Question: Which direction defines a nucleic acid sequence?
About the article "Nucleic acid sequence", section "Abstract".

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KH domains bind to either RNA or single stranded DNA.
The nucleic acid is bound in en extended conformation across one side of the domain.
The binding occurs in a cleft formed between alpha helix 1, alpha helix 2 the GXXG loop (contains a highly conserved sequence motif) and the variable loop.
The binding cleft is hydrophobic in nature with a variety of additional protein specific interactions to stabilise the complex.
Valverde and colleagues note that, "Nucleic acid base-to-protein aromatic side chain stacking interactions which are prevalent in other types of single stranded nucleic acid binding motifs, are notably absent in KH domain nucleic acid recognition". 
Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation.
Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing.
It is necessary because there are many possible sequences of nucleic acid strands that will fold into a given secondary structure, but many of these sequences will have undesired additional interactions which must be avoided.
In addition, there are many tertiary structure considerations which affect the choice of a secondary structure for a given design.
Nucleic acid design has similar goals to protein design: in both, the sequence of monomers is rationally designed to favor the desired folded or associated structure and to disfavor alternate structures.
However, nucleic acid design has the advantage of being a much computationally simpler problem, since the simplicity of Watson-Crick base pairing rules leads to simple heuristic methods which yield experimentally robust designs.
Computational models for protein folding require tertiary structure information whereas nucleic acid design can operate largely on the level of secondary structure.
However, nucleic acid structures are less versatile than proteins in their functionality.
Nucleic acid design can be considered the inverse of nucleic acid structure prediction.
In structure prediction, the structure is determined from a known sequence, while in nucleic acid design, a sequence is generated which will form a desired structure. 
Dda is a molecular motor, specifically a helicase that moves in the 5' end to 3' direction along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands, using the free energy released by the hydrolysis of adenosine triphosphate.
The National Center for Biotechnology Information (NCBI) Reference Sequence accession number is NP_049632. 
Information about the secondary structure of a nucleic acid complex along with its sequence can be used to predict the thermodynamic properties of the complex.
When thermodynamic models are used in nucleic acid design, there are usually two considerations: desired hybridizations should have melting temperatures in a narrow range, and any spurious interactions should have very low melting temperatures (i.e.
they should be very weak).
The Gibbs free energy of a perfectly matched nucleic acid duplex can be predicted using a nearest neighbor model.
This model considers only the interactions between a nucleotide and its nearest neighbors on the nucleic acid strand, by summing the free energy of each of the overlapping two-nucleotide subwords of the duplex.
This is then corrected for self-complementary monomers and for GC-content.
Once the free energy is known, the melting temperature of the duplex can be determined.
GC-content alone can also be used to estimate the free energy and melting temperature of a nucleic acid duplex.
This is less accurate but also much less computationally costly.
Software for thermodynamic modeling of nucleic acids includes Nupack,mfold/UNAFold, and Vienna.
A related approach, inverse secondary structure prediction, uses stochastic local search which improves a nucleic acid sequence by running a structure prediction algorithm and the modifying the sequence to eliminate unwanted features. 
A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule.
By convention, sequences are usually presented from the 5' end to the 3' end.
Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule.
For this reason, the nucleic acid sequence is also termed the primary structure.
The sequence has capacity to represent information.
Biological DNA represents the information which directs the functions of a living thing.
In that context, the term genetic sequence is often used.
Sequences can be read from the biological raw material through DNA sequencing methods.
Nucleic acids also have a secondary structure and tertiary structure.
Primary structure is sometimes mistakenly referred to as "primary sequence".
Conversely, there is no parallel concept of secondary or tertiary sequence.