◽  
Ionic Binding

DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics.

scholarly journals Construction of a novel phagemid to produce custom DNA origami scaffolds

2018 ◽  
Author(s):  
Parsa M. Nafisi ◽  
Tural Aksel ◽  
Shawn M. Douglas
Keyword(s):  
Dna Sequences ◽  
Dna Origami ◽  
Single Strand ◽  
Base Pairs ◽  
Fixed Sequence ◽  
Design Processes ◽  
Low Level ◽  
Structural Details ◽  
Filamentous Bacteriophages ◽  
Fixed Region

AbstractDNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the “scaffold” to template assembly of numerous short DNA oligonucleotide “staples”. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and thus cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of only 381 bases. We used pScaf to generate new scaffolds ranging in size from 1,512 to 10,080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.

scholarly journals New Code for DNA Nucleotide Sequences

2020 ◽  
Author(s):  
Charles Schaper
Keyword(s):  
Hydrogen Bonds ◽  
Gene Transcription ◽  
Dna Sequences ◽  
Structural Characteristics ◽  
Intermolecular Hydrogen Bond ◽  
Regulatory Elements ◽  
Initiation Site ◽  
Nucleotide Sequences ◽  
Base Pairs ◽  
Ionic Binding

DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics.

Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 661-668
Author(s):  
Mandy Kim ◽  
Erika Wolff ◽  
Tiffany Huang ◽  
Lilit Garibyan ◽  
Ashlee M Earl ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Deinococcus Radiodurans ◽  
Genetic System ◽  
Base Change ◽  
Base Substitution ◽  
Wild Type ◽  
Base Pairs ◽  
E Coli ◽  
Radiation Induced ◽  
Induced Mutagenesis

Abstract We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

scholarly journals THE DNA OF CAENORHABDITIS ELEGANS

Genetics ◽  
1974 ◽  
Vol 77 (1) ◽  
pp. 95-104
Author(s):  
J E Sulston ◽  
S Brenner
Keyword(s):  
Caenorhabditis Elegans ◽  
Chemical Analysis ◽  
Dna Sequences ◽  
Base Composition ◽  
Nematode Caenorhabditis Elegans ◽  
5S Rna ◽  
Base Pairs ◽  
Small Component ◽  
E Coli ◽  
The Mean

ABSTRACT Chemical analysis and a study of renaturation kinetics show that the nematode, Caenorhabditis elegans, has a haploid DNA content of 8 x IO7 base pairs (20 times the genome of E. coli). Eighty-three percent of the DNA sequences are unique. The mean base composition is 36% GC; a small component, containing the rRNA cistrons, has a base composition of 51% GC. The haploid genome contains about 300 genes for 4s RNA, 110 for 5s RNA, and 55 for (18 + 28)S RNA.

The Order of Phase Transition of Solvable DNA Melting Models

2003 ◽  
Vol 17 (16) ◽  
pp. 885-896 ◽  
Author(s):  
Su-Long Nyeo ◽  
I-Ching Yang
Keyword(s):  
Phase Transition ◽  
Hydrogen Bonds ◽  
Short Range ◽  
Scaling Laws ◽  
Dna Melting ◽  
Thermodynamic Quantities ◽  
Base Pairs ◽  
Order Of Phase Transition ◽  
Exactly Solvable ◽  
Dna Models

The phase transition of DNA molecules is studied in an exactly solvable formalism with the Morse and Deng–Fan potentials for the interstrand hydrogen bonds of nucleotide base pairs. It is shown that although the two potentials have different short-range behaviors, the thermodynamic quantities of the DNA system in these potentials enjoy the same scaling laws with the associated critical exponents, which are explicitly calculated. These exactly solvable DNA models are shown to exhibit a phase transition of the second order and the results of the analysis agree with previous studies.

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